13th Annual
Solanaceae Conference
SolGenomics: From Advances to Applications
CONFERENCE
PROGRAM
September 12 — 16, 2016
Davis, California USA
www.SolGenomics2016.ucdavis.edu
Solanaceae Conference 2016 • UC Davis | SolGenomics2016.ucdavis.edu
SCIENTIFIC COMMITTEE
Siobhan Brady,UCDavis
Glenn Bryan,TheJamesHuttonInstitute
Anne Britt,UCDavis Roger Chetelat,UCDavis
Gitta Coaker,UCDavis
Luca Comai,UCDavis
Ellen Dean,UCDavis Massimo Delledonne,UnivofVerona
Allen Van Deynze,UCDavis James Giovannoni,USDA/BTI/Cornell
Antonio Granell,ConsejoSuperiordeInvestigacionesCientificas
Phyllis Himmel,UCDavis
Jeanne Jacobs,Plant&FoodResearch,NewZealand
Julin Maloof,UCDavis
Cathie Martin, JohnInnesCentre
Rich Ozminkowski,Heinz
Ann Powell,UCDavis
Neelima Sinha,UCDavis
LOCAL ORGANIZING COMMITTEE
Susan DiTomaso
Ann Powell
Allen Van Deynze
Phyllis Himmel
Amanda Saichaie
UC Davis, USA
Rebeca Madrigal
Julie Tillman
GENERAL CONFERENCE INFORMATION
• Conference Center building will open daily at 7:30 am.
• Conference Center restrooms are located adjacent to the registration desk; Additional restrooms
are available on the second floor.
• Meal and drink tickets are placed in the plastic sleeve of the name badges.
• Drink tickets are needed for beer and wine at all evening social events. Non-alcoholic drinks and
water available at no cost. Additional beer and wine drinks may be purchased (cash only, USD).
• All conference abstracts available at SolGenomics2016.ucdavis.edu/program
• Platinum and Gold level sponsor representatives are encouraged to be present at their company
hosted lunch tables.
• Emergency help is available by dialing 911 from a land line or (530) 752-1230 from a mobile
phone. Do not dial 911 from a mobile phone. For additional campus emergency and safety
information, visit www.ucdavis.edu/emergency/. For status or information during an emergency,
call the campus Emergency Status Line at (530) 752-4000.
• In case of emergency, conference attendees should gather on VanderHoef Quad.
CONFERENCE POLICIES
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Name badges should be worn at all Conference functions.
For all evening social events, guests may not leave event area with alcohol in hand.
Lunch, reception and banquet tickets must be turned in at each meal.
Cell phones should be turned off during all scientific sessions.
Photos are discouraged during talks.
Photos of posters may be taken only with presenter’s permission.
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CONFERENCE TOURS • THURSDAY, SEPTEMBER 15, 8:00 AM DEPARTURE
Pre-registration required.
For all tours: Closed toe shoes and long pants are required; Jewelry or hair ornaments prohibited.
Detailed tour information and tour-specific dress requirements are available at
SolGenomics2016.ucdavis.edu/in-meeting-tours/
TOURS:
Buses depart from the Conference Center at 8:00 am, unless noted otherwise.
Ø Tomato Genetics Resource Center Field Plot and Pepper Diversity Plot (UC Davis)
Ø HM.Clause Field Commercial Breeding Facility, Davis
Ø Monsanto Phenotyping & Genotyping Lab and Greenhouse Facility, Woodland
Ø Commercial Scale Conventional Farm, Davis area
Ø Morning Star Tomato Processing Facility, Williams
Buses return back to the Conference Center at approximately 12:00 pm, unless noted otherwise.
CONFERENCE WORKSHOPS • Thursday, SEPTEMBER 15, 4:20 PM
Workshops will be held in the Conference Center. Detailed workshop information is available at
SolGenomics2016.ucdavis.edu/program/
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Sol Genomics Network workshop: New features and data in the SGN database, Ballroom A
Government, Industry, Academics Career Panel (for students and postdocs), Ballroom B
Collaboration for Plant Pathogen Strain Identification (CPPSI), Ballroom C
Accelerating Plant Science with CyVerse ­— Genomics Workflows, Data Management and
Training, 2nd floor, Room 2207
Conference organizers would like to extend a special THANK YOU to the following individuals:
• Our conference tour hosts and workshop chairs
• Alfred Huo and Cai-Zhong Jiang (poster coordination and set-up)
• Kathy Esparza (registration and general assistance)
• Joy Patterson and Sally Mohr (catering arrangements, attendee and invited speaker gifts, conference
packet assembly)
• Susan Hendrickson (general assistance)
• Ryan Eadry and Garry Pearson (centerpiece plants)
• Chris Durand and Andrew Hutchinson (conference supplies transportation)
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SESSION CHAIRPERSONS
Session I • DIVERSITY-TAXONOMY/CROP GERMPLASM DIVERSITY
EllenDean,UCDavis•IrmaOrtiz,UCRiverside
Session II • BARRIERS TO BREEDING
RogerChetelat,UCDavis•BennyJulissaOrdonezAquinno,UCDavis
Session III • GENOMES & GENOME TECHNOLOGIES
MassimoDelledonne,Univ.ofVerona•ArsenioNdeve,UCRiverside
Session IV • HIGH-THROUGHPUT PHENOTYPING
AllenVanDeynze,UCDavis•LavYadav,WestVirginiaStateUniv.
Session V • GENE-EDITING AND NEW BREEDING TECHNOLOGIES
AnneBritt,UCDavis•JuliePedraza,CaliforniaStateUniv.,Fresno
Session VI • EPIGENOMICS AND METHYLATION
LucaComai,UCDavis•BrittanyDavenport,WestVirginiaStateUniv.
Session VII • GENOMICS-ASSISTED BREEDING
JeanneJacobs,Plant&FoodResNZ•KieuNgaTran,LouisianaStateUniv.
Session VIII • SYSTEMS BIOLOGY AND NETWORKS
SiobhanBrady,UCDavis•SophiaJinata,UCDavis
Session IX • ABIOTIC STRESSES
JulinMaloof,UCDavis•LumarizHernandez-Rosario,Univ.ofPuertoRico
Session X • RESISTANCE, PATHOGENS, PESTS AND MICROBIOMES
GittaCoaker,UCDavis•KevinBabilonia,TexasA&M
Session XI • TUBERS AND ROOT SYSTEMS
GlennBryan,TheJamesHuttonInstitute•JustinMedina,CalPolyPomona
Session XII • FLOWERS, SEEDS AND FRUIT
JamesGiovannoni,USDA/BTI/Cornell•KimberlyRodriguez,NewMexicoStateUniv.
Session XIII • PLANT DEVELOPMENT AND REGULATION
NeelimaSinha,UCDavis•TimothyBatz,Calif.StatePolytechnicUniv.,Pomona
Session XIV • METABOLITES, FLAVOR AND QUALITY
CathieMartin,JohnInnesCentre•SassoumLo,UCRiverside
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SESSION STUDENT CO-CHAIRPERSONS
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SESSION I • DIVERSITY-TAXONOMY/CROP GERMPLASM DIVERSITY
CO-CHAIRPERSON: IRMA ORTIZ (UC RIVERSIDE, USA)
Irma Ortiz is a Ph.D. candidate at the University of California, Riverside.
Irma received her B.S. in Molecular, Cell and Developmental Biology from
UCLA in 2011. She studied the interactions of a new plant growthpromoting bacterium (Bacillus simplex) and peas in Ann Hirsch’s
laboratory. This full-time, research-intensive experience confirmed her
passion for plant and biotic interactions and a life in research. She is
currently a graduate student in Linda Walling’s laboratory. Her current
research focuses on understanding resistance mechanisms to insects. In
response to wounding and insect attack, tomato plants express toxic
chemicals and anti-nutritive proteins that interfere with insect growth and
development.
_______________________________________________________________________________
SESSION II • BARRIERS TO BREEDING
CO-CHAIRPERSON: BENNY ORDONEZ (UC DAVIS, USA)
Benny is a Peruvian citizen. She holds an MSc in Plant Breeding. She
currently works at the Chetelat Lab in UC Davis and as a Research
Assistant in the International Potato Center (CIP). Benny’s research
interests focus on interspecific reproductive barriers, haploid induction,
unreduced gametes, and she is developing new potato pre-bred lines
with late blight and bacterial wilt resistance. Besides, she studies the
mechanism of introgression of the S locus inhibitor gene into diploid
potatoes.
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SESSION III • GENOMES AND GENOME TECHNOLOGIES
CO-CHAIRPERSON: ARSENIO NDEVE (UC RIVERSIDE, USA)
Arsenio Ndeve is originally from Mozambique, South East Africa. He
received his BSc degree in 2005 in Agronomy at Eduardo Mondlane
University, and in 2008 obtained his MSc in Agricultural Development,
with focus on Crop Production, at Copenhagen University. After finishing
his MSc studies he got a teaching appointment at Eduardo Mondlane,
where he taught Crop Production, Feed and Industrial Crops and Crop
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Physiology for four years before he joined to Dr. Philip Roberts lab for his PhD studies at the University
of California Riverside in 2012. Currently he is fifth year PhD student in the Plant Pathology Program,
and his research is focused on cowpea (black-eye-pea) pathology, with focus on the genetics of
resistance to Root-knot nematodes, Fusarium Wilt and Ashy Stem Blight diseases in novel cowpea
germplasm. His research interest is focused on the integration of agronomy related subjects such as
crop physiology, plant pathology, genetics and plant breeding, to contribute to the enhancement of
food crop productivity in an environmentally sound manner.
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SESSION IV • HIGH-THROUGHPUT PHENOTYPING
CO-CHAIRPERSON: LAV KUMAR YADAV (WEST VIRGINIA STATE UNIV., USA)
I am originally from Nepal belonging to farming family. I have an
undergraduate degree in Agriculture (BSc.Ag) majoring in plant breeding.
I have a GPA of 4.00. I am the first one to go to college in my family, I
came to USA in 2015 to pursue my Master’s degree in Biotechnology at
West Virginia State University. I am currently working in Dr. Umesh
Reddy's lab. I am working primarily in peppers, focusing on the
characterization of ankyrin gene family. My interests are in biostatistics,
bioinformatics work to explore the genome of pepper in every way
possible. Also I have a keen interest in pepper breeding to get plants
with large size fruit and high capsaicin content. I am also doing some
work in this direction.
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SESSION V • GENE-EDITING AND NEW BREEDING TECHNOLOGIES
CO-CHAIRPERSON: JULIE PEDRAZA (CSU, FRESNO, USA)
Julie J. Pedraza, California State University-Fresno, Fresno, CA – Ms.
Pedraza is a graduate student at California State University, Fresno
(Fresno State) studying herbivore induced plant volatiles in agricultural
crops. She graduated Fresno State in 2016 with a BS in Plant Science with
an emphasis in Plant Health. She plans to further her education at a
doctorial school to study economic entomology and integrated pest
management. Julie interns as a Biological Science Technician with Dr.
Christopher Wallis, a Research Plant Pathologist with the USDA,
Agricultural Research Service in Parlier, CA. She is actively involved in
research projects investigating the biology and ecology of number of
plant pathogens including: Xylella fastidiosa in grapevine and almond,
‘Liberibacter solanacearum’ in potato, and Verticillium dahliae in olives.
In addition, she researches herbivore-plant interaction in grapevines, tomatoes, and brassicas with a
variety of insects and nematodes. Ms. Pedraza is active in her community, promoting agriculture and
higher education. She has received several honors and awards including the Golden Opportunity
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Scholar, Jim Patterson Ag-Science Student of the Year and the Fresno State Alumni Association Top
Dog Award.
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SESSION VI • EPIGENOMICS AND METHYLATION
CO-CHAIRPERSON: BRITTANY DAVENPORT (WEST VIRGINIA STATE UNIV., USA)
Brittany Davenport is a native of West Virginia. She holds an MS degree in
Biotechnology. Currently, she works as a Lab Technician in the Reddy Lab
at WVSU. Brittany is a mother of 1 and an active participant in her
community. Brittany's research focuses on association mapping of fruit
colors in various Capsicum species as well as high/low density trichome
crosses in Citrullus species.
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SESSION VII • GENOMICS-ASSISTED BREEDING
CO-CHAIRPERSON: KIEU-NGA T. TRAN (LOUISIANA STATE UNIV., USA)
Kieu is currently a first year PhD student at Louisiana State University. She
started as a volunteer research assistant in Dr. Maheshi Dassanayake’s
lab in Fall 2013. She joined Dr. Dassnayake’s group as a full time research
assistant in June 2015 after graduating from LSU and as a graduate
student in Spring 2016. She is currently investigating the stress responses
to multiple salts in the extremophile plants, Schrenkiella Parvula and
Eutrema salsugineum compared to the model plant, Arabidopsis thaliana
using comparative genomics and transcriptomics methods. She uses a
custom hydroponics system she has optimized for synchronized growth of
extremophytes with control species to monitor their different stress
responses. She plans to use other Brassicaceae genomes that represent
stress sensitive species together with the A. thaliana genome as control species to study genomic
elements in the extremophyte genomes that may have contributed to their stress adapted lifestyles.
The use of extremophytes to harness genetic mechanisms that respond to abiotic stress and as a
repository of genomic elements naturally selected for environmental stress adaptations will provide
critical resources to design crops better adapted to a changing climate.
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SESSION VIII • SYSTEMS BIOLOGY AND NETWORKS
CO-CHAIRPERSON: SOPHIA JINATA (CSU SACRAMENTO, USA)
Sophia Jinata was born and raised in the eastern region of the Bay Area.
She is currently an undergraduate in her senior year studying General
Biology at California State University, Sacramento. In the summer of 2016,
she completed an internship at the UC Davis Genome Center in the
laboratory of Dr. Luca Comai, where she worked on a project focused on
targeted gene editing and bioinformatics in potatoes. After graduation,
she hopes to continue working in the realm of molecular biology and
bioinformatics and is considering pursuing graduate school later on in her
career.
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SESSION IX • ABIOTIC STRESSES
CO-CHAIRPERSON: LUMARIZ HERNANDEZ (UNIV. OF PUERTO RICO)
Lumariz Hernández Rosario is a master’s degree student currently
working as research assistant in the laboratory of plant biotechnology
and molecular biology of the professor Dimuth Siritunga at the University
of Puerto Rico at Mayaguez. Her interest is in plant molecular biology
and her thesis research project aims to assess the Genetic Diversity of
Solanaceae in Puerto Rico using DNA barcoding. With this research
project, she has been training undergraduate students with this
technique and encouraging them to pursue graduate studies in plant
molecular biology.
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SESSION X • RESISTANCE, PATHOGENS, PESTS AND MICROBIOMES
CO-CHAIRPERSON: KEVIN BABILONIA (TEXAS A&M, USA)
Kevin Babilonia is a Ph.D. candidate in Texas A&M University. He
received BA and M.S. degrees in the University of Puerto Rico at
Mayagüez, in industrial biotechnology and Plant Molecular Biology,
respectively. As an undergrad student he went to Texas A&M for a
summer internship program in the biochemistry department where he
worked with Dr. Ping He and Dr. Libo Shan. During this summer he used
forward genetics to screen mutants with altered immune defense
responses. After receiving his M.S., he decided to go back to Dr. Ping
He’s lab at Texas A&M to continue working with some of the mutants. His
main focus is to characterize, map and identify novel components in the
plant defense signaling pathway. In addition, he is also working with the
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functional characterization of genes in cotton drought stress responses by using VIGS (Virus-Induced
Gene Silencing) as a novel approach.
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SESSION XI • TUBERS AND ROOT SYSTEMS
CO-CHAIRPERSON: JUSTIN MEDINA (CAL POLY POMONA, USA)
My name is Justin Medina. I am a 25-year-old Mexican-American born and
raised here, in southern California. My immediate family consists of my
mother, my father, and my younger sister. I currently reside in Ontario, CA
and I am a senior at Cal Poly Pomona and will be graduating with a
Bachelors in General Biology. I have two jobs, one at night working at the
Ontario International airport for UPS and the other at Cal Poly working in
Dr. David Still’s Lab. In Dr. Stills lab, or The Still Lab as we call it, we as
students conduct many of the projects and/experiments needed for Dr.
Still’s research. Much of our current research is done on a variety of
lettuce ranging from lactuca serriola, virosa, sativa, etc. We do seed
germination projects, DNA isolation & sequencing, cross breeding and
NUE/WUE studies. My day-to-day tasks in the lab include setting up experiments, incubators, grow
rooms, etc., successful germinating and growing many varieties of lettuce in our greenhouse which we
collect seeds, DNA samples and preform crosses on, data collection and some analysis, as well as
maintaining the lab materials and equipment which includes proper storage of chemicals or tools and
also washing glass wear.
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SESSION XII • FLOWERS, SEEDS, AND FRUIT
CO-CHAIRPERSON: KIMBERLY RODRIGUEZ (NEW MEXICO STATE UNIV., USA)
Kimberly Rodriguez is a M.S. graduate student at New Mexico State
University majoring in Horticulture with a minor in Applied Statistics. Her
major professor is Dr. Paul Bosland, Chile Pepper Breeding and Genetics
Program, and Chile Pepper Institute. Kimberly is currently investigating
disease resistance, specifically Verticillium and Phytophthora resistance,
and the inheritance of genetic mutations in chile peppers. In 2015, she
obtained her Bachelor’s Degree in Horticulture, at New Mexico State
University. While an undergraduate student, Kimberly worked in Dr.
Bosland’s research program aiding with field work, greenhouse work, and
data collection, and the Chile Pepper Institute providing answers to chile
pepper questions and giving garden tours to the public.
Kimberly grew up in Sunland Park, NM, a small city near El Paso, TX. Both sets of her grandparents
were born in Mexico and then migrated to United States where they settled in New Mexico. She
graduated from high school as Valedictorian of her class and is the first college graduate in her family.
She plans on continuing research and improving her skills in the fields of plant breeding and molecular
genetics, as well as conveying valuable knowledge to the scientific community.
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__________________________________________________________________________________________
SESSION XIII • PLANT DEVELOPMENT AND REGULATION
CO-CHAIRPERSON: TIM BATZ (CAL POLY POMONA, USA)
Timothy Batz is a recent plant science graduate from California State
Polytechnic University, Pomona. He is currently a first year master’s
student in the lab of Dr. Bharti Sharma studying the morphological and
genetic dynamics involved in inflorescence formation in Columbine
(Aquilegia). Timothy is interested in the evolution and morphological
diversity of inflorescence branching within the Ranunculaceae family as
well as potential applications of these traits in agriculture.
__________________________________________________________________________________________
SESSION XIV • METABOLITES, FLAVOR AND QUALITY
CO-CHAIRPERSON: SASSOUM LO (UC RIVERSIDE, USA)
My name is Sassoum Lo and I am from Senegal. I am a Ph.D. student in
Plant Biology, working in Timothy Close Lab, at the University of California
Riverside. I received my B.S. in Applied Biology from Cheikh Anta Diop
University (Senegal). I am interested in crop domestication and crop
genetic improvement. Specifically, my research is focused on determining
the genetic basis of domestication-related traits in cowpea (Vigna
unguiculata), including pod shattering and seed size, and on studying the
effect of increasing seed size on the nutritional quality of the cowpea
grain. Currently I am identifying QTL for seed size and introgressing them
into a Senegalese cultivar.
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PLENARY AND KEYNOTE SPEAKERS
Richard Michelmore • Welcome Keynote Speaker
Richard Michelmore has been the founding Director of the Genome Center at the
University of California at Davis since 2003. He received BA and Ph.D. degrees in
Natural Sciences from the University of Cambridge, UK and joined the faculty of UC
Davis in 1982. He is currently a Distinguished Professor in the Departments of Plant
Sciences, Molecular & Cellular Biology, and Medical Microbiology & Immunology.
He has published over 160 scientific papers. His multidisciplinary research utilizes a
synthesis of molecular, genetic, and evolutionary approaches. His interests span
basic research into the molecular basis of specificity in plant-pathogen interactions
to translational plant genetics and crop improvement. His research is focused on
comparative and functional genomics with an emphasis on plant disease resistance
and pathogen variability (http://michelmorelab.ucdavis.edu). In addition, his program
coordinates and hosts the bioinformatics component of the Compositae Genome Project
(http://compgenomics.ucdavis.edu/). His interests include applications of next-generation DNA sequencing
approaches to all areas of biology and its imminent impact on society in general. In particular, he aims to
exploit such approaches for information-driven deployment of resistance genes in plants to provide durable
disease resistance. He is also interested in fostering research to enhance food security internationally.
Talk title: Disruptive Technologies and Improvement of Disease Resistance in Lettuce
Roger Chetelat • Banquet Keynote Speaker
Roger Chetelat‘s research encompasses the molecular and classical genetics of
tomato; wide hybridization and interspecific incompatibility; use of molecular
markers in breeding; and germplasm conservation. His work on reproductive
barriers is revealing how plants control pollination to avoid both inbreeding and
excessive outcrossing. Using this information, he is developing new types of
prebred germplasm sources that broaden the genetic base of cultivated tomato.
These research projects are synergistic with the C.M. Rick Tomato Genetics
Resource Center, a national and international genebank of tomato wild species and
genetic stocks. The Rick Center distributes seed samples to interested researchers,
breeders and educators around the world.
Talk title: Charlie Rick and the Origins of the Tomato Genetics Resource Center
During his 60-year career at UC-Davis, the late Prof. Charles M. Rick isolated and
mapped hundreds of mutants, collected wild tomato relatives throughout South
America, and founded a seed bank to preserve these and other stocks. His work
helped establish tomato as a model system for genetic studies, and made available
rich germplasm resources with which to analyze the Solanum genome. Rick led 13
major expeditions to the native region to collect and study wild tomatoes. His
photographic and written account of these trips form the basis for this retrospective
view of the ups and downs of plant collecting in the Andean region and the
Galapagos Islands. The C.M. Rick Tomato Genetics Resource Center, established in
1976, now maintains and distributes over 3,900 accessions of wild species and
genetic stocks. Current research on wide hybridization and self- and interspecific
incompatibility is generating new sources of germplasm and fresh insights into reproductive barriers between
tomato and its wild relatives.
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Session I - Diversity-Taxonomy/Crop Germplasm Diversity • Sandy Knapp, Plenary Speaker
Sandy Knapp leads the Natural History Museum’s team of 20 botanists, and is
herself a specialist in the nightshade (or potato) family, Solanaceae. She originally
came to the Museum to lead the international project Flora Mesoamericana – a
synoptic account of the 18,000 species of flowering plants and ferns that occur in
tropical Mexico and Central America. The Flora is the first major regional floristic
project to be published in Spanish. She has published more than 150 peer-reviewed
scientific papers, ranging from description of more than 100 new species, to
evolutionary analyses of the entire nightshade family. She has written 11 popular
books and field guides; one of these, Potted Histories (re-titled as Flora in its second
and third editions) won the Prix J. Redouté in its French translation.
She leads collecting expeditions in the Americas, Asia, and Africa as part of her work, and has a wide range
of collaborations worldwide. She served as the first female President of the Nomenclature Section of the
International Botanical Congress in Melbourne in 2011, and has been elected to the same role for the
Congress in Shenzhen, China in 2017. Her current research is focused on the wild relatives of cultivated
plants, and explores aspects of domestication, distribution, and diversification in these complex groups of
species.
Talk title: Diversification in Solanaceae: More Than Meets the Eye
Session I - Diversity-Taxonomy/Crop Germplasm Diversity • Elizabeth McCarthy, Invited Speaker
Elizabeth McCarthy is an Assistant Project Scientist at the University of California,
Riverside. She obtained her BA from Smith College and her PhD from Queen Mary,
University of London. Her research interests include the effects of allopolyploidy on
floral evolution, using Nicotiana as a study system. During her PhD, she quantified
floral shape, size, and color for Nicotiana allopolyploids of different ages and
examined floral evolution in polyploids based on the morphology of their diploid
progenitors. Currently, she works with Amy Litt, and their research focuses on how
the merger of distinct genomes results in the transgressive phenotypes observed in
allopolyploids. Specifically, they are using transcriptome analyses along with floral
pigment quantification to explore the genetic basis of transgressive and diverse
floral colors in Nicotiana allopolyploids. In addition, they are using ancestral state
character reconstruction to determine whether there are differences in the trends of
floral evolution in polyploids versus diploids.
Talk title: Diverse and Novel Phenotypes in Nicotiana Allopolypoids: The Genetic Basis of Floral
Pigments
Session II - Barriers to Breeding • Pat Bedinger, Plenary Speaker
Patricia Bedinger investigated the genetics of pollen development and the cell
biology of pollen tube growth for a number of years. More recently she has
refocused her research on a fundamental biological question: how do closely related
species occurring in sympatry avoid hybridization? In particular, her current research
aims to elucidate the molecular mechanisms underlying reproductive isolation
between species, and how mutations can impact species interactions. This highly
integrative project involves a team of researchers with expertise encompassing
bioinformatics, evolution, genetics and molecular biology. The study system for the
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project is the tomato clade of Solanum, which, in addition to the cultivated tomato, includes a diverse set of
wild species found Ecuador, Peru and Chile. Dr. Bedinger conducted field work on wild tomatoes in
Ecuador as a Fulbright Scholar in 2014-2015.
Talk title: Interspecific Reproductive Barriers in the Wild Tomatoes
Session II - Barriers to Breeding Session • Ian Beddows, Invited Speaker
Ian Beddows is a PhD student at the Institute of Population Genetics, Heinrich Heine
University, Duesseldorf. He received a B.A. in ecology from Northern Michigan
University in 2013 and an M.Sc. from Heinrich Heine University in 2015. His thesis is
focused on natural diversity in wild tomato with a special interest on two very
diverse species Solanum chilense and S. peruvianum. In addition to the central
topics of speciation and hybridization, he is currently studying natural selection in
biosynthetic pathways and disease resistance loci using genomic datasets.
Talk title: Wild Tomato: Population Structure and Evidence of Natural S. chilense
x S. peruvianum Hybrid Populations
Session III - Genomes and Genome Technologies • Dario Cantu, Plenary Speaker
Dario Cantu is an Associate Professor in the department of Viticulture and Enology at
UC Davis. He obtained a Ph.D. in Plant Biology form UC Davis in Fall 2009. During his
Ph.D. he investigated the molecular bases of the intersection between tomato
ripening and susceptibility to Botrytis cinerea. Since graduating from UCD, he
conducted research in the laboratory of Prof. Dubcovsky where he applied novel
sequencing and large dataset technologies and made significant contributions to the
field of plant genomics, including the first epigenome analysis of wheat transposable
elements, the first assembly and annotation of the wheat stripe rust genome, a large
scale transcriptome analysis of polyploidy wheat, and a comparative study of the
defense response interactomes in rice and wheat. Since 2012, as Faculty member at
UC Davis, he has been leading an independent research group that integrates
principles of systems biology and quantitative genetics and uses genomics and bioinformatics to dissect
the molecular networks underlying grapevine responses to the environment, including biotic and abiotic
stresses. Research topics range from (i) grapevine resistance to pathogens, (ii) the evolution of
pathogenicity in fungal plant pathogens, (iii) berry ripening and its association with pathogens and microbial
communities, and (iv) the molecular determinants of fruit development and ripening.
Talk title: Democratization of Reference Quality Genome Sequencing for Non-model Organisms
Session III - Genomes and Genome Technologies • Lidija Berke, Invited Speaker
Lidija Berke received her PhD from Utrecht University, the Netherlands, in 2015 for
work on evolution of epigenetic mechanisms in plants, focusing on the repressive
histone modification H3K27me3. She is currently a postdoctoral researcher at the
Biosystematics group at Wageningen University, the Netherlands, where she is
exploring the evolution of specific traits in several Solanaceae and Asteraceae
genomes. For example, the genome of Solanum etuberosum as an outgroup species
to tomato and potato provides important insights into evolution of tuberisation. A
second Solanum species, S. cardiophyllum, is the only edible wild potato species
due to its low glycoalkaloid content. Its genome is thus a valuable resource to
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explore the mechanism for the loss of glycoalkaloids.
Talk title: You Say Tomato, I Say Potato: High-Quality Genome Assembly of the Sister-Group Species,
Solanum etuberosum, Provides Insights into Genome and Trait Evolution
Session IV - High-throughput Phenotyping • David Slaughter, Plenary Speaker
David Slaughter is a considered a worldwide leading expert in the development of
nondestructive and noninvasive sensing systems for determining the quality and
identity of agricultural commodities, and he has made tremendous contributions
toward the development of automation technologies for precision, on-farm,
individualized plant care. Moreover, he has spent much of his career improving the
long-term sustainability of U.S. specialty crop production by developing smart
agricultural machines that can simultaneously reduce the drudgery of menial labor
associated with fruit and vegetable production and the need for and negative
environmental impact of pesticides. He was a pioneer in the development of one of
the first robotic fruit-harvesting systems. He developed and patented one of the
first machine-vision-based automatic guidance systems for precision inter-row
weed control and for automated spray bandwidth control in row crops. He has
developed several novel technologies for automated, pesticide-free, intra-row weed control in specialty
crops, and has developed and demonstrated a robust on-farm system for plant species determination in
tomato and lettuce.
Talk title: In-field High-throughput Phenotyping for Plant Architecture and Internal Fruit Quality in
Tomato
Session IV - High-throughput Phenotyping • Mao Li, Invited Speaker
Mao Li is a mathematician whose research interests lie in geometric and
topological data analysis, the study of complex shapes and network. She is in the
position of Postdoctoral Associate in Topp Lab and Chitwood Lab at the Donald
Danforth Plant Science Center. Her current focus is to apply mathematical methods
and algorithms such as persistent homology to quantify plant morphology----root,
leaf, or floral structures, branching architecture, or other geometric and topological
phenomena. Such quantitative analyses are applied to discovering the genetic and
molecular mechanisms underlying the plant form.
Talk title: Persistent Homology: A Tool to Universally Measure Plant Morphologies Across Organs and
Scales
Session V - Gene Editing and New Breeding Technologies • Joyce Van Eck, Plenary Speaker
Joyce Van Eck is a faculty member at the Boyce Thompson Institute (BTI) at
Cornell University and is also the director of the BTI Center for Plant
Biotechnology Research. She received her undergraduate degree in Plant Biology
from the Pennsylvania State University, a M.S. from the University of Delaware, and
a Ph.D. in Plant Breeding and Genetics from Cornell University. The focus of
research in the Van Eck laboratory is biotechnological approaches to the study of
gene function and crop improvement with an emphasis on plants for human
health. For her studies, she applies genetic engineering strategies to food crops,
such as grape, potato, and tomato, in addition to several model species (Setaria
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viridis, Brachypodium distachyon, and Asclepias syriaca).
Talk title: Genetic Engineering and Genome Editing in the Solanaceae
Session V - Gene Editing and New Breeding Technologies • Angela Chaparro-Garcia, Invited Speaker
Angela Chaparro-Garcia is a postdoctoral researcher at The Sainsbury Laboratory.
She obtained her Bachelor degree in Microbiology from Universidad de Los
Andes, Colombia. During her PhD she studied the molecular mechanisms of PTI
suppression by the Phytophthora infestans effector AVR3a. Convinced of the
importance of bridging the gap between basic science and agricultural
applications, she is pursuing her main research interest of transforming our
understanding of molecular host-pathogen interactions into new solutions to
improve plant disease resistance. She is taking advantage of the latest genomeediting technologies to deliver sustainable and durable traits against the
devastating plant-pathogen Phytophthora infestans.
Talk title: Susceptibility Genes for Resistance Against Phytophthora infestans
Session VI - Epigenomics and Methylation • Philippe Gallusci, Plenary Speaker
Philippe Gallusci is full professor at University of Bordeaux. He received his PhD in Plant
Molecular Biology from the University of Toulouse in 1991. After a 4 years long
postdoctoral stay at the Max Planck Institute (Cologne) where he studied maize
endosperm development, he was hired as associate professor at Bordeaux University in
1994 to initiate research on volatile terpene synthesis in plants. He then studied the
interplay between sugar metabolism and carotenoid accumulation in tomato fruits. In
2005, he initiated research on tomato epigenetics and since that time was leading the
epigenetic research team at the Fruit Biology Laboratory (INRA Bordeaux) before
moving in January 2016 to the Grape Ecophysiology and Functional Biology Laboratory
(ISVV, Bordeaux). His actual research interests concern the functional analysis of
epigenetic mechanisms in fleshy fruits, with a focus on Polycomb group proteins and
DNA methylation, using tomato and grape as models. He is now initiating research to
analyze the relevance of epigenetic mechanisms in the adaptation of grapevine to climate changes Pr Gallusci
conducted research on DNA methylation in tomato fruits at the Boyce Thompson Institute in Pr J Giovannoni
laboratory (Cornell University) as a Fulbright Scholar in 2014.
Talk title: The Functions of DNA Methylation in Fleshy Fruits
Session VI - Epigenomics and Methylation • Subha Damodharan, Invited Speaker
Subha Damodharan, completed her PhD from Madurai Kamaraj University, India.
Currently working as a post-doc with Tzahi Arazi team in Volcani Centre, Israel. The
main interest of the lab includes identifying and deciphering the role of miRNAs in
tomato development. She is involved in a project to understand the role of miR160 in
reproductive development of tomato. Techniques like STTM and CRISPR-cas9 have
been used to reveal the importance of this miRNA in auxin signalling. Her research
interests include plant development, phytohormones, small RNA, reproductive
development and genome editing.
Talk title: miR160 is a Master Regulator of Auxin Mediated Developmental
Processes in Tomato
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Session VII - Genomic-assisted Breeding • David Douches, Plenary Speaker
David Douche‘s research interests involved Potato breeding and genetics:
Development and utilization of molecular markers for gene mapping, breeding and
fingerprinting; Utilization of exotic germplasm; Cytogenetics of 2n gametes; Late
blight, scab and Colorado potato beetle resistance; Transformation of potato to
introgress economically important genes.
Talk title: Genomics Assisted Breeding in Potato
Session VII - Genomic-assisted Breeding • Debora Liabeuf, Invited Speaker
Debora Liabeuf is a PhD candidate in Horticulture and Crop Sciences with a focus in
Genetics and Plant Breeding. She is advised by Dr David Francis. She is originally
from France where she earned her M.S. in Horticulture and Plant Breeding (2012).
She started her PhD program in 2013. Her research focuses on breeding for
resistance to the complex of Xanthomonas species causing bacterial spot of
tomato. She identified wild accessions resistant to X. gardneri and mapped QTLs
associated with the trait. Additionally, she empirically evaluated the accuracy of
genomic selection for resistance to X. euvesicatoria, and characterized wild genetic
regions introgressed in an elite S. lycopersicum line carrying resistance to bacterial spot using whole
genome sequencing. Her anticipated graduation is December 2016. After her PhD, she will pursue her goal
of being a plant breeder in the industry.
Talk title: Empirical Evaluation of Genomic Selection for Resistance to Bacterial Spot of Tomato
Session VIII - Systems Biology and Networks • Rob Last, Plenary Speaker
Rob Last is Barnett Rosenberg Professor of Plant Biochemistry at Michigan State
University. His research interests focus on metabolic pathways of nutritionally
important and protective small molecules in Arabidopsis and Solanaceae. He
currently serves on the American Society of Plant Biologists Program Committee and
the Science Advances Editorial Board.
Talk title: The Tip of the Trichome: Specialized Metabolic Diversity in the
Solanaceae
Session VIII - Systems Biology and Networks • Yoshihito Shinozaki, Invited Speaker
Yoshihito Shinozaki investigated floral organ development, particularly
reproductive responses in petals and ovaries, with focusing on hormones. He
obtained his Ph.D. in 2012 and then did postdoctoral research in University of
Tsukuba (Japan), where he studied molecular and biochemical mechanisms of
fruit setting depending on auxin, gibberellin, and ethylene signaling triggered by
pollination. He then moved to the laboratory of Prof. J Rose at Cornell University in
2015 and has been investigating transcriptome of specialized cell/tissue-types in
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developing tomato fruits using laser microdissection.
Talk title: A High-resolution Spatiotemporal Atlas of the Tomato Fruit Transcriptome
Session IX - Abiotic Stresses • Francisco Borja Flores Pardo, Plenary Speaker
Borja Flores is a researcher from the Spanish Scientific Research Council (CSIC,
Spain). He obtained his Ph.D. in Biochemistry in 2001 and then he fulfilled
postdoctoral stages in ENSAT-INP/INRA (Toulouse, France) and the University of
Nottingham (United Kingdom), where his research was focused on fruit ripening,
quality and postharvest physiology of horticultural crops. In 2007 he joined the
group of Abiotic Stress in the research centre CEBAS-CSIC (Murcia), where its
research is focused on the tomato tolerance against abiotic stress, mainly salt and
water stress, using different approaches. In order to identify key genes involved in
salinity and water stress tolerance, my group together with other two Spanish
Groups (IBMCP-UPV/CSIC of Valencia and Agro-Food Biotechnology Research
Centre from the University of Almeria) are generating an insertional mutant
collection in cultivated and wild tomato species. Some remarkable genes involved in salt and drought
tolerance have already been identified and cloned thanks to the identification and characterization of
mutants from these collections, and functional analysis of them is currently being carried out.
Talk title: New Tomato Mutant Collections for the Identification of Key Genes Involved in Tolerance to
Salinity and Drought
Session IX - Abiotic Stresses • Yveline Pailles, Invited Speaker
Yveline Pailles is a PhD candidate in Plant Sciences at King Abdullah University of
Science and Technology in Saudi Arabia. She received her BS. with honors in Food
Science and Biotechnology from the Monterrey Institute of Technology and Higher
Education in Mexico, before moving to Saudi Arabia to pursue postgraduate studies,
where she obtained an MSc. in Biosciences and is currently working towards her
PhD. Her research focuses on studying salinity tolerance of wild relatives of tomato.
Her research interests also include plant physiology and evolutionary biology.
Talk title: Galapagos Tomatoes as a Genetic Source for Salinity Tolerance
Session X - Pathogens, Pests and Microbiomes • Francine Govers, Plenary Speaker
Francine Gover‘s Phytophthora research group focuses on the biology and
pathology of Phytophthora species, in particular the late blight pathogen
Phytophthora infestans, and aims at further unravelling Phytophthor – host
interactions. Website: http://www.php.wur.nl/uk
Publications: http://www.researcherid.com/rid/A-5616-2009
Talk title: Phytophthora Blight in Potato: Tipping the Balance Between
Resistance and Susceptibility
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Session X - Pathogens, Pests and Microbiomes • Sarah Hind, Invited Speaker
Sarah Hind is a postdoctoral research associate at the Boyce Thompson Institute at
Cornell University (Ithaca, New York). She received her Ph.D. in Molecular, Cell, and
Developmental Biology at the University of South Carolina in 2010. During her
graduate studies Sarah examined the function of a multi-protein complex in tomato
plant responses to herbivorous insects and pathogens. Since 2011 she has worked
in the laboratory of Gregory Martin and investigates signaling proteins involved in
immunity to Pseudomonas syringae pv. tomato which causes bacterial speck
disease in tomato. The overall focus of her research is on how plants defend
themselves from pathogens and insect pests, with a specific emphasis on the
identification and characterization of plant immune receptors and signaling components. Throughout her
career Sarah has worked on tomato using a variety of molecular, genetic, and biochemical techniques, and
hopes to continue contributing toward the improvement of tomato in the areas of disease and pest
resistance.
Talk title: Tomato Receptor FLAGELLIN-SENSING 3 Binds FLGII-28 and Activates the Plant Immune
System
Session XI - Tubers and Root Systems • Salomé Prat, Plenary Speaker
Salomé Prat‘s research group aims to identify which signaling cascades govern
etiolated seedling development in the dark and how these cascades are affected by
light, with a particular focus in the mechanisms involved in integration of the light
signal with the own running developmental programs of the plant. The plant
hormones gibberellins (GA) and brassinosteroids (BRs) play a central role in
transducing the light signal as judged from the dark de-etiolated phenotype of
mutants with a block in the synthesis or response to these hormones.
Talk title: Control of Potato Tuberization by the CONSTANS-FT Module
Session XI - Tubers and Root Systems • Craita Elena Bita, Invited Speaker
Craita Elena Bita was born in Bucharest (Romania) in 1978, graduated in Plant
Biotechnologies at USAMV Bucharest in 2001 and continued with a Master Degree in
Horticultural Biotechnologies at MAICh (Greece) in 2003 where she investigated the
genetic diversity within cultivated olive germplasm from the Eastern Mediterranean
Basin. Later on she took on postgraduate research projects at several laboratories in
Germany, the Netherlands and Greece, using molecular markers and transcriptomics
tools to investigate the molecular response of environmental effects on plant growth
and reproductive development in various plant species. She completed her PhD
project in 2011 at the Wageningen University and Research Centre in the Netherlands
on fingerprinting heat stress effects during reproductive development in heat-sensitive and heat-tolerant
tomato plants. In 2014 she returned to MAICh to study several aspects of growth and development in
tomato fruits including abscission and ripening. At present she is working at the James Hutton Institute in
Dundee, UK, decrypting mechanisms of acquired thermotolerance in potato and developing varieties with
improved yield performance under heat stress conditions.
Talk Title: Characterization of Acquired Thermotolerance in Potato
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Session XII - Flowers, Seeds, and Fruit • Mondher Bouzayen, Plenary Speaker
Mondher Bouzayen: Ph.D. 1989, University of Toulouse, France; Postdoc. 19901992, Nottingham University, UK; Current position: Full Professor, University of
Toulouse, Head of the GBF laboratory (Genomics and Biotechnology of Fruits), INRA
/ INPT, France. He is the Chair of the European research network on fleshy fruit
(COST Action FA1106) and the coordinator of TomGEM project within the EU
Framework Programme for Research and Innovation H2020. His research deals
with developmental transitions during fleshy fruit development, particularly the
flower-to-fruit transition (fruit setting) and the shift from immature to mature (fruit
ripening). His main interest is cross-talk hormone signalling. Tomato is the main
model plant for its economic importance and the advanced genomics tools and
genetic resources available in this species. His research addresses the integration
of ethylene and auxin signaling. GBF actively contributes to major international
initiatives on the tomato such as the genome sequencing project and the generation of tools for high
throughput expression profiling.
Talk title: The Regulatory Network Controlling Fruit Ripening: A Complex Interaction Between MultiHormonal Signaling and Developmental Factors
Session XII - Flowers, Seeds, and Fruit • Barbara Blanco-Ulate, Invited Speaker
Barbara Blanco-Ulate has recently been appointed as an Assistant Professor in the Department of Plant
Sciences at UC Davis with an emphasis on postharvest physiology. She obtained a
Ph.D. in Plant Biology from UC Davis in 2014, investigating the developmental
control of tomato fruit susceptibility to Botrytis cinerea. Her dissertation research
characterized fruit responses to fungal infection and explored pathogen infection
strategies. She did her postdoctoral research in the Department of Viticulture and
Enology at UC Davis, characterizing the impact of pathogen infections on the
ripening and quality of grape berries. She established innovative approaches
integrating transcriptional profiling with metabolite and biochemical data to study
the development and metabolism of ripening berries under field conditions. She
will focus on tomato and pepper fruit, which represent economically valuable
postharvest commodities worldwide and in California. Her research interests
include the control of fruit ripening, softening, improvement of flavor and aroma,
and fruit-pathogen interactions.
Talk title: Acceleration of Ripening-related Host Cell Wall Disassembly During Botrytis cinerea
Infections of Unripe Tomato Fruit
Session XIII - Plant Development and Regulation • Jose M. Jiménez-Gómez
Frontiers sponsored Plenary Speaker
Jose M. Jiménez-Gómez obtained his Ph.D. at the CNB-CSIC in Madrid performing a
QTL analysis for flowering time in tomato. He then moved to the Maloof lab at
UCDavis, where he learned to use genomics and bioinformatics to study natural
variation in Arabidopsis and to perform comparative transcriptomics in tomato.
Since that time, he has headed a group in the Max Planck Institute for Plant
Breeding Research in Germany and currently at IJPB, INRA-Versailles in France. His
research group is interested in the study of molecular mechanisms involved in plant
adaptation to natural and artificial environments. Relevant for this meeting, part of
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his lab studies the effect of domestication in flowering time and circadian rhythms in tomato.
Talk title: Domestication Delayed Circadian Rhythms in Tomato
Session XIII - Plant Development and Regulation • Hester Sheehan
Plant Physiology Sponsored Invited Speaker
Hester Sheehan a Swiss National Science Foundation-funded postdoctoral fellow at
the University of Cambridge, currently working on the evolution of betalain
pigmentation in the Caryophyllales. She is interested in the evolution of secondary
metabolites and understanding the molecular evolution of the structural genes and
genetic networks that control the production of these specialized compounds. She
completed her PhD in 2016 at the University of Bern where she worked on
characterising the molecular basis of adaptation to pollinators in Petunia. In
particular, she focused on alterations in anthocyanin pigments and the UVabsorbing pigments, flavonols.
Talk title: Examining the Molecular Basis of Speciation in Petunia Through Flavonoid-tinted Glasses
Session XIII - Plant Development and Regulation • Kaisa Kajala, Invited Speaker
Kaisa Kajala (https://twitter.com/kaisakajala?lang=en) is a postdoctoral scholar in the
Brady lab (http://www-plb.ucdavis.edu/labs/brady/) at UC Davis. She received BA and
Ph.D. degrees in Natural Sciences from the University of Cambridge, UK before
joining the Brady lab in 2012. For the past four years she has been working on
tomato root development in S. lycopersicum cv. M82 and S. pennellii as part of the
NSF-funded Integrative Plasticity project (http://plant-plasticity.github.io/index.html).
She’s generated nuclear-tagging and ribosome-tagging marker lines in order to
characterize gene expression in a dozen different cell types and developmental
stages. These marker lines are currently used to elucidate the underlying molecular
mechanisms of cell type differentiation, especially in response to drought and
flooding. Her favourite cell type is exodermis, which contains apoplastic barriers to
protect the root from drying and drowning.
Talk title: Regulation of Tomato Meristems in Response to Submergence
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Session XIV - Metabolites, Flavor and Quality • Harry Klee, Plenary Speaker
Harry Klee received a Ph.D. in Biochemistry from the University of Massachusetts.
He did postdoctoral research on Agrobacterium tumefaciens at the University of
Washington. He was employed by Monsanto Company from 1984-1995 where he
developed technologies for plant transformation and transgene expression and
participated in the team that developed Roundup resistant crops. He has worked on
ethylene for the last three decades, with emphasis on its role in tomato fruit
development. In 1995, he joined the University of Florida where he established a
program to understand the biochemistry and genetics underlying flavor of fruit
crops. He is a member of the National Academy of Sciences and is President-elect
of the American Society of Plant Biologists. His laboratory has identified many of the
genes encoding important flavor synthesis activities. That work has transitioned into
large-scale genomics approaches for improvements of tomato flavor, initially focusing on varieties for the
home garden market and expanding into commercial germplasm.
Talk title: The Genetic Blueprint for Developing a Better Tasting Tomato
Session XIV - Metabolites, Flavor and Quality Session • Gaurev Moghe, Invited Speaker
Dr. Gaurav Moghe is a postdoctoral researcher in Dr. Robert Last’s lab at Michigan
State University. While working on understanding the architecture and evolution of
plant genomes during his PhD, Dr. Moghe developed interest in investigating the
origins of biological complexity. His postdoctoral research focuses on unraveling the
various modes by which metabolic pathways evolve and create chemical novelty in
the plant world, using acylsugar biosynthesis in Solanaceae as an example. His
research integrates diverse approaches and themes from biochemistry, genomics,
bioinformatics and evolution. Dr. Moghe has published 12 papers on topics related to
plant molecular evolution.
Talk title: Comparative Biochemical Genomics of Solanaceae Acylsugars Illustrates
the Mechanisms of Evolutionary Diversification in Plant Specialized Metabolism
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CONFERENCE PROGRAM
MONDAY, SEPTEMBER 12
1 - 4:30 pm
Conference Check-In
Conference Center Lobby
4:30 - 6:00 pm
Opening Ceremony, Conference Center Ballroom
Welcome Address: Secretary Karen Ross, California Department of Food and Agriculture
Plenary Talk: Richard Michelmore, UC Davis Genome Center
Talk Title: Disruptive technologies and improvement of disease resistance in lettuce.
6:00 - 9:00 pm
Welcome Reception
VanderHoef Quad (in front of Conference Center)
Appetizers, food trucks, dessert, local wine and beer, Mariachi music
TUESDAY, SEPTEMBER 13
8:00 am Announcements
Session I • DIVERSITY-TAXONOMY/CROP GERMPLASM DIVERSITY
Ellen Dean and Irma Ortiz, Chairs
8:15 — 9:45 am, Conference Center Ballroom
8:15 am
DIVERSITY AND DISTRIBUTION IN THE SOLANACEAE - NOT QUITE WHAT IT MIGHT SEEM!
Knapp S.1, Echeverria-Londoño S.1,2, Sarkinen T.3, Purvis A.1
1
Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United
Kingdom; 2Imperial College London, London SW7 2AZ, United Kingdom; 3Royal Botanic Garden
Edinburgh, 20A Inverleith Way, Edinburgh EH3 5LR, United Kingdom
Contact: Sandra Knapp, [email protected]
Solanaceae – the family conjures up images of foods galore and the power of human domestication to
manage and exploit the diversity of plant life. But Solanaceae are much more than just the foods we eat;
the family comprises some 3000 species distributed worldwide, almost half of these in the mega-diverse
genus Solanum. The richest area of the world in terms of both generic and species diversity is South
America, but Solanaceae have radiated in other areas as well. In this talk we will explore the diversity of the
family, both in terms of patterns and origins. New data from taxonomy and phylogenetics coupled with
analyses using the tools of macroecology and evolution show that diversification of the family at the
generic level does not mirror that in the large and complex genus Solanum– where diversification rates are
highest not in South America, where species numbers are greatest, but in the arid zones of Australia and
Africa, where long-distance dispersal at just the right time from perhaps just the right lineage led to an
explosion in species diversity. We will explore some of the consequences of this for the study of
Solanaceae diversity worldwide, and suggest new avenues for collaborative research involving the whole
SOL community – from genomics to biodiversity.
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8:45 am
DIVERSE AND NOVEL PHENOTYPES IN NICOTIANA ALLOPOLYPLOIDS: THE GENETIC BASIS OF
FLORAL PIGMENTS
McCarthy E.W.1, Berardi A.E2,+, Smith S.D.2, and Litt A.1
1
Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA;
2
Department of Ecology and Evolutionary Biology, University of Colorado-Boulder, Boulder, CO, USA;
+
Current address: Institute of Plant Sciences, University of Bern, Bern, Switzerland
Contact: Elizabeth McCarthy, [email protected]
Approximately half of the species in the genus Nicotiana (tobacco) are allotetraploids of different ages,
arising from whole genome duplication and interspecific hybridization. The diploid progenitors of these
polyploids have been well-established. Polyploidy is a widespread phenomenon in the evolution of
flowering plants, and allopolyploids often display diverse and even transgressive (outside the range of
the progenitors) phenotypes. Here, we investigate the genetic and regulatory basis for the diverse and
transgressive floral color phenotypes found in Nicotiana allopolyploids. Floral color affects pollinator
attraction and thus floral color differences may lead to reproductive isolation and species
diversification.
Nicotiana displays substantial diversity in floral morphology, and allopolyploids from the same
progenitors often have divergent floral phenotypes. Using two accessions of N. tabacum that display
different floral colors (magenta and pink), we tested the hypothesis that differences in homeolog
(progenitor gene copy) expression ratios underlie floral color variation in allopolyploids. To address this
hypothesis, we quantified pigment gene expression from transcriptome data and measured the
composition and concentration of floral flavonoids (anthocyanins and flavonols). We mapped our
pigment data and homeolog expression ratios onto the flavonoid biosynthetic pathway to determine
whether differential homeolog expression between magenta and pink allopolyploids yields different
pigment composition or concentration. Magenta N. tabacum flowers have an increased concentration
of cyanidin pigment compared to pink ones. However, at anthesis, there are no differences in
homeolog expression ratios or overall expression of anthocyanin biosynthetic genes, which does not
support our hypothesis. It is possible that differential expression earlier in floral development yields
floral color differences. Magenta buds start producing pigment at 75% of full length whereas pink buds
are 95% of full length when pigment is first observed. Preliminary semi-quantitative RT-PCR data show
that late anthocyanin biosynthetic genes are upregulated earlier in development in magenta flowers.
These results suggest that production of cyanidin over a longer period may explain the observed
increase in concentration. In addition, Nicotiana allopolyploids produce novel pigments not observed
in either progenitor, suggesting that allopolyploidy yields shifts in the regulation and flux of the
flavonoid pathway that create transgressive phenotypes, which may affect pollinator attraction.
9:00 am
RECENT INSIGHTS INTO SPECIES DIVERSITY AND RELATIONSHIPS IN CAPSICUM L.
Carrizo García C.1, Ehrendorfer F.2, Barboza G.E.1,3
1
IMBIV, CONICET-UNC, Córdoba, Argentina; 2Dept. of Botany and Biodiversity Research, Vienna
University, Vienna, Austria; 3Faculty of Chemical Sciences, Córdoba University, Córdoba, Argentina
Contact: Gloria Barboza, [email protected]
Capsicum L. (Solanaceae) is a genus of great economic importance because it includes the renowned
sweet and hot chili peppers. Apart from the five cultivated species, there are ca. 30 poorly known wild
species, distributed from Mexico to Brazil, Paraguay and Central Argentina. The species diversity of the
genus has not been exhaustively analyzed so far, and therefore, the number of species, their
delimitation and relationships are not yet completely understood. Capsicum species predominantly
have the chromosome base number of x = 12, but x = 13 is also registered. There are several partial
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studies that deal with different groups of species but only recently a comprehensive analysis of the
total genus diversity and evolution has been done by our research group. The current meeting offers
the opportunity to present our results on Capsicum species diversification and relationships, and to
discuss them within the context of our more recent phylogenetic analyses.
Altogether, several clades of more closely allied species and some isolated species are recognized.
The most basal and unique Capsicum species belong to a clade native to the northern Andes and
adjacent Central America with non-pungent red fruits and x = 13. The current territories of Bolivia and
Peru as well as the Andes of NW South America have to be regarded as the most important centers of
diversification concerning several not closely related lineages with x = 12. The Atlantic Forest of SE
Brazil is another relevant center of diversification of wild chilies, mostly with greenish yellow fruits and
x = 13. The cultivated species belong to three different lineages among the most derived clades of the
genus; no closer wild relatives can be suggested for C. pubescens.
Even though at least 35 Capsicum species can be distinguished today, both cultivated and wild, a
number of populations are still under study to define their identity. All this suggests that the species
number of Capsicum may still increase. Thus, new and extensive field expeditions are obligatory to
obtain a better understanding of the total Capsicum diversity.
9:30 am
TRADITOM: DIGGING IN THE TRADITONAL VARIABILITY POOL OF EUROPEAN TOMATO FOR
FRUIT QUALITY AND RESILIENCE
The TRADITOM partners as in traditiom.eu (presented by Anthony Granell1)
1
IBMCP (CSIC-UPV), Valencia, Spain
Contact:Tony Granell, [email protected]
Europe can be considered a secondary diversification for tomato since its introduction in XVII century
Europe by Spanish Conquistadores. In the frame of the EU-funded project TRADITOM we have started
to characterize the genotypic and phenotypic variability of 1500 traditional varieties available on farms
and in public repositories throughout Europe. A total of 300Gb of genotype information (equivalent to
300 tomato genomes) have been produced during this first year. Approximately 2x the whole
TRADITOM collection has been cultivated (over 15k plants), with different subpopulation growing in a
total of 12 location spreading over 5 different countries. For each of the 1500 varieties a total of 19
qualitative and 117 quantitative traits have been measured and recorded. In addition, a total of >100 Gb
of images, scans at the plant of fruit level has been recorded.
The genotyping by GBS of this TRADITOM collection has revealed that despite the limited variability, there
is still a possibility to associate it with geographical and phenotypic characteristics. Despite the reduced
genetic variability the extensive phenotyping revealed ample variability in traits related to plant architecture
and fruit characteristics. Large variability has been found in fruit size, shape, Brix and also in fruit ripening
time. A subset of the European traditional varieties show extended shelf life and the ability to grow and set
fruit under limited water which is of high interest. I will present some of this variability present in the
TRADITOM collection and our progress in understanding the basis of this variability.
COFFEE Break (9:45 — 10:05 am), Conference Center lobby and patio
Session II • BARRIERS TO BREEDING
Roger Chetelat and Benny Ordonez, Chairs
10:05 — 11:30 am, Conference Center Ballroom
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10:05 am
ELUCIDATING MECHANISMS AND DYNAMICS OF REPRODUCTIVE ISOLATION IN WILD TOMATO
SPECIES
Bedinger, P.A.1, Baek, Y. S.1, Broz, A.K.1, Randle, A.M.2, Royer, S.M.1, Chetelat, R.T.3, Tovar-Méndez, A.4,
McClure, B.4
1
Biology Department, Colorado State University, Fort Collins, CO, USA; 2Department of Environmental
Science, University of San Francisco, San Francisco CA, USA; 3Plant Sciences Department, University
of California, Davis, CA, USA; 4Department of Biochemistry, University of Missouri-Columbia, Columbia
MO, USA
Contact: Pat Bedinger [email protected]
Interspecific Reproductive Barriers (IRBs) prevent hybridization between closely related species, such
as the wild tomato species (Solanum sect. Lycopersicon). Active rejection of interspecific pollen tubes
within styles often follows the SI x SC rule, a type of unilateral incompatibility (UI): crosses between
females of self-incompatible (SI) species and males from self-compatible (SC) species fail, while
reciprocal crosses succeed. We tested the generality of the SI × SC rule, examining pollen tube growth
in crosses between all 13 clade members, and found that pistils of SI species always reject pollen of SC
species. However, pistils of some SC species and SC populations of otherwise SI species also rejected
interspecific pollen. Thus, an intact SI system is sufficient for the rejection of interspecific pollen, but
partial SI systems, or redundant non-SI systems, can also contribute to UI pollen rejection. Using
transgenic approaches, we directly demonstrated that both pollen and style SI factors also function in
UI. To further explore the relationship between SI and UI, we investigated mating system dynamics and
IRBs at the margins of the wild tomato Solanum habrochaites range. At the southern margin, an SRNase allele encoding a low-activity protein is associated with the loss of SI and pistil IRBs seem to be
unaffected. At the northern margin, loss of SI is associated with the at least two independent events
causing loss of S-RNase expression. In the north, IRBs are weakened, and in some cases are lost
altogether, due to subsequent accumulation of additional mutations. When pollen-side mutations also
become fixed, SC populations become reproductively isolated from the ancestral SI populations. In
parallel experiments using interspecific crosses between accessions from 10 sympatric sites in Peru,
we documented prezygotic IRBs including pollen tube rejection, conspecific pollen precedence, and
lack of ovule targeting. We also found postzygotic IRBs leading to defective seed development in
these populations. In a minority of interspecific crosses, normal seed formed and normal fertile F1
hybrid plants were produced, demonstrating that even with the array of reproductive barriers found in
wild tomato species, hybridization in natural populations could occur at a low frequency.
10:30 am
WILD TOMATO: POPULATION STRUCTURE AND EVIDENCE OF NATURAL S. CHILENSE X S.
PERUVIANUM HYBRID POPULATIONS
Beddows I., Kloesges, T., Rose, L. E.
Institute of Population Genetics, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
Contact: Ian Beddows, [email protected]
The wild tomato clade (Solanum sect. Lycopersicon) is native to the western coast of South America.
The section shared a last common ancestor approximately 2-3 Mya, but has since diversified into
upwards of 12 species. Intraspecific variation in plant size, shape, habit, and other characters has made
systematics following the morphological species concept very difficult in the group, and widespread
incomplete lineage sorting (ILS) has hampered genetic studies.
To better understand the ancestry of two allogamous-SI sister species, S. chilense and S. peruvianum,
we conducted individual RNA sequencing on a total of 36 individuals from different populations of the
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two species. Two outgroup species from neighboring sections were also sequenced, and previouslypublished sequence data from 59 additional wild tomato accessions (11 species total) was included to
investigate the full evolutionary history of sect. Lycopersicon. Our comprehensive analyses confirmed
four main species groups within the section, but widespread admixture between groups has resulted in
para- and polyphyly for some taxa.
Using the synonymous JSFS, we model the S. chilense - S. peruvianum speciation event at 1.4 million
Ne generations ago. We find that the population size of S. peruvianum is 3.78 times larger than the
shared ancestral population size (Ne). The genetic diversity is distributed into two demes: a coastal
lomas deme and a more mountainous south-central Peru deme. In contrast, S. chilense has a smaller
effective population size (1.28 Ne individuals) and less population structure. Heterozygosity decreases
with longitude, indicating a recent S. chilense expansion south.
In contrast to previous studies, we detect little evidence for post-divergence gene flow between these
sister species. In fact, earlier reports of gene flow were confounded by the inclusion of disjunct
northern populations of S. chilense. We discovered that these populations are in fact S. chilense x S.
peruvianum interspecific hybrids with transgressive phenotypes in several characters including habit,
leaf size, stem width, branching pattern, and trichome density. The hybrid populations are stable
through time and may therefore be an example of homoploid hybrid speciation. These populations
present a new opportunity to study hybrid zones, crossing barriers, and speciation in plants.
10:50 am
THE GAMETE ELIMINATOR AS A MECHANISM OF ISOLATION IN WILD POPULATIONS AND A
REMNANT OF INTROGRESSION IN CULTIVATED TOMATO
Francis D.M.1, Barrantes W.2,3, Fakhet D. 2, Pons C.2, Blanca J. 4, Granell A.2, Monforte A.J.2
1
The Ohio State University, Wooster, OH, USA. 2IBMCP and 3COMAV, Universidad Politécnica de
Valencia, Spain. 4Universidad de Costa Rica, La Garita-Alajuela, Costa Rica
Contact: Dave Francis, [email protected]
Segregation distortion on chromosome 4 is associated with undeveloped ovules and pollen abortion.
Classical genetics defined “gamete eliminator” (Ge), with at least three alleles GeP, GeC and Genin
cultivated varieties. Female and male gametes are affected to the same extent, elimination of gametes
is dependent on the interaction of GeP and GeC in heterozygotes, and Ge behaves as if it were
incompletely penetrant. To investigate the origin of Ge, we used a combination of genetic mapping,
analysis of haplotype and allele frequencies, and re-sequencing. Segregation distortion on
chromosome 4 in some S. lycopersicum x S. pimpinellifolium crosses, but not others, suggested that
more than one Ge allele might be present in S. pimpinellifolium accessions. Fine mapping in S.
lycopersicum x S. lycopersicum and S. lycopersicum x S. pimpinellifolium populations narrowed Ge to a
100 Kb region. There are both potential candidate genes and structural variations in the region
identified. Analysis of linkage disequilibrium demonstrates a strong isolating influence on chromosome
4. Clustering of haplotypes from 1,250 accessions of wild and domesticated tomatoes suggests a role
for this region in enforcing population sub-division. The same clustering was observed based on
sequence analysis. The Gep haplotype and gene sequences identified in some processing tomato
varieties are identical to a haplotype/sequence shared by S. pimpinellifolium accessions from
previously identified Ecuadorian sub-populations. Two other haplotypes identified in processing
tomato lineages cluster with fresh-market, vintage, and S. lycopersicum var cerasiformae accessions.
These results suggest that Gep, originally described in Pearson a precursor to Californian processing
varieties, resulted from an introgression from S. pimpinellifolium. In wild populations, gamete abortion
in Gec and GeP hybrids potentially serves as an isolating mechanism and may reinforce population
substructure by limiting interbreeding of some parental combinations.
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11:10 am
LIFTING BARRIERS IN DIPLOID HYBRID POTATO BREEDING
Lindhout P., Viquez-Zamora M. Ying, S. ter Maat M. de Vries M. van Heusden A.W.
Solynta, Wageningen, The Netherlands
Contact: Pim Lindhout, [email protected]
A prerequisite for hybrid potato breeding is the development of homozygous lines, preferably at the
diploid level. However, diploid potato breeding is blocked by self-incompatibility and severe
inbreeding depression. Recently, Solynta has lifted these barriers by introgression the Sli-gene from S.
chacoense and by dedicated breeding, consisting of many generations of crossings, selections and
selfings.
The first essentially homozygous self-compatible potato genotypes have already been generated in
2012. Since then new crosses between inbred lines were made and the progenies selfed to gradually
remove the alleles that are associated with inbreeding depression and hence increasing the
performance of the new inbred lines. Typically, the higher level of homozygosity is associated with
reduction of self-compatibility, plant vigour and tuber yield, but it does not affect quality traits like chips
frying quality and dormancy.
The most advanced inbred lines are used for two purposes:
1). Hybrid breeding
The best performing lines are assumed to have the best potential breeding value and these are
crossed to generate experimental hybrids. In the summer season of 2015 the first series of diploid
experimental hybrids were evaluated in the field. Seedlings and greenhouse grown seed tubers were
used as starting materials and compared with tetraploid controls. The results of these premature test
were encouraging and in 2016 series of hundreds of newer hybrids are tested at several locations in
EU.
2). Genetic studies
Our most homozygous inbred lines are used for genetic studies on important potato traits, like
earliness, plant vigor, tuber quality, etc.
In addition, advanced inbred lines are used to introgress resistance genes to Phytophthora infestans
by marker assisted backcrossing, whereby an existing hybrid variety is enriched with two stacked
resistance genes in only two years. Moreover, a mutant population is being developed for tilling
purposes and to identify useful mutants. Finally, The Solynta inbred lines are also used by national and
EU (public / private) consortia in studies on plant development, efficiency of photosynthesis, heat
tolerance, metabolism of tubers pigments and predicting breeding value.
LUNCH Break (11:30 am — 12:45 pm)
Mondavi Center lobby (across the quadrangle from Conference Center)
Session III • GENOMES AND GENOME TECHNOLOGIES
Massimo Delledonne and Arsenio Ndeve, Chairs
12:45 — 2:15 pm, Conference Center Ballroom
12:45 pm
DEMOCRATIZATION OF REFERENCE QUALITY GENOME SEQUENCING FOR NON-MODEL
ORGANISMS
Cantu D.
Department of Viitculture and Enology, University of California, Davis, CA, USA
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Contact: Dario Cantu, [email protected]
Biotic interactions in the vineyard contribute to define grape productivity. Many microorganisms,
including viruses, bacteria and fungi are capable of infecting grapevines causing important damage if
left uncontrolled. Many more microorganisms, endophytic or epiphytic, are not pathogenic and may
play a positive role in wine grape yield and chemical composition. Although recent reports have shown
that composition of microbial communities correlates with quality characteristics and regional variation
among wine grapes, our understanding of the interactions between microbial communities and
grapevines is still limited. Here, I will discuss the use of whole genome sequencing based on single
molecule real time sequencing (SMRT) technology to generate high-quality genome references for the
plant host and the associated microorganisms to study their interactions under natural field settings.
The highly heterozygous genome of Cabernet Sauvignon was sequenced at 140x coverage with the
PacBio RSII using a combination of 20kb and 30kb DNA libraries. Reads were assembled into 788
contigs of total length of 590Mb, achieving a contig NG50 and NG90 of 2.1Mb and 1Mb, respectively.
Genetic and optical maps are being used to improve contig scaffolding. The same approach was used
to sequence the genomes of some of the most common and economically important fungal grape
pathogens. For most species, SMRT sequencing yielded the reconstruction of entire chromosomes in
individual contigs from telomore-to-telomere. These high quality genome sequences have provided us
with the references necessary to apply metatranscriptomics and profile genome-wide gene expression
of all interacting organisms simultaneously, including the grapevine host. Resequencing using short
read technologies of multiple isolates and metatranscriptomic sequencing of vineyard samples has
given us the opportunity to associate microbial activity, gene expression with genetic diversity. To
study the impact of microbial activity on grape metabolism we have been integrating transcriptomics,
metabolomics, and enzyme activity assays. Integrative systems-level analysis of grape berries during
the interaction with biotrophic and necrotrophic pathogens is shading light on how microbial activities
can reprogram berry development and metabolism.
1:15 pm
YOU SAY TOMATO, I SAY POTATO: HIGH-QUALITY GENOME ASSEMBLY OF THE SISTER-GROUP
SPECIES SOLANUM ETUBEROSUM PROVIDES INSIGHTS INTO GENOME AND TRAIT EVOLUTION
Berke L.1, Grandont L.1, Aflitos S.A.2, Bachem C.W.B.3, Becker F.1,4, Bouwmeester K.5, van de Geest H.2,
Govers F.5, de Jong J.H.4, Peters S.A.1,2, Sanchez-Perez G. F.2,6, Schijlen, E.2, van den Berg R. G.1,
Schranz M.E.1
1
Biosystematics, Wageningen University & Research Center, Wageningen, The Netherlands, 2 Plant
Research International, Wageningen University & Research Center, Wageningen, The Netherlands,
3
Laboratory of Plant Breeding, Wageningen University & Research Center, Wageningen, The
Netherlands, 4 Laboratory of Genetics, Wageningen University & Research Center, Wageningen, The
Netherlands, 5Laboratory of Phytopathology, Wageningen University & Research Center, Wageningen,
The Netherlands, 6Bioinformatics, Wageningen University & Research Center, Wageningen, The
Netherlands
Contact: Lidija Berke, [email protected]
To elucidate the evolutionary history and basis of chromosomal, molecular and phenotypic differences
between tomato and potato, genomic data from a key outgroup species is needed. Solanum
etuberosum, a non-tuber-bearing species from Chile, fulfills this requirement: its ancestors diverged
from the tomato-potato lineage shortly before the split of the tomato and potato clades. With the aim of
investigating both genome and trait evolution, we sequenced and assembled the genome of S.
etuberosum. The initial Illumina assembly consisted of 3666 scaffolds with the N50 statistic of 1.7Mb
and captured 94% of the predicted 702 Mb genome size. The assembly was further scaffolded using
BioNano genome mapping, yielding a final genome assembly that surpassed an N50 of 5Mb. Hence, it
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is one of the most contiguous Solanum genome assemblies thus far, and with 97% coverage of the
expected gene space, also one of the most complete ones. We subsequently annotated the genome
sequence and reconstructed the evolution of genes crucial to potato and/or tomato phenotypes and
specifically related to tuber formation, pathogen resistance, flower color and glycoalkaloid
biosynthesis. The genome of S. etuberosum thus proved to be an invaluable resource for novel
insights in the Solanum genus.
1:35 pm
UTILIZING LONG-RANGE SHORT-READ TECHNOLOGY FOR A BETTER PEPPER GENOME
Hulse-Kemp A.M.1, Maheshwari S.1, Stoffel K. 1, Hill T.A.1, Jaffe D.2, Weisenfeld N.2, Kumar V.2, Shah P.2,
Schatz M.C.3, Church D.M.2, and Van Deynze A.1
1
Plant Sciences Department,University of California, Davis, USA, 210X Genomics Inc., Pleasanton,
California, USA; 3Department of Computer Science, John Hopkins University, Baltimore, Maryland,
USA
Contact: Amanda M. Hulse-Kemp, [email protected]
The pepper genome is one of the largest in Solanaceae at approximately 3.5 Gigabases and is
comprised largely of repetitive elements estimated at 75-80% of the genome. As pepper is a diploid
species, the genome structure has not inhibited production of multiple draft genome reference
sequences using next generation sequencing technology with short reads. However, these genomes
are largely comprised of a large number of small scaffolds with 37,989 scaffolds in the CM334, 967,017
scaffolds in the Zunla-1, and 1,973,483 scaffolds in the Chiltepin genomes with the largest scaffold N50
at 2.47Mb in the CM334 assembly. Recently third generation technologies have been released that
capture long range sequence information in order to enhance the ability of generating higher quality
reference sequences with a smaller number of larger scaffolds. These results have been promising on
many different species in not only improving existing genomes, but generating new genomes de novo.
Ability of breeders and researchers to use the pepper genome for improvement of the crop is
dependent on a high-quality reference that provides anchoring and ordering of the majority of the
sequence. Thus we have targeted the second generation 10X Genomics Chromium® technology for
improving the pepper genome, by taking advantage of the long-range information together with
affordable short-read technology. 10X Chromium not only builds on scaffolds, but allows for de novo
genome assembly in a fraction of the time and cost with little input DNA. Importantly, the resulting
assembly is phased as part of the assembly process, something that is not currently achievable using
other technologies. Initial results indicate a significant improvement over any pepper short read
genome assembly. We will report on the progress of generating a high quality pepper genome using
this technology.
1:55 pm
NICOTIANA GENOMES: BEYOND TOBACCO
Sierro N., Battey J., Ouadi S., Thomas J., Liedschulte V., Bovet L., Broye H., Laparra H., Vuarnoz A.,
Lang G., Goepfert S., Peitsch M.C., Ivanov N.V.
Philip Morris International R&D, Philip Morris Products S.A., Neuchatel, Switzerland (part of Philip Morris
International group of companies)
Contact: Nicolas Sierro, [email protected]
While Nicotiana tabacum is likely the most notable species from the Nicotiana genus, various other
Nicotiana species are cultivated as crops, grown as ornamental garden plants, or used as model
organisms in research. Within Solanaceae, Nicotiana species are peculiar first because although most
Solanaceae species are diploids, a high number of Nicotiana species are tetraploids; and second
because they have relatively large genomes that are similar in size with Capsicum species and two to
three times larger than Solanum and Petunia species.
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To date, the genomes of N. benthamiana, N. otophora, N. sylvestris, N. tabacum and N.
tomentosiformis have been sequenced and draft assemblies published, enabling genome-based
evolutionary studies of Nicotiana species. With the exception of N. benthamiana, all the published
Nicotiana genomes are however closely related to N. tabacum. To complement these already
published genomes we present here new draft genomes for additional Nicotiana species, which we
expect will contribute to further our understanding of the diversity and of the impact of polypoidization
in the Nicotiana genus.
Session IV • HIGH-THROUGHPUT PHENOTYPING
Allen Van Deynze and Lav Kumar Yadav, Chairs
2:15 — 3:25 pm, Conference Center Ballroom
2:15 pm
IN-FIELD HIGH-THROUGHPUT PHENOTYPING FOR PLANT ARCHITECTURE AND INTERNAL FRUIT
QUALITY IN TOMATO
Slaughter D.C.1, Nguyen T.T.1, Maloof J.2, Sinha N.2 Max N.3
Departments of 1Biological and Ag. Engineering, 2Plant Biology, and 3Computer Science, University of
California, Davis
Contact: David Slaughter, [email protected]
As a society, we face multiple challenges in our endeavor to provide food security to all people. The
global population growth (a 30% increase, to 9 billion people, in the next 35 years) will add to the 2
billion people (~28% of the current population) who are now food insecure. Unmitigated climate
change is projected to increase the frequency of extreme weather events and decrease the yields of
our cropping systems in California by ~15% over this same period with prolonged drought depressing
yields even further.
Currently, a lack of smart machines and technologies in agriculture, coupled with the need for realworld, on-farm research at scale is dramatically limiting our ability to increase our understanding of how
plants sense and react to their environments and therefore limits our capacity to accelerate the rate of
food crop improvement. Efficient use of genomics-enabled breeding for new crops that are productive
under and biotic and/or abiotic stress are severely hindered by the high cost and time-intensive
manual methods of evaluating traits in field-grown crop plants in the Solanaceae family.
This presentation describes the development of a novel smart machine for automated high-throughput
phenotyping of Solanaceae food crops that is capable of creating 3D models of showing the
morphology of individual plants growing in the natural outdoor environment of a farm. The system uses
robotic technology and multi-view stereovision to create a high-resolution 3D reconstruction model of
each plant. From this model, the system is capable of making automatic, non-destructive rapid
phenotype measurements of plant height, a count of the number of leaves on the plant, an estimate of
area of individual leafs, total leaf area, and plant biomass, for example. This novel technology will help
to eliminate the current phenotyping bottleneck and to accelerate breeding of novel Solanaceae food
crops adaptable to climate change.
2:40 pm
PERSISTENT HOMOLOGY: A TOOL TO UNIVERSALLY MEASURE PLANT MORPHOLOGIES
ACROSS ORGANS AND SCALES
Li M.1, Frank M. H.1, Coneva V.1, Mio W.2, Topp C. N.1, Chitwood D. H.1
1
Donald Danforth Plant Science Center, St. Louis, MO USA; 2Department of Mathematics, Florida State
University, Tallahassee, FL USA
Contact: Mao Li, [email protected]
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Genetic contributions to plant morphology are not restricted to either shoot or root architectures. Yet,
shoot and root morphologies are rarely measured in the same plants. Even if the architecture of the
shoot and root are measured, the application of mathematical methods flexible enough to
accommodate the disparate topologies and shapes within a plant are lacking. Here, we advocate the
use of persistent homology, a method robust to noise, invariant with respect to orientation, capable of
application across diverse scales, and importantly, compatible with diverse functions to quantify
disparate plant morphologies, architectures, and textures. To demonstrate the usefulness of this
method, we apply persistent homology approaches to the shape of leaves, serrations, and root
architecture as measured in the same plants of a domesticated tomato Solanum pennellii introgression
line population under field conditions. We find that genetic alterations to morphology affect the plant in
a concerted fashion, affecting both the shoot and root, revealing a pleiotropic basis to natural variation
in tomato.
3:00 pm
FIELD PLATFORMS FOR HIGH-THROUGHPUT PHENOTYPING IN ARIZONA
Andrade-Sanchez P.1
1
Agricultural and Biosystems Department, University of Arizona, Maricopa, AZ, USA
Contact: Pedro Andrade, [email protected]
In Maricopa AZ a synergistic relationship was created between scientists at the University of Arizona
and USDA-ARS Arid-Land Agricultural Research Center (ALARC) to advance the study of crop plants
with proximal sensing techniques for applications to crop management in precision agriculture and
field-based phenomics. One approach has been the use of ground platforms retrofitted with
ruggedized field-ready instrumentation for high-throughput data acquisition of electronic signals at
close range (~ 1m above the top of the plant canopy). In the context of our research and extension
work, a typical sensor package includes multiple units of active radiometers for canopy light
reflectance, thermal infra-red sensors with analog outputs, and displacement sensors to characterize
canopy architecture. These signals are time-stamped and geo-referenced with strings of GPS-RTK data
collected simultaneously. The group’s success in developing efficient field-ready systems is the result
of intense peer collaboration and the ability to integrate mechanical and electronic components to this
field of study.
New developments in the group include the construction of a field scanner deployed in 0.61 ha of land.
This scanner is instrumented with a variety of imaging systems including two hyperspectral imagers
(VIS-NIR and SW), thermal, RGB and fluorescence cameras, and laser displacement sensors. A PLCbased control system enables xyz motion of the camera box with better than one millimeter accuracy.
This system generates large data streams that are taken from the field and into I2 through a 1 Gbps
circuit. This system has been functional since April of 2016, currently we are carrying out research on
energy sorghum panels as part of the Department of Energy TERRA-REF program.
Session V • GENE EDITING AND NEW BREEDING TECHNOLOGIES
AnneBritt and Julie Pedraza, Chairs
3:45 — 4:55 pm, Conference Center Ballroom
3:45 pm
GENETIC ENGINEERING AND GENOME EDITING IN THE SOLANACEAE
Van Eck J.1, Wang W.1, Brooks C.2, Nekrasov V.3, Xu C.2, Du C.1, Lippman Z.2
1
The Boyce Thompson Institute, Ithaca, NY, USA; 2Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY, USA; 3Sainsbury Laboratory, Norwich Research Park, Norwich, UK
Contact: Joyce Van Eck, [email protected]
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The Solanaceae is a family of very diverse plant species that includes important food crops, medicinal
plants, and models used for various areas of research. A number of the species are amenable to plant
tissue culture and genetic engineering, which has been key for advancement of biological and genetic
studies. Research in the Van Eck laboratory is centered on biotechnological approaches, including
genome editing by CRISPR/Cas9 technology. The majority of their work is focused on gene function
studies in the Solanaceae family for the purpose of identifying potential strategies for crop
improvement.
Tomato (Solanum lycopersicum) has quickly become a tractable model plant for genetic, biological,
and functional genomics studies. Its adoption as a model resulted from readily available resources
such as mutant collections, a high quality genome sequence, mapping populations, and efficient
transformation methodology. These resources provided the ideal platform for testing the feasibility of
the genome editing technology, CRISPR/Cas9. We started with a proof-of-concept experiment to target
a gene (ARGONAUTE7; SlAGO7) that when function was lost would result in an easily recognizable
phenotype (needle-like leaves; wiry) evident as early as the plant regeneration stage following
Agrobacterium-mediated transformation of cotyledon explants. The CRISPR construct contained two
single guide RNAs (sgRNAs) to produce large deletions to ensure disruption of gene expression. DNA
sequencing of PCR amplicons revealed the CRISPR lines were comprised of a range of mutations
including homozygous, biallelic or chimeric small insertions and deletions (indels). The indels were
present at various locations near both sgRNA targets. Following this success, we have designed more
than 50 CRISPR constructs to target genes that were shown through RNAseq analysis to possibly play
a role in plant stem cell proliferation, flowering, and inflorescence branching. The CRISPR/Cas9
technology has been a powerful tool for our reverse genetics approach to elucidate the roles of these
genes. Genes found to be of interest in tomato will also be targeted in otherSolanaceae members,
such as pepper, Physalis peruviana, Solanum prinophyllum, and tomatillo to determine cross species
effects on meristem development and shoot architecture.
4:10 pm
SUSCEPTIBILITY GENES FOR RESISTANCE AGAINST PHYTOPHTHORA INFESTANS.
Chaparro-Garcia A., Nekrasov V., Dagdas Y., Kamoun S.
The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
Contact: Angela Chaparro-Garcia, [email protected]
Phytophthora infestans is the most devastating pathogen of potato and a growing threat for tomato
production causing annual losses of up to 6.7 billion dollars. Most disease resistance breeding
programs currently focus on transferring dominant resistance genes from wild species into cultivated
crop varieties. However, new virulent races of the pathogen often overcome late blight resistance
mediated by cell-surface or intracellular immune receptors that recognize pathogen-derived molecules
or effectors. An alternative plant breeding strategy that could provide a more durable type of
resistance is to alter plant genes that facilitate infection and support pathogen growth. These
components, termed susceptibility genes, are an untapped resource for finding novel resistance
against P. infestans and other oomycetes. Here, we identified and targeted several diseasesusceptibility (S) genes for P. infestans using the CRISPR/Cas9 system in tomato, including SlCMPG1.
We recovered around 80% T0 plants carrying various mutations along the SlCMPG1 locus and 10% of
those had homozygous deletions. We found that several T1 mutant lines that harbored different types of
deletions in the SlCMPG1 locus conferred partial resistance to P. infestans to a similar extent.
Moreover, Cas9-induced mutations in SlCMPG1 were heritable and stable in both T1 and T2 generations.
In addition, we recovered T-DNA free plants in the T2 generation that still had the desired gene
modification and enhanced resistance phenotype. Importantly, none of the mutations in SlCMPG1
seemed to cause any obvious pleiotropic effects. Our results demonstrate that targeting susceptibility
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genes using genome-editing technologies is a fast route to develop transgene-free disease resistant
crops and accelerate research and deployment of valuable resistance traits.
4:30 pm
CREATING TOMATO HAPLOID INDUCER THROUGH SINGLE AMINO ACID SUBSTITUTIONS IN
CENH3 HISTONE FOLD DOMAIN
Kuppu S., Li G., Rodgers A., Terry J., Britt A.B.
Dept. Plant Biology, University of California, Davis, CA 95694
Contact: Anne Britt, [email protected]
Haploids are of great value to plant breeding. Circumventing the many generations of back crossing
required to obtain true-breeding lines. We have shown that plants carrying a variety of single amino
acid substitutions in the highly conserved histone fold domain of the Arabidopsis thaliana centromere
specific histone 3 variant (CENH3) produced haploids on crossing by pollen from CENH3 wild-type
plants (Kuppu et al., PLOSGen, 2015). The frequency of haploid induction ranges from 0.5% to 12% of
progeny. Since CENH3 is present in all plant species, mostly as a single copy gene, this approach has
potential applications to crop breeding. Moreover, the single amino acid substitutions we tested are
inducible by chemical mutagen EMS by G to A or C to T transition in a wide variety of angiosperm
crops. Here we are analyzing the effect of 47 such single amino acid substitutions in
the CENH3 histone fold domain for their ability to complement endogenous null and their potential to
produce haploids on out crossing to parent carrying wild-type CENH3. These findings using facile
arabidopsis genetics have the potential to create non-transgenic haploid inducers in most if not all
crop species.
4:45 pm
ASSESSING THE IMPACT OF GENE REPLACEMENT AND GENE MODIFICATION METHODS IN A
CROP SPECIES AT THE WHOLE GENOME LEVEL
Starker C.G.1, Nadakuduti S.S.2, Crisovan E. 3, Konecna, E.1, Butler N.M.2, Buell C.R.3, Voytas D.F.1,
Douches D.S.2
1
Department of Genetics, Cell Biology and Development and Center for Genome Engineering,
University of Minnesota, USA, 2Department of Plant, Soil and Microbial Sciences, Michigan State
University, USA, 3 Department of Plant Biology, Michigan State University, USA
Contact: Colby G. Starker, [email protected]
Genetically engineered (GE) crops are a key component of U.S. agriculture and quantitative data to
facilitate informed risk assessment of GE crops is important. The aim of this project is to utilize the
targeted genome editing technologies, Transcription Activator–like Effector Nucleases (TALENs) and
Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated systems (CRISPR-Cas)
to engineer a crop species and detect the variability generated at the genomic and transcriptomic level
by quantifying off-target effects.
We are using the diploid line, DMRH S5 28-5, an inbred progeny (S5) of a cross between DM (S.
tuberosum group Phureja, homozygous doubled monoploid) and RH (S. tuberosum group Tuberosum,
a heterozygous diploid clone) to minimize interpretations due to genome heterozygosity and ploidy.
CRISPR/Cas9 and TALENs reagents have been developed that target two regions of Acetolactate
synthase1 (ALS1) and two copies of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) genes in
DMRH S5 and are being used in protoplast transformations followed by GUIDE-seq. In addition to an
Arabidopsis codon optimized Cas9, improved variants of Cas9, eCas9(1.1) and Cas9-HF, which are
shown to reduce off-target effects yet maintain robust on-target cleavage, are being used with the
guide RNAs for comparison of efficiencies as well as off-target effects of various Cas9 nucleases.
Gene-targeting constructs to edit ALS1 in vivo have also been developed in which the ALS1 donor
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molecule contains point mutations that confer herbicide resistance. Agrobacterium mediated
transformation has been successful in DMRH S5 to generate transgenic lines using conventional TDNA transformation with a modified ALS1 transgene conferring herbicide resistance to permit
comparison with genome engineered lines at the transcriptomic, genomic, and phenotypic levels.
Session VI • EPIGENOMICS AND METHYLATION
Luca Comai and Brittany Davenport, Chairs
4:55 — 6:05 pm, Conference Center Ballroom
4:55 pm
THE FUNCTIONS OF DNA METHYLATION IN FLESHY FRUITS
Gallusci P.
Laboratory of Grape Ecophysiology and Functional Biology, Bordeaux University, INRA, Bordeaux
Science Agro, 33882, Villenave d’Ornon, France
Contact: Philippe Gallusci, [email protected]
The concept of epigenetic refers to heritable changes in chromatin organization, which may lead to
modifications in gene expression but the underlying genomic DNA sequence remains unchanged.
DNA methylation which occurs on the 5th carbon of cytosine (5mC) is an essential epigenetic mark that
is involved in controlling gene expression and transposon mobility during plant development. Recent
discoveries have demonstrated that important changes in the DNA methylation landscape over the
tomato genome occur during fruit ripening suggesting that fruit development not only relies on
hormones and genetic factors, but also on epigenetic regulations. Most notably a 30% decrease in
global DNA methylation level and demethylation at ripening specific genes were observed.
We have now shown that the balance between active DNA demethylation and methylation is critically
important to tomato fruit development. Plants with modified methylation patterns present altered fruit
ripening processes. In particular inhibition of DNA demethylation leads to fruit ripening inhibition
following hypermethylation and repression of the expression of genes encoding ripening transcription
factors and rate-limiting enzymes of key biochemical processes. The results are consistent with DNA
demethylation being an essential actor of tomato fruit ripening control and suggest crosstalks with
other developmental factors. The results obtained are the foundation of a new paradigm where the
DNA methylation/demethylation balance is central to the regulation of tomato fruit development that
might have evolved as a ‘double-lock’ mechanism, to prevent premature dispersal of seeds prior to
their full maturation. We are currently determining the network of genes and related processes under
direct methylation control in tomato fruits. The potential application of DNA methylation control and
variability to tomato breeding will be discussed
In addition, whether the epigenetic control of ripening has emerged similarly in other types fleshy fruits
or is limited to the tomato and related wild species is now an open question that we are starting to
address by studying the function of DNA methylation during grape berry development.
5:20 pm
miR160 IS A KEY REGULATOR OF AUXIN MEDIATED DEVELOPMENTAL PROCESSES IN TOMATOz
Damodharan S.1, Arazi T.1
1
Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 6, Bet Dagan
50250, Israel
Contact: Subha Damodharan, [email protected]
Auxin plays an important role in many aspects of vegetative and reproductive development in plants.
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Several miRNAs regulate the expression of Auxin Response Factors (ARFs) central components of the
auxin signaling cascade. MiR160 is one such miRNA that regulates a group of ARFs 10/16/17. We found
that reduction of tomato miR160 (sly-miR160) levels by Short Tandem Target Mimic (STTM 160)
modified ovary patterning, blade outgrowth and floral organ abscission, all of which were shown to be
regulated by auxin. We found that sly-miR160 depletion was always associated with strong
upregulation of SlARF10A and SlARF17 of which SlARF10A increased the most. This suggested a
common mechanism behind these auxin regulated processes, involving sly-miR160 guided cleavage of
corresponding targets. In contrast, SlARF16A was not upregulated as a result of sly-miR160 depletion
suggesting it is regulated by mechanism other than mRNA cleavage. Does this mode of regulation
have any significance? We further probed into the functions of sly-miR160 by knocking out SlMIR160a
using CRISPR/Cas9 technology. This strategy resulted in the isolation of sly-miR160 allelic series
including loss-of-function mutant. The analysis of these mutants is ongoing and already revealed novel
sly-miR160 functions which will be discussed.
5:40 pm
AN ERF TRANSCRIPTION FACTOR ACTS AS A POSITIVE REGULATOR IN THE ANTIVIRAL RNA
SILENCING IN PETUNIA
Jiang C-Z.1,2, Daoyang Sun2,3, Yanlong Zhang3, Lixin Niu3, Michael Reid2
1
Crops Pathology and Genetic Research Unit, USDA-ARS, Davis, CA, USA; 2Department of Plant
Sciences, University of California Davis, Davis, CA, USA: 3Department of Landscape Architecture and
Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
Contact: Cai-Zhong Jiang, [email protected]
Virus-induced RNA silencing is involved in plant antiviral defense and requires key enzyme
components, including RNA-dependent RNA polymerases (RDRs), Dicer-like RNase III enzymes (DCLs),
and Argonaute proteins (AGOs). However, the transcriptional regulation of these critical components is
largely unknown. We identified an ethylene-responsive element binding factor (PhERF2) that is induced
by Tobacco rattle virus (TRV) infection in petunia. Inclusion of a fragment in a TRV silencing construct
containing reporter fragments of phytoene desaturase (PDS) or chalcone synthase (CHS) substantially
impaired silencing efficiency of both the PDS and CHS reporters. Silencing was also impaired in
PhERF2-RNAi lines, where TRV-PhPDS infection did not show the expected silencing phenotype
(photobleaching). In contrast, photobleaching in response to infiltration with the TRV-PhPDSconstruct
was enhanced in plants overexpressing PhERF2. Transcript abundance of the RNA silencing-related
genes RDR2, RDR6, DCL2, and AGO2 was lower in PhERF2-silenced plants but higher in PhERF2overexpressing plants. Moreover, PhERF2-silenced lines showed higher susceptibility to Cucumber
mosaic virus (CMV) than wild-type (WT) plants, while plants overexpressing PhERF2 exhibited
increased resistance. Taken together, our results indicate that PhERF2 acts as a positive regulator in
antiviral RNA silencing and is essential for efficient silencing of genes in plants.
POSTER SESSION I (6:05 — 7:30 pm) • ABSTRACTS ON PAGE 64
Appetizers and beverages served, Welcome Center (adjacent to Conference Center)
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WEDNESDAY, SEPTEMBER 14
Session VII • GENOMICS-ASSISTED BREEDING
Jeanne Jacobs and Kieu-Nga T. Tran, Chairs
8:00 — 9:30 am, Conference Center Ballroom
8:00 am
GENOMICS ASSISTED BREEDING IN POTATO
Douches D.S.1, Massa A.1, Manrique N.1, Coombs J.1, de Los Campos G.2, Islam S.1, Alsahlany M.1, Enciso
F.1
1
Plant Soil and Microbial Sciences Department, 2Department of Statistics, Michigan State University,
East Lansing, MI, USA
Contact: Dave Douches, [email protected]
The potato (Solanum tuberosum L.) plays an important role in human nutrition as a staple food. It is
considered one of the main sources of carbohydrates, providing the energy needed for development
and function. Potato breeding is being transformed by the use of genome-wide SNPs. The current
version of the SolCAP array has over 12,000 SNPs that provide better genome coverage and up to
8,000 co-dominant SNPs that can be used in tetraploid populations. A new array is being designed
that will be expanded to over 30,000 SNPs and identify polymorphism in the broader Solanum species
germplasm. We are using the genome-wide SNPs for multiple breeding related problems including: (i)
mapping in diploid and tetraploid populations; these analyses are providing additional markers for
disease resistance that can be used for marker-assisted breeding, (ii) confirming and quantifying ploidy
level of breeding selections and clones (diploid, triploid, or tetraploid), (iii) monitoring the cycles of
selection for diversity and heterozygosity, (iii) monitoring the backcross introgression of PLRV
resistance from unadapted tetraploid germplasm and (iv) for identifying SNPs associated with late
blight (Phytophthora infestans) and common scab (Streptomyces scabies) resistance in tetraploid
potato. For the latest we developed additive and dominance models for tetraploids, to determine
associations between SNP dosage and resistance to late blight and common scab, using six years of
phenotypic data. We tested the association between resistance and SNP dosage correcting for
structure and for population structure. Some of the late blight resistance associations found were
located in resistance hot-spots previously reported for potato. However, for common scab resistance,
there were SNPs located in non-reported genes, with a LRR-kinase protein domain, known for their
role in the first layer of plant resistance.
8:25 am
EMPIRICAL EVALUATION OF GENOMIC SELECTION FOR RESISTANCE TO BACTERIAL SPOT OF
TOMATO
Liabeuf D.1, Sim S.-C.2, Francis D. M.1
1
Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research
and Development Center; 2Department of Bioresources Engineering, Sejong University, Korea
Contact: Debora Liabeuf, [email protected]
Bacterial spot of tomato affects fresh market and processing tomatoes (Solanum lycopersicum) grown
under humid conditions throughout the world. Multiple genes and QTLs for resistance have been
identified and need to be combined to improve disease control. We evaluated the prediction accuracy
of genomic selection (GS) models for resistance to Xanthomonas euvesicatoria based on empirical
data. The training population consisted of 109 directionally selected families combining resistance from
at least four different sources. The training population was evaluated in the field after inoculation with
X. euvesicatoria. We compared GS models developed with sets of 24 to 397 markers. Markers were
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selected based on their distribution in the genome, or based on their association with resistance.
Genomic Estimated Breeding Values (GEBVs) were evaluated using Bayesian LASSO (BL) and ridge
regression (RR). RR models were either completely random or mixed, with the markers significantly
associated to disease resistance used as fixed effects. Prediction abilities of the models were
evaluated based on leave-one-out cross validation and empirically. Empirical validation was conducted
with sets of inbred families derived from the training population and F1 hybrids test crosses evaluated
in replicated field trials. Model performances were evaluated based on prediction ability and
percentage of co-selection. Prediction ability was the correlation coefficient of the regression between
GEBVs and phenotypic values. Percentage of co-selection, evaluated only empirically, was the
percentage of lines with superior observed phenotypes that were also selected based on GS models.
Prediction abilities evaluated by cross validation were underestimates compared to the empirical
observations. Results for BL models and RR random models were similar. Prediction abilities ranged
from 0.04 to 0.49 based on cross validation and from 0.20 to 0.58 empirically. The highest prediction
ability was obtained with models using only markers significantly associated with resistance. The
highest percentage of co-selection was obtained with the RR mixed model (67%). GS models, even
with low marker coverage, offer the potential for genetic gain for resistance to bacterial spot of tomato.
Such models are not a replacement for phenotypic selection, but offer opportunities for off-cycle
selection in the absence of disease pressure to advance populations.
8:40 am
GBS-ASSISTED RECOVERY OF “LOST” INTROGRESSIONS IN ADVANCED BACKCROSSES OF
SOLANUM INCANUM TO CULTIVATED EGGPLANT (S. MELONGENA)
Gramazio P., Prohens J., Plazas M., Herraiz F.J., Ziarsolo P., Cañizares J., Vilanova S
Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de
València, Valencia, Spain
Contact: Pietro Gramazio, [email protected]
Although the common eggplant (Solanum melongena) displays a huge phenotype variation, its genetic
base is quite narrow. Here we present the results of the development of a collection of introgression
lines (ILs) of S. incanum in the genetic background of common eggplant. Solanum incanum grows in
the wild in semi-desertic areas of Africa and the Middle East and is cross-compatible with eggplant.
This species has been reported as highly tolerant to drought and also presents resistances to some
diseases. Additionally, it also shows high levels of bioactive phenolics acid. Therefore, S. incanum is
considered as a highly valuable source of variation for several traits in eggplant breeding. The starting
population for developing the ILs collection was a set of 93 BC1 obtained from a cross between the
Spanish S. melongena accession AN-S-26 (SM) and S. incanum accession MM577 (SI) collected in the
wild in Israel. Due to a lack of previous genomic information, a genetic map was developed, mostly
using AFLPs, SSRs and COS markers. A set of 12 BC1 plants, one per SI chromosome introgressed, was
selected. From the BC2 to the BC5 generations, the plants were genotyped with 4-5 SSRs per
chromosome, although the genotyping was exclusively made for the target SI chromosome, avoiding
screening the rest of genetic background. In the BC5S1 generation a GBS (genotyping by sequencing)
analysis was performed, which enabled to discover more than 50,000 SNPs. The screening of the
whole genomic background by GBS allowed recovering some introgressions that were thought lost
during the backcross process and revealed that some advanced introgression generations had
introgressed fragments in the non-targeted chromosomes. At the same time non-targeted introgressions
were identified. This shows that GBS, as other high-throughput genotyping techniques, increases
tremendously the precision of the plant selection over strategies based on a limited number of markers
per chromosome. This indicates that the use of GBS in early generations will increase the efficiency of
the development of ILs sets.
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9:00 am
ANALYZING AND EVALUATING THE USEFULNESS OF EXISTING MOLECULAR MARKERS FOR BREEDING
OF ELITE TETRAPLOID POTATO
Sundmark E.H.R., Sønderkær M., Kirk H.G., Nielsen K.L.
Department of Chemistry and Bioscience, Aalborg University, Aalborg, 2 LKF Vandel, Denmark
Contact: E H. R. Sundmark, [email protected]
In a world with increasing demands for high quality potatoes, both for direct consumption and
industrial processing, breeding companies struggle to keep up. Potato breeding is largely carried out
as traditional selective breeding with crossing of two tetraploid parental lines, followed by extensive
phenotyping and selection of offspring, which can take 10-15 years. Thus, there is a significant interest
for enhancing traditional breeding as has been done for many other crops. However, this is
complicated by the extreme genetic diversity of potato, few meiotic cell divisions since introduction
into Europe, and its autotetraploid nature. Nonetheless, breeding enhancement might be obtained
through the use of molecular markers in marker assisted selection programs or through predictive
algorithms to shorten the selection process. Molecular markers for both simple and complex traits in
potatoes have been around for 20 years, but have only been applied in breeding practices to a small
extent, and largely only to follow dominant resistance genes against late blight. The reason for this is
that more complex molecular markers have often been derived from populations with little relevance
for elite breeding programs and because marker linkages to traits are frequently lost.
With publicly available molecular markers as starting point, we have designed a pipeline for conducting
analysis and evaluation of the usefulness of markers in an industrially relevant population of breeding
clones and cultivars from the Danish breeding company LKF Vandel. Using the potato genome model
(DM v4.03), CLC Genomics Workbench 8.0 and Illumina high throughput sequencing of multiple
amplicons enabled us to map, select and, if necessary, redesign markers for genotyping a small
population of 48 potato plants. Sequencing and analysis of haplotypes from each individual plant
enabled both evaluation of the markers for different traits simultaneously and calculation of a
reasonably predictive value for each trait.
9:15 am
GENOMICS-ASSISTED QTL MAPPING FOR AGRONOMICAL TRAITS IN PEPPER
Han K.1, Jeong H-J.1, Yang H-B.1, Kang S-M.2, Kim S.1, Choi D.1, Kang B-C.1
1
Department of Plant Science,Seoul National University,Seoul, Republic of Korea; 2Departmentof
Computer Science, College of Information Science and Technology, KAIST, Daejeon, Republic of
Korea
Contact: Koeun Han, [email protected]
Pepper (Capsicum annuum) genome published in 2014 allows rapid identification of the genetic loci
controlling agronomically important traits. To identify QTLs controlling pepper traits including plant
height, fruit color, weight, and pungency, we constructed high-density maps by re-sequencing 120
recombinant inbred lines (RILs) derived from an intraspecific cross (C. annuum ‘Perennial’ × C. annuum
‘Dempsey’) and by genotyping-by-sequencing (GBS) of 96 RILs from an interspecific cross (C. annuum
‘TF68’ × C. chinense ‘Habanero’). Single nucleotide polymorphisms (SNPs) were detected by aligning
sequences obtained from resequencing and GBS to the C. annuum ‘CM334’ reference genome. To
improve efficiency of genetic map construction, adjacent SNPs were combined to bins using sliding
window approach. Genotypes of the bins were determined based on the ratio of SNPs with different
genotypes. Also parental SNPs from GBS were imputated using a haplotype map derived from GBS of
pepper germplasm. From resequencing of intraspecific population, 1.4 million SNPs were detected and
a linkage map with a total map length of 1,372 cM was constructed using 2,578 SNP bins. A total of 17
horticultural traits including plant architecture, leaf, flower, and fruit were evaluated for three
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consecutive years in two different regions. Using the linkage map and three-year phenotype data, 86
significant QTLs were detected for 32 horticultural traits, and among them 32 QTLs were major QTLs.
For mapping QTLs controlling pungency levels, we used both intraspecific and interspecific population.
From GBS, a total of 8,500 highly reliable SNPs were obtained for the interspecific population and
used for a linkage map construction resulting in a map length of 1,186 cM. In our ongoing research,
QTLs for pungency levels were mapped using the phenotype data obtained from the two different
populations. Physical locations of commonly detected pungency QTLs were compared, and molecular
markers linked to the major QTLs are being developed. Our study shows that genomics-assisted QTL
mapping is powerful tool to find the valuable locus for molecular breeding of pepper.
COFFEE Break (9:30 — 9:55 am), Conference Center lobby and patio
Session VIII • SYSTEMS BIOLOGY AND NETWORKS
Siobhan Brady and Sophia Jinata, Chairs
9:55 — 11:25 am, Conference Center Ballroom
9:55 am
THE TIP OF THE TRICHOME: SPECIALIZED METABOLIC DIVERSITY IN THE SOLANACEAE
Last R.L.1,2, Fan P.1, Moghe G.1, Miller A.1, Leong B.1, Lybrand D.1, Hurney S.3, Jones A.D.1,3
1
Department of Biochemistry and Molecular Biology, 2 Department of Plant Biology,
3
Department of Chemistry, Michigan State University, USA
Contact: Robert Last, [email protected]
The tomato clade of Solanum -- and indeed the entire Solanaceae family -- is an excellent model for
analysis of evolution of morphological, defensive and metabolic traits. Plants produce hundreds of
thousands of specialized metabolites, typically in specialized cell types. Tomato and other members of
the Solanaceae synthesize protective metabolites known as acylsugars in the tip cells of glandular
secreting trichomes. We have characterized the metabolic network that produces acylsucroses in S.
lycopersicum and wild tomato relatives. Four BAHD acyltransferases are sufficient to produce the full
repertoire of cultivated tomato compounds in vitro starting with sucrose (table sugar) and varied acylCoA esters. There is a striking amount of intra- and interspecific structural variation in the products of
this network within the tomato group of Solanum, suggesting that the enzymes have evolved new
activities in relatively short evolutionary time. Surveys across the Solanaceae are revealing even
greater structural diversity of acylated trichome products, and in vitro reconstruction of the metabolic
networks leading to these products, coupled with viral induced gene silencing, allows us to explore the
biochemical basis of this metabolic novelty. This work is beginning to reveal the genetic and
biochemical mechanisms by which specialized metabolism has evolved over tens of millions of years.
10:25 am
A HIGH-RESOLUTION SPATIOTEMPORAL ATLAS OF THE TOMATO FRUIT TRANSCRIPTOME
Shinozaki Y.1, Fernandez-Pozo N.2, Nicolas P.J.2, Martin L.B.B.1, Snyder S.I.1, Ma Q.2, Xu Y.2,3, Zheng Y.2,3,
Catalá C.1,2, Fei Z.2,3, Mueller L.A.2, Giovannoni J.J.2,3, Rose J.K.C.1
1
Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA; 2Boyce
Thompson Institute, Ithaca, NY, USA; 3U.S. Department of Agriculture/Agriculture Research Service,
Robert W. Holley Centre for Agriculture and Health, Ithaca, NY, USA
Contact: Yoshihito Shinozaki, [email protected]
Fleshy fruits, including tomato, are organs with complex anatomies and functional structures consisting
of distinct tissue and cell types. However, essentially all biochemical and molecular studies of fruit
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biology to date have used homogenized amalgam of different fruit cell/tissue-types as a source of
target molecules. Such an approach limits insights into cell/tissue specialization, and lower abundance
molecules that are present only in certain cells/tissues and having specific roles unique to the
cells/tissues are often diluted below the level of quantitation or even detection. The lack of spatial data
at the cell/tissue level leads to a critical 'information void', resulting in an incomplete picture of fruit
development and other aspects of fruit biology. Our consortium has been using RNA sequencing
(RNA-seq) coupled with laser microdissection (LMD), which allows precise isolation of specific
tissue/cell types, to generate comprehensive transcript profiles of tomato fruit development, spanning
fruit set, expansion and ripening, at an unprecedented level of resolution. Importantly, we have
included the less studied interior tissues, such as the columella, placenta and septa, as well as seeds,
to give a comprehensive coverage of the gene expression landscape throughout the fruit. The
transcriptomic data has been incorporated into a new publicly accessible database, the Tomato
Expression Atlas (TEA), which also houses two- (2D) and three-dimensional (3D) imaging data sets of
tomato tissues reconstructed from microscopic sections and X-ray computed tomography (CT),
respectively. The database has a graphical interface that allows the identification of co-expressed
gene sets with particular spatiotemporal patterns, including those that are tissue/cell type-specific. This
high-resolution profiling approach allows us to address questions that previously could not be readily
addressed, such as the cell/tissue origin of the ripening signal(s), the identity and spatiotemporal
characteristics of cell type specific transcription factors and hormone signal networks, and the
biochemical and regulatory gene pathways associated with cell type specific structures, such as the
cuticle and specialized cell wall polymers. Examples of the many fundamental new insights into fruit
biology that we have generated, together with a summary of the TEA database, will be presented.
10:45 am
A SYSTEMS-LEVEL STUDY ON THE EFFECTS OF ELEVATED ATMOSPHERIC CO2 ON SOLANUM
LYCOPERSICUM AND SOLANUM PENNELLII
Gray S.B.1, Toal T.W.2, Kajala K.1, Brady S.M.1,2
1
Department of Plant Biology, 2 Genome Center, University of California, Davis, CA, USA
Contact: Sharon Gray, [email protected]
Atmospheric CO2 is projected to reach up to 1000 ppm by the end of this Century. Elevated CO2 will
increase photosynthesis of C3 plants, stimulating biomass. Increased root biomass is predicted to
improve plant access to water or nutrient resources in the future, but questions remain as to the
molecular mechanisms and developmental changes that underlie enhanced root biomass in response
to elevated CO2, and the genetic variation in these responses. To elucidate this aspect of plant
response to global climate change, we used domesticated tomato (Solanum lycopersicum, cv ‘M82’)
and a wild species (Solanum pennellii, ‘LA0716’) as models. We measured the effect of elevated CO2
on the transcriptome and metabolome of roots and shoots, root cellular anatomy and morphology and
whole-plant physiological and morphological responses over developmental time. Gene expression
responses to elevated CO2 varied with species, age, and tissue type, with the strongest transcriptional
responses occurring in S. pennellii at 12 days after planting. Genes that were differentially expressed in
elevated CO2 in M82 and S. pennellii shoots were significantly enriched for GO categories related to
translation and ribosome biosynthesis. Elevated CO2 also affected amino acid content of shoots.
Specifically, elevated CO2 significantly increased shoot content of aspartic acid in both species.
Aspartic acid content is negatively correlated with photorespiration, which is often reduced in elevated
CO2. Ongoing work is using Translating Ribosome Affinity Purification (TRAP) to profile CO2 effects on
the translatome of both species. Root vascular anatomy responses to elevated CO2 varied throughout
development and between species, suggesting the potential for developmental variation in plant
hydraulic responses to global change. There were no significant interactive effects of elevated CO2
and species on root or shoot biomass, or photosynthesis, suggesting that these species share similar
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responses in terms of carbon gain and root-shoot partitioning. These results suggest that differences
between M82 and S. pennellii in early developmental and molecular responses to elevated CO2 are
largely buffered, resulting in similar morphological responses in mature plants.
11:05 am
NETWORK ANALYSIS UNRAVELS CROSSTALK BETWEEN ETHYLENE AND SALICYLIC ACID
SIGNALLING PATHWAYS IN VIRUS-INFECTED POTATO
Baebler S.1, Ramšak Z.1, Stare T.1, Coll A1, Tzfadia O.2,3, Gruden K.1
1
Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia;
2
Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; 3 Department of Plant Biotechnology
and Bioinformatics, Ghent University, 9052 Ghent, Belgium
Contact: Špela Baebler, [email protected]
Worldwide, potato represents the fourth most widely grown food crop and the Potato virus Y (PVY) is
one of its most important pathogens. The plant-pathogen interaction causes an extensive
reprogramming of a complex signalling network, resulting in gene activity and metabolic changes. To
understand the mechanisms and dynamics involved, a systems biology approach was adopted to
model the complex biological processes associated in the interplay between potato and viral
components following PVY infection.
Previously, a topological plant defence signalling model was constructed. It described the biosynthesis,
signal transduction and transcriptional regulation leading to activation of effector molecules of crucial
phytohormones involved in plant defence: salicylic acid (SA), jasmonic acid (JA) and ethylene (ET).
Manually gathered knowledge in the model was complemented with information from publicly
available high-throughput experimental datasets, namely protein-protein interactions, transcription
factor regulation and non-coding RNAs. Additionally, datasets describing the interaction between viral
and plant components were included. Subsequently, the network was transferred from model plant
Arabidopsis to potato using published orthologue information.
In parallel, a time-series transcriptomics experiment was performed, capturing 11 different time points
following PVY infection of potato. To study the effect of SA, expression profiles of two genotypes (one
non-transgenic and another deficient in SA signalling) were used in the study. This transcriptomics data
was used for the creation of two co-expression networks, one using a targetted approach and the
other using the BioLayout algorithm.
Integrating the potato defence signalling model with our own experimental data offers new insights
into the plant-virus interaction by expanding the knowledge on critical components of plant defence
signaling. One of the most interesting findings, which was also functionally validated, is the previously
unknown crosstalk between the ET and SA signalling pathways.
ONE-MINUTE Oral POSTER SESSION II Presentations – ABSTRACT PAGE 96
11:25am — 12:15pm, Conference Center Ballroom
LUNCH Break (12:15 — 1:30 pm)
Mondavi Center lobby (across the quadrangle from Conference Center)
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Session IX • ABIOTIC STRESSES
Julin Maloof and Lumariz Hernandez, Chairs
1:30 — 3:00 pm, Conference Center Ballroom
1:30 pm
NEW TOMATO MUTANT COLLECTIONS FOR THE IDENTIFICATION OF KEY GENES INVOLVED IN
TOLERANCE TO SALINITY AND DROUGHT
Flores F.B.1, Angosto T.2, Moreno V.3, Lozano R.2, Bolarín M.C.1
1
Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Espinardo-Murcia, Spain; 2AgroFood Biotechnology Research Centre (BITAL), University of Almería (UAL), Almería, Spain;3Department
of Plant Biotechnology and In Vitro Culture, IBMCP-UPV/CSIC, Valencia, Spain
Contact: [email protected]
Development of crops tolerant to stress is vital to meet the growing food demand from a rising world
population and to confront the increasing impact of abiotic stresses, especially salt and water stresses,
due to environmental factors derived from climate change. Tomato is the sixth most important crop in
worldwide agriculture in value terms, and its production as well as the area devoted to its cultivation
has doubled during the last 20 years. Moreover, this species has also become a model crop plant in
agronomic research programs thanks to its genetics and relatively small genome. The identification of
key genes involved in salt and water stress tolerance mechanisms is critical for the breeding of new
crop cultivars with improved resistance to these abiotic stresses. One biotechnological approach to
identify such genes is by means of the analysis of mutants. Such strategy is being developed in tomato
by a consortium of three Spanish research groups leaded by Prof. V. Moreno (IBMCP, Valencia), Prof. R.
Lozano (UAL, Almeria), and Prof. M.C. Bolarin (CEBAS, Murcia), making use of the insertional
mutagenesis tool. The insertional mutagenesis programme is being carried out using T-DNA and
enhancer trapping in cultivated tomato and the wild tomato species Solanum pennellii and S.
cheesmaniae. Up to our knowledge these collections of T-DNA lines are the first ones from
commercial tomato cultivars and wild-related species. In this communication it is going to be presented
the methodology of generation and screening of the mutant collections, as well as several of the most
interesting mutants exhibiting phenotypes of differential susceptibility to water and salt stress. Some of
the mutants identified and characterized are not insertional but somaclonal, as it has already been
observed in other insertional mutant collections like those of Arabidopsis and rice. Regarding the
insertional mutants the genes responsible of the mutant phenotypes have already been identified in
some cases, and they code for products of very different nature and function, such as stress receptors
and transcription factors. These findings reveal the complexity of the plant response to abiotic stress
and the diversity of molecular stakeholders involved in the process.
2:00 pm
GALAPAGOS TOMATOES AS A GENETIC SOURCE FOR SALINITY TOLERANCE
Pailles Y.1, Ho, S.1, Lightfoot D.1, Pires I. 2, Mitchell C. 3, Negrão S.1, Schmoeckel S.1, Tester M.1
1
Plant Science Program, Biological and Environmental Sciences & Engineering Division (BESE), King
Abdullah University of Science and Technology, Thuwal, Saudi Arabia; 2GPlantS Lab, ITQB-UNL,
Oeiras, Portugal ; 3Red Sea Research Center, King Abdullah University of Science and Technology,
Thuwal, Saudi Arabia
Contact: Yveline Pailles, [email protected]
Wild relatives of modern crops hold valuable genes for environmental stress tolerance and disease
resistance. Of particular interest are two species of wild tomato endemic to the Galapagos Islands: S.
cheesmaniae and S. galapagense, which often grow near the coast and are tolerant to salinity. For the
purpose of studying salinity tolerance in tomatoes, we characterized 68 accessions of Galapagos
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tomatoes and two varieties of S. lycopersicum.
We have sequenced and assembled the draft genomes of the two Galapagos tomato species. In
addition, genotyping by sequencing has been performed on all 68 accessions to establish the
population structure of the germplasm collection.
Phenotypic studies at the seedling stage have been performed, subjecting the seedlings to 200mM
NaCl for 10 days after fourth leaf emergence. The NaCl was administered gradually and supplemented
with CaCl2, to maintain constant Ca2+ availability. Various phenotypes were recorded and analysed for
their contribution to salinity tolerance, compared to control conditions. Six out of the 68 accessions
were selected based on their good performance under salinity. The six accessions were then studied
for their performance under salinity throughout their life cycle, up to the reproductive stage, under
three different NaCl concentrations. This experiment included the scoring of several physiological
parameters and RNA sequencing for transcriptome analyses. We have identified natural variation in
salinity tolerance of Galapagos tomatoes, as well as, the physiological and genetic basis for the
variation in tolerance.
2:20 pm
GENETICS AND GENOMICS OF TRAITS ASSOCIATED WITH WATER STRESS TOLERANCE IN WILD
TOMATO (SOLANUM HABROCHAITES)
St. Clair D.A.
Plant Sciences Department, University of California, Davis, CA 95616 USA
Contact: Dina St. Clair, [email protected]
Climate change and limited fresh water resources pose significant challenges to agricultural
production. Breeding crops for water stress tolerance and water use efficiency (WUE) would increase
sustainability of crop production. Cultivated tomato (Solanum lycopersicum) is sensitive to abiotic
stresses, including limited water and temperature extremes, while wild tomato (S. habrochaites)
exhibits tolerance to limited water and chilling temperatures. Water stress can be rapid-onset or slowonset. Rapid-onset water stress induced by root chilling (6°C) reduces water movement from roots to
shoots. S. habrochaites responds to root chilling by closing stomata and maintaining shoot turgor,
while cultivated tomato fails to close stomata and wilts. This trait (shoot turgor maintenance under root
chilling) is controlled by a major QTL (stm9) and we used sub-near-isogenic lines (sub-NILs) to highresolution map stm9 to a 0.32 cM region on S. habrochaites chromosome 9. To investigate if other
water stress tolerance-related traits map to chromosome 9, we evaluated these sub-NILs in multi-year
replicated field experiments under slow-onset water stress (induced by severely restricted irrigation).
Traits phenotyped included fruit yield, shoot dry weight, specific leaf area, and leaf delta-13C (carbon
isotope discrimination; correlated with WUE). All trait QTL were closely linked to, but not coincident
with, stm9. Almost all traits evaluated in the field segregated in the sub-NILs, but some QTL positions
were not fully resolved. Consequently, we generated a new set of sub-NILs with S. habrochaites
introgressions extending towards the centromere. These sub-NILs are being evaluated in field
experiments under severely restricted irrigation and phenotyped for the same set of traits to resolve
QTL locations and effects. A reference genome for S. habrochaites is not available, therefore we are
sequencing S. habrochaites genomic BACs from chromosome 9 to help identify QTL candidate genes
and regulatory elements. We are also using mRNA-Seq to analyze transcriptional regulation of plant
responses to water stress. Collectively, our data suggests that genetic elements on S. habrochaites
chromosome 9 play essential roles in plant responses to water stress.
2:40 pm
DISSECTING THE GENETIC BASIS OF POLLEN THERMOTOLERANCE IN TOMATO
Driedonks N.1, Wolters-Arts M.1, de Boer G.J.2, Vriezen W.3, Mariani C.1, Rieu I.1
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Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud
University Nijmegen, The Netherlands; 2 Enza Zaden Research and Development B.V., the
Netherlands; 3 Bayer Vegetable Seeds, PO Box 4005, 6080 AA Haelen, the Netherlands
Contact: Nicky Driedonks, [email protected]
1
Temperature increases associated with climate change have become a major challenge with respect
to agricultural output. Despite the urgent need to improve crop thermotolerance, only a limited number
of heat-tolerant varieties have been developed. Heat can affect the whole plant, but development of
male gametophytes seems to be particularly sensitive. Only a few degrees above optimal growth
temperature results in male sterility, which is a primary cause lower yields. To better understand the
problem underlying heat sterility, we aimed to examine the genetic basis of pollen thermotolerance,
using tomato as a model. Within the tomato clade (Solanum section Lycopersicon), we screened 61
accessions of 13 wild species by exposing them to continuous mild heat (CMH) and found high natural
variation for pollen viability (PV), the number of pollen (PN) and reproductive organ sizes. Using the
most thermotolerant wild plant and a thermosensitive tomato cultivar, an interspecific bi-parental F2
mapping population of 218 individuals was generated, phenotyped under CMH. Following genotyping
of all individuals, composite interval mapping revealed Quantitative Trait Loci (QTLs) for all traits. A
dominant and an additive QTL for PV with a LOD score of 4.4 and 7.3 explaining 8.9 and 13.4% of the
phenotypic variance, respectively, showed the complexity of the PV trait. QTLs for organ size traits
were co-localized and also identified in independent F2 mapping populations, indicating a potentially
broad and conserved genetic effect. To downsize the number of candidate genes underlying the PV
QTLs and study the physiological consequence of the QTLs, premature anthers of 20 F2 individuals
with varying tolerance levels and QTL composition were used for RNA-seq. We hypothesize that a
wide range of genes determines PV in tomato.
COFFEE Break (3:00 — 3:20 pm), Conference Center lobby and patio
Session X • RESISTANCE, PATHOGENS, PESTS and MICROBIOMES
Gitta Coaker and Kevin Babilonia, Chairs
3:20 — 4:50 pm, Conference Center Ballroom
3:20 pm
PHYTOPHTHORA BLIGHT IN POTATO: TIPPING THE BALANCE BETWEEN RESISTANCE AND
SUSCEPTIBILTY
Govers F., Wang Y., Du Y., Yang S., Bouwmeester K.
1
Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
Contact: Francine Govers, [email protected]
Plants are continuously challenged by pathogens but because of their effective multi-layered defence
system plant diseases are an exception rather than a rule. The first layer of defence is governed by
plasma membrane-associated receptors known as pattern recognition receptors (PPRs). The second
layer is mediated by intracellular receptors, which are largely nucleotide-binding leucine-rich repeat
(NLR) proteins also known as resistance (R) proteins. Our research focuses on late blight, a devastating
disease on potato and tomato that is caused by the oomycete pathogen Phytophthora infestans, and
infamous because of the Irish potato famine in the mid 19th century. To colonize host plants, pathogens
secrete effectors that can modulate host defence. Well-known are the RXLR effectors that are
produced by Phytophthora species and related oomycetes, and translocated into host cells. To
counteract the pathogen, potato exploits R proteins, the intracellular NLR immune receptors that confer
resistance to P. infestans upon recognition of a RXLR effector, with each R protein having its own
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matching RXLR effector (or AVR protein). In the absence of a matching R protein, RXLR effectors
manipulate the cell machinery by targeting host proteins, the so-called effector targets, thereby paving
the way for successful infection. As an example I will elaborate on the NLR R1 in potato, its matching
effector AVR1 in P. infestans, and the AVR1 effector target Sec5, a subunit of the exocyst complex. In
addition to R proteins there are also some PRRs known that confer resistance to Phytophthora. We
identified a family of cell surface receptors classified as L-type lectin receptor kinases (LecRKs).
Arabidopsis has 45 LecRK genes, of which several play a role in resistance to a variety of plant
pathogens including Phytophthora. LecRKs are wide-spread in plants, and this justifies exploitation of
LecRKs as novel sources for disease resistance. A further understanding of the mechanisms underlying
R protein- and PPR-mediated resistance is crucial to design novel strategies for introducing resistance
traits in crops.
3:50 pm
TOMATO RECEPTOR FLAGELLIN-SENSING 3 BINDS FLGII-28 AND ACTIVATES THE PLANT
IMMUNE SYSTEM
Hind S.1, Strickler S.1, Boyle P.1, Dunham D.1, Bao Z.1, O’Doherty I.1,2, Baccile J.1,2, Hoki J.1,2, Viox E.1, Clarke
C.3, Vinatzer B.3, Schroeder F.1,2, Martin G.1,4
1
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA; 2Department of Chemistry and
Chemical Biology, Cornell University, Ithaca, NY 14853, USA; 3Department of Plant Pathology,
Physiology and Weed Sciences, Virginia Tech, Blacksburg, VA 24061, USA; 4Section of Plant
Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca,
NY 14853, USA
Contact: Sarah Hind, [email protected]
The recognition of conserved microbe-associated molecular patterns (MAMPs) by pattern recognition
receptors (PRRs) is one of the initial events that activates pattern-triggered immunity (PTI) in both plants
and animals. This immune response leads to the rapid generation of reactive oxygen species (ROS),
activation of mitogen-associated protein kinases (MAPKs), and extensive changes in the transcriptome
that together hinder the infection process. The first plant PRR-MAMP pair, consisting of FLS2 and its
ligand the flagellin epitope flg22, works in concert with the co-receptor BAK1 to activate immune
signaling.
Certain solanaceous plants, including tomato, potato and pepper, detect flgII-28, a region of bacterial
flagellin that is distinct from that perceived by the well-characterized FLS2 receptor. The discovery that
tomato recognizes a second flagellin MAMP, combined with extensive natural variation and recent
availability of the genome sequence for this species, offered the opportunity to identify the flgII-28
receptor using a genetic approach. Here, we use natural variation in tomato heirloom varieties and a
mapping-by-sequencing approach to identify a receptor-like kinase gene, named FLAGELLIN-SENSING
3 (FLS3), which confers responsiveness to flgII-28. We demonstrate that FLS3 is the flgII-28 receptor
and show that FLS3-mediated immunity enhances resistance to a bacterial pathogen. In addition, FLS3
signaling is BAK1-dependent and is suppressed by bacterial effectors AvrPto and AvrPtoB. The
emerging awareness that pathogens have numerous ways to subvert or evade host immunity has
highlighted the need for identifying new mechanisms to enhance the plant immune system.
Introduction of novel immune receptors into crop plants offers the potential to improve food quality
and yield.
4:10 pm
LOCAL SMRT RENSEQ ENABLES RAPID CLONING OF RPI-SMIRA1 AND R10 FROM POTATO
CULTIVAR SARPO MIRA
Witek K.1, Xing L.1,2, Jupe F.1,4, Bryan G.3, Hein I.3, Jones J.D.G.1
1
The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom, 2Nanjing Agricultural
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University, Nanjing, Jiangsu, China, 3 Cell and Molecular Sciences, James Hutton Institute, Dundee, UK,
4
Current address: Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
Contact: Kamil Witek, [email protected]
We recently demonstrated that R gene enrichment sequencing (RenSeq) coupled with long read
sequencing technologies like PacBio (SMRT RenSeq) allows to capture, sequence and assemble
complete nucleotide-binding, leucine-rich repeat receptor (NLR) genes, their regulatory elements and
multi-NLR loci from uncharacterized germplasm. This allowed us to accelerate cloning of the novel
Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr3i, from a wild Solanum sp.
We further applied RenSeq to the organically grown, tetraploid cultivar Sarpo Mira, known for strong
resistance towards a wide array of P. infestans genotypes present in the UK and mainland Europe. To
map the underlying resistance, we phenotyped an existing Sarpo Mira x Maris Piper population using
two contemporary UK late blight isolates, 6_A1 and 13_A2, and performed RenSeq together with
Illumina short-read sequencing on small bulks of highly resistant and susceptible plants. While we
positioned the resistance against both isolates to the R3 NLR cluster on chromosome 11 (named RpiSmira1), the recognition of 6_A1 isolates co-segregated also with another locus, Rpi-Smira2, within the
Sw5 cluster on chromosome 9.
We set out to clone Rpi-Smira1 using a modified local SMRT RenSeq approach. The R3 locus contains
over 40 highly similar sequences in the doubled-monoploid reference genome, and presumably ~160
in the tetraploid Sarpo Mira. We developed long probes specific to R3-like sequences, captured DNA
from a 3-kb library with high specificity and sequenced on the PacBio platform. Illumina gDNA and
cDNA RenSeq data on bulked susceptible and resistant samples from the segregating population
allowed us to rapidly predict candidate genes within ~140 de novo assembled R3-like gene-harbouring
contigs. Linked candidate genes were subsequently tested in transient complementation assays in
Nicotiana benthamiana, and it revealed that four genes confer partial resistance against P. infestans.
One candidate gene recognizes the effector AvrSmira1, and another candidate the effector Avr10,
confirming that we cloned the functional Rpi genes Rpi-Smira1 and R10. Interestingly, the identified
functional resistance genes reside on three different haplotypes. This suggest that recreating a
genotype carrying all three resistant R3/Smira1 locus haplotypes by classical breeding might be
challenging, but could be facilitated using molecular markers for each haplotype.
4:30 pm
OPPORTUNITIES TO IMPROVE TOMATO FRUIT BY TARGETING EARLY DEVELOPMENT AND
RIPENING PROCESSES CO-OPTED BY PATHOGENS
Powell A.L.T.1, Tang Y.1,2, Yang S.B.1,2, An Y.1,3, Blanco-Ulate B.1,4, Cantu D.1,4, Vincenti-Martinez E.1, Wang
B.2, Li N..,2, Yu, Q.2, Bennett A.1, Labavitch J.1
1
Plant Sci. Dept., Univ. Calif. Davis; 2Xinjiang Acad. of Ag. Sci., Urumqi, China; 3Beijing Forestry Univ.,
China; 4Dept. of Vit. and Enol., Univ. Calif. Davis CA 95616
Contact: Ann Powell, [email protected]
Tomato fruit comprise 15-40% of the vegetables consumed worldwide. Harvested fruit quality
determines crop value. Loss of ripe fruit to infections by opportunistic fungal pathogens is costly and
wasteful. Major challenges for producing fruit uncompromised by pathogens but developing the colors,
flavors and sugars preferred by consumers include understanding the pleiotropic effects of
development and ripening processes.
Early in tomato fruit development, anti-pathogen polygalacturonase (PG) inhibiting proteins (PGIPs)
bind wall pectin polysaccharides in the fruit pericarp and inhibit fungal virulence enzymes. PGIPs
contribute to young fruit defenses and are strategically positioned to inhibit pathogen PGs expressed
quickly and abundantly during the host-pathogen interaction. Constitutive PGIP over-expression
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obviates the ripening-associated fruit cell wall disassembly that is required for susceptibility. The
development of young fruit chloroplasts also affects ripe fruit attributes. As ripening begins, SlGLK2
expression decreases and chloroplasts are remodeled into chromoplasts. Prior SlGLK2 expression
increases ripe fruit soluble solids, sugars and metabolites and may thereby impact pathogen success.
Wild and heirloom SlGLK2 alleles are available to improve fruit quality.
Non-ripening mutant and modified tomato lines resistant to infections identify alterable events and
regulators that promote B. cinerea infections of fruit and suggest that some, but not all, of ripening is
required for susceptibility. B. cinerea infections accelerate ripening and prematurely induce fruit cell
wall modifying enzymes. Before ripening, successful infections require the pathogen’s polysaccharide
degrading enzymes. Reduced expression of tomato wall disassembling enzymes modestly but
significantly decreases softening, improves pathogen resistance, impacts substrate availability for
fungal metabolism and virulence functions and enhances binding site retainage for anti-pathogen
proteins in ripe fruit. Understanding how fruit development and ripening restrict or support pathogens
informs effective future modifications to improve quality.
5:00 - 6:00 pm
Conference Keynote Address
Conference Center Ballroom
Roger Chetelat, Tomato Genetics Resource Center, UC Davis
Talk title: Charley Rick and the Origins of the Tomato Genetics Resource Center
6:00 - 9:00 pm
Gala Garden Banquet
Good Life Garden, Robert Mondavi Institute
Appetizers, beer/wine, and dinner with regional specialities, live music (UC Davis
Marching Band and Amplified DNA Band)
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THURSDAY, SEPTEMBER 15
7:45 — 8:00 am, Pre-Tour Announcements, Conference Center Ballroom
OFF-SITE TOURS, 8:00 — 12:00 pm
Pre-registration required. Please wear sun protection, closed toe walking shoes, long pants and no
jewelry. Water provided on buses.
Buses depart from front of Conference Center at 8 am, unless noted otherwise.
• Tomato Genetics Resource Center Field Plot and Pepper Diversity Plot, UC Davis
• HM.Clause Field Commercial Breeding Facility, Davis
• Monsanto Phenotyping & Genotyping Lab and Greenhouse Facility, Woodland
• Commercial Scale Conventional Farm, Davis area
• Morning Star Tomato Processing Facility, Williams
Buses return to Conference Center by 12 pm, unless noted otherwise.
LUNCH Break (12:00 — 1:00 pm) Boxed lunches
Mondavi Center lobby (across the quadrangle from Conference Center)
Session XI • TUBERS AND ROOT SYSTEMS
Glenn Bryan and Justin Medina, Chairs
1:00 — 2:30 pm, Conference Center Ballroom
1:00 pm
CONTROL OF POTATO TUBERIZATION BY THE CONSTANS-FT MODULE
Cruz-Oró E., Abelenda J.A., Sanz R., Prat S.
Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
Contact: Salomé Prat, [email protected]
Potato is worldwide the third crop in economical importance, after wheat and rice. It is cultivated for its
underground tubers, highly rich in starch and a good source of vitamin C and essential amino acids,
when compared to other storage organs. Tubers serve as vegetative propagation organs to the plant
and in wild Andean species, their formation is strongly dependent on short days and cooler
temperatures, two informational cues of winter proximity. Although Tuberosum species were selected
against this strict environmental control, short days still promote tuber formation in these genotypes.
Day length is perceived by the leaves, suggesting that under inductive short days, a mobile signal is
produced in the vasculature and transported to the underground stolons to signal tuber formation.
Work by our group has established that this mobile signal is encoded by a member of the potato FT
family (SP6A), and that expression of this gene is regulated by an homolog of the B-box CCT-domain
CONSTANS factor. Notably, StCOL1 shows a different oscillation pattern than the
Arabidopsis AtCO gene, high transcript levels for the potato factor being observed at dawn. Also, its
peak of expression is shifted in long days towards early morning, which allows stabilization of the
protein in the light. Reduced StCOL1 expression in RNAi lines causes tuber formation in LDs, indicating
that StCOL1 suppresses tuberization under non-inductive day lengths. We observed that inhibition
of StCOL1 leads to up-regulated levels of the SP6A mobile signal, but that levels of this factor show a
strong correlation with another member of the FT family, the SP5G gene, expressed under non
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inductive LDs. SP5G-RNAi lines tuberize in LDs, and tuber formation is associated with strong
activation of theSP6A signal in the stolons, which indicates that SP5G indeed acts as a repressor
of SP6A expression. Thus, rewiring of the CO-FT module from direct mobile signal activation, to
activation of an additional FT family member (SP5G) that acts as a negative regulator of SP6A provided
a robust day length-dependent mechanism for SD tuberization control.
Temperatures over 25ºC are inhibitory for tuber formation, partly due to suppression
of SP6A expression. Remarkably, over-expression of SP6A revokes this inhibition and preserves high
tuber yields. SP6A-ox tubers display high starch levels and unaltered dormancy traits, highlighting the
SP6A regulatory pathway as one of the primary targets for increasing potato productivity.
1:30 pm
CHARACTERISATION OF ACQUIRED THERMOTOLERANCE IN POTATO
Bita C.E.S., Ducreux L., Hancock R., Hedley P., Morris J., Morris W., Trapero-Mozos A., Wiese C., Taylor
M.
Cell and Molecular Sciences Group, James Hutton Institute, Dundee, United Kingdom
Contact: Mark Taylor, [email protected]
For many commercial potato cultivars, tuber yield is optimal at average day time temperatures in the
range of 14-22°C. Further rises in ambient temperature can reduce or completely inhibit potato tuber
production, with damaging consequences for both producer and consumer. Despite centuries of
potato breeding, high temperature tolerance has not been significantly improved. In the field, in the
major European growing regions, it is more likely that plants will be exposed to short periods of
elevated temperature rather than continuous high temperatures and so acquired thermotolerance is
likely to be an important trait. Acquired thermolerance is a powerful adaptive response that has been
observed in many plant species. Following exposure to sub-lethal heat stress, plants acquire enhanced
tolerance to subsequent exposure to more severe levels of heat stress. Many temperature profiles
have been reported to induce thermotolerance, with different plant species having different
requirements for acquiring heat tolerance. Recent studies have started to address molecular
mechanisms that underpin acquired thermotolerance in Arabidopsis. Direct exposure to high
temperature elicited a very different transcriptional response compared with plants that are acclimated
at a moderately high temperature prior to high temperature treatment. Furthermore, different
acclimation treatments resulted in different transcriptional profiles although the plants appeared to
have a similar degree of priming to the high temperature condition.
Although acquired thermotolerance has been characterized in Arabidopsis, little detail is available of
the process in potato, despite its prospective significance. Here we describe the temperature and light
conditions that elicit acquired thermotolerance in potato. Notably we demonstrate the inability of plants
to acquire thermotolerance in the dark, potentially implicating light signaling in the acclimation
response. In time course experiments we describe gene expression and metabolite changes
associated with acquired thermotolerance. We also define changes in the main cellular redox buffers
associated with thermotolerance and subsequent exposure to severe heat stress. Using an electrolyte
leakage test to monitor cell damage, comparison of different potato genotypes indicated considerable
variation for this trait. Ultimately, our results will be used to develop genetic screens for heat tolerance
identification and to implement novel targeted breeding approaches.
1:50 pm
BIOLOGICAL PREDICTORS FOR TUBER SWEETENING DURING LONG TERM COLD STORAGE
Neilson J.1, Lagüe M.1, Thompson S.3, Aurousseau F.2, Murphy A.1, Bizimungu B.1, Deveaux V.2, Begue
Y.2, Jacobs J.3, Tai H.1
1
Agriculture and Agri-Food Canada Potato Research Centre, P. O. Box 20280, 850 Lincoln Rd.,
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Fredericton, N. B., Canada E3B 4Z7; 2Sipre-Responsable Scientifique Creation Varietale, Station de
Recherche du Comite Nord, 76110 Brettevukke du Grand Caux, France; 3The New Zealand Institute for
Plant and Food Research Limited, Private Bag 4704, Christchurch, New Zealand
Contact: Jonathan Neilson, [email protected]
Cold temperature (4 degrees Celsius) is routinely used in potato agriculture to prevent budding during
storage. However, this leads to a phenomenon known as cold-sweetening where sugars accumulate in
tuber tissue. The presence of reducing sugars in tuber tissue during frying results in an undesirable
browning and production of toxic substances, such as acrylamide. Potato cultivars exhibit different
levels of cold-sweetening, suggesting an underlying genetic mechanism controlling sugar
accumulation during cold storage. To untangle the mechanism behind cold-sweetening we measured
glucose concentration and sequenced the transcriptomes of 10 different potato cultivars that show
different levels of glucose accumulation before and 3 months after cold storage. Many of the genes
that exhibit a transcriptome expression profile similar to differences observed in glucose levels appear
to be involved in post-translational regulation, particularly protein degradation through ubiquitination.
From this data we have identified a candidate list of genes that may be used as biomarkers to predict
the magnitude and kinetics of cold-sweetening over the storage period. We are currently in the
process of validating these genes as a test to be used by growers during long term, cold storage to
make better informed crop management decisions and by plant breeders as markers for susceptibility
to cold-sweetening.
2:10 pm
TRANSCRIPTION ACTIVATOR-LIKE EFFECTOR NUCLEASES (TALEN)-MEDIATED TARGETED DNA
INSERTION IN POTATO PLANTS FOR ENGINEERING TUBER TRAITS
Duan H., Forsyth A., Richael C., and Weeks T.
Simplot Plant Sciences, JR Simplot Company, Boise ID 83706, USA
Contact: Hui Duan, [email protected]
Silencing of the Polyphenol oxidase2 gene (Ppo2) to minimize enzymatic browning and bruising in
potato tubers has practical benefits for the potato industry to reduce waste. Low bruising and
browning Innate® potatoes were engineered via Agrobacterium-mediated transformation and a
number of elite events containing the randomly inserted Ppo2 silencing cassette were
selected. Targeted DNA integration into known locations in the genome has potential advantages
over the random insertional events used to create Innate® potatoes. Control of transgene expression
level is conceivably more predictable, making downstream characterization for line selection more
manageable. Described is a method that combines TALEN-mediated induction of double strand
breaks and non-autonomous marker selection to insert a transgene into a pre-selected
transcriptionally active region in the potato genome. In our experiment, TALEN was designed to create
a double strand break in the genome sequence following an endogenous constitutive promoter. A
promoter-less plant-derived herbicide resistant gene was positioned close to the T-DNA left border
and was used to select desired transgenic events. Gene-of-interest cassettes within the same T-DNA
were consequently inserted into the same location. Our results indicated that TALEN was able to
induce a high frequency of targeted integration and resulting events have more consistent expression
of the genes-of-interest than random events. An efficient transient assay for TALEN activity verification
and a cytokinin vector for selecting against stable integration of nucleases are also described.
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Session XII • FLOWERS, SEEDS AND FRUIT
Jim Giovannoni and Kimberly Rodriguez, Chairs
2:30 — 4:00 pm, Conference Center Ballroom
2:30 pm
THE REGULATORY NETWORK CONTROLLING FRUIT RIPENING: A COMPLEX INTERACTION
BETWEEN MULTI-HORMONAL SIGNALING AND DEVELOPMENTAL FACTORS
Bouzayen M.
University of Toulouse, INPT, INRA, Genomics and Biotechnology of Fruits, France
Contact: Mondher Bouzayen [email protected]
While ethylene is the major phytohormone regulating climacteric fruit ripening, it is becoming clear that
the ripening process is under multi-hormonal control in combination with the intervention of known
developmental factors like RIN and NOR. However, how this complex regulatory mechanism operates
still remains quite elusive. Auxin has long been assigned a role in fleshy fruit ripening because
treatment with this hormone results in delayed ripening. We recently showed that among all members
of the Auxin Response Factor (ARF) gene family in the tomato, SlARF2 displays the most prominent
ripening-associated pattern of expression. Interestingly, SlARF2 down-regulation results in strong
ripening defects and conversely its over-expression accelerates ripening. ARF2 emerges therefore as
a new component of the regulatory network controlling tomato ripening working along with known key
regulators of fruit ripening, such as RIN, CNR and NOR. On the other hand, the regulatory mechanisms
underlying ethylene action during climacteric fruit ripening are poorly understood, and in particular, the
role of Ethylene Response Factors (ERFs) in mediating the ripening-associated ethylene responses still
awaits clear demonstrated. A small subset of ERF genes displaying consistent ripening-associated
expression pattern were identified and showed to be linked to the mechanism underlying ethyleneand RIN/NOR-dependent ripening. In particular, sub-class E ERFs are shown to be the most active
during ripening and considering their function as oxygen sensors, they might represent the missing link
between the climacteric rise in respiration and the autocatalytic ethylene production. The data provide
a new insight into the mechanisms underlying the control of fleshy fruit ripening, and open new
avenues towards manipulating the ripening process through yet undescribed means.
2:55 pm
ACCELERATION OF RIPENING-RELATED HOST CELL WALL DISASSEMBLY DURING BOTRYTIS
CINEREA INFECTIONS OF UNRIPE TOMATO FRUIT
Blanco-Ulate B.1,2, Cantu D.2, Vincenti E.1, van Kan J.A.L.4, Hahn M.G.3, Labavitch J.M.1, Powell A.L.T.1.
1
Department of Plant Sciences, University of California, Davis, CA, USA. 2Department of Viticulture and
Enology, University of California, Davis, CA, USA. 3Complex Carbohydrate Research Center, University
of Georgia, Athens, GA, USA. 4Laboratory of Phytopathology, Wageningen University, Wageningen,
The Netherlands
Contact: Barbara Blanco, [email protected]
The ripening of tomato fruit is an example of a developmental transition that coincides with increased
susceptibility to necrotrophic pathogens, such as Botrytis cinerea. Ripening processes that promote
susceptibility include softening-associated disassembly of the fruit host cell wall polysaccharide
networks, modulation of the fruit’s synthesis and perception of plant hormones, accumulation of
organic acids and losses of preformed or induced defense responses.
As an opportunistic pathogen, B. cinerea modifies its infection strategy to take into account the
ripening stage of the host. The diverse and versatile infection mechanisms that B. cinerea deploys on
fruit help to define processes that the pathogen may use to hasten fruit susceptibility but also
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demonstrate that B. cinerea takes advantage of opportune ripening events that render its host
vulnerable to aggressive infections.
B. cinerea utilizes a large repertoire of enzymes that degrade multiple components of the cell walls of
unripe tomato fruit. However, fruit susceptibility to B. cinerea not only depends on the array of
enzymes secreted by the pathogen during infection, but also on modifications that alter the fruit cell
wall as part of ripening. We have determined that B. cinerea induces the expression of tomato genes
coding for cell wall degrading proteins that enhance the deconstruction and softening of the fruit
tissues. Tomato and B. cinerea genes coding for pectin degrading enzymes are expressed more in
infected unripe fruit than in infected ripe fruit. Glycome profiling of cell walls from B. cinerea-infected
and healthy tomato fruit identified changes in the composition and structure of the wall caused by
infections that are associated with fungal infections and the normal ripening process. Specific classes
of cell wall polysaccharides that are depolymerized by B. cinerea during tomato fruit infections include
the backbones and side-chains of homoglacturonan pectins. We detected significant correlations
between the modifications in the fruit cell walls that occurred during B. cinerea infections of unripe fruit
and those that occurred as a result of uninfected fruit ripening. Fruit susceptibility assays using B.
cinerea knockout mutants of pectin degrading enzymes validated the role of particular enzymes during
interactions between tomato fruit and B. cinerea.
3:10 pm
GENETICS AND MACROEVOLUTION OF FLOWER COLOR IN SOLANACEAE
Smith S.D.
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO.
Contact: Stacey D. Smith, [email protected]
Genetic and developmental studies in model species of Solanaceae have provided insights into the
mechanisms underlying many ecologically important traits, such as fruit size, leaf shape and flower
color. In the case of flower color, early work in the model system petunia elucidated the biochemistry
and regulation of anthocyanin pigmentation, enabling parallel work in many other taxa. Building on this
now rich body of literature, I will discuss how the genetic basis for different classes of flower color
transitions relates to different macroevolutionary patterns. A priori, we might expect that colors that can
arise from simple loss-of-function mutations would be common across the phylogeny while those that
with a more complex genetic basis would be rare. Indeed, white flowers, which typically have a simple
genetic basis, are extremely common in Solanaceae. Because these mutations are predominantly
regulatory, lineages that have transitioned to white flowers are often able to regain floral pigmentation
in the course of evolution. We observed a marked difference in phylogenetic distribution of red flower
color, which appears to evolve through a combination of regulatory and structural mutations. Species
with red flowers are exceptionally rare in Solanaceae (34 species or ca. 1% of the family), and we find
no clear evidence of evolutionary reversals following transitions to red. These patterns suggest that
understanding the genetic mechanisms responsible for different classes of transitions may help us to
explain why some colors are common and others remain rare.
3:22 pm
REGULATORY VARIATION IN TOMATO: HARNESSING GENETIC DIVERSITY TO UNDERSTAND
THE REGULATION OF FRUIT DEVELOPMENT
Elroub, N.1, Pattison, R.J.1, Zheng, Y.1, Fei, Z.1,2, Giovannoni, J.1,2, and Catalá, C.1,3
1
Boyce Thompson Institute, Ithaca, NY, USA; 2USDA, Robert W. Holley Centre for Agriculture and
Health, Ithaca, NY, USA; 3School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
Contact: Carmen Catalá, [email protected]
The wild relatives of tomato represent a rich reserve of phenotypic variation in fruit development traits
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including fruit size, morphology and valuable metabolic diversity. However, the genetic basis for this
variation remains mostly unexplained. Differences in gene expression are thought to be an important
source of phenotypic variation between crop species and their wild progenitors. For example, tomato
genes involved in fruit size and shape, style length, cuticle development and starch accumulation,
produce phenotypic differences due to cis-regulatory changes in their expression profile rather than
coding sequence changes. However, comparative transcriptomic approaches to identify genes
responsible for phenotypic variation are complicated by over-riding differences in morphology, growth
habit and development between species. As a result, such “apples-to-oranges” type comparisons tend
to identify large numbers of differentially expressed genes, yet uncovering meaningful changes can be
difficult.
We have characterized genome-wide regulatory variation between S. lycopersicum and S.
pimpinellifolium fruit using RNA-seq based allele-specific expression analysis in F1 hybrids at different
developmental stages. By simultaneously analyzing the expression of wild and cultivated alleles in the
hybrid fruit, background effects on gene expression are eliminated and cis and trans-regulatory
variants are distinguished. We show that the regulatory landscape is characterized by a combination of
cis, trans and compensatory factors and that cis-regulatory differences are found for the majority of
divergently expressed genes. We provide an index of cis-regulated genes at each stage of tomato fruit
development, correlate our findings to previous QTL studies, and identify candidate genes related to
phenotypic variation including sugar and secondary metabolite content and hormone biosynthesis. Our
approach provides a blueprint for understanding regulatory differences between the parent species
and explaining the molecular basis for phenotypic variation.
3:34 pm
GENOME-WIDE ANALYSIS REVEALS THE ROLES OF TRANSPOSABLE ELEMENTS IN THE ORIGIN
OF NOVEL LNCRNAS AND THEIR FRUIT RIPENING IN TOMATO
Ze, Y.1, Wang, X.1, Zhang, J.1, Li, H.2, Cui, L.2, Wang, J.2
1
Key Laboratory of Horticultural Plant Biology, MOE, and 2Key Laboratory of Horticultural Crop Biology
and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei
430070, China
Contact: Zhibiao Ye, [email protected]
Long non-coding RNA (lncRNA), with a transcript length between 200nt and 100kb, has the capability
of protein coding RNA fragments. In recent years, lncRNAs have been widely studied with the
development of sequencing technology. However, the lncRNA expression and origin in plant are still
unclear. In order to understand the lncRNA expression features and evolution patterns in plants. In our
study, we identified 413 and 709 multi-exon non-coding transcripts from 353 and 595 loci of the
cultivar tomato Heinz1706 and the wild species LA1589, respectively. Systematic comparison of the
sequence and expression of lncRNAs showed that they are poorly conserved in Solanaceae, with only
<0.4% lncRNAs present in all sequenced genomes of tomato and potato. Approximately 75% of
Lycopersicon-specific lncRNA loci contain one or more deletions in their transcribed or promoter
regions compared with that in the genome of Solanum pennellii and the origin of some lncRNAs are
closely related to transposable events. Further analysis a fruit-specific expressed lncRNA (named
lncRNA-314), revealed that it originated through two evolutionary events: speciation of S. pennellii
resulted in insertion of a long terminal repeat (LTR) retrotransposon into chromosome 10 and
contributed to most of the transcribed region of lncRNA-314; and a large deletion in Lycopersicon
generated the promoter region and part of the transcribed region of lncRNA-314.Co-expression
analysis indicated that lncRNA-314 co-expressed with a neighboring ABC transport gene which located
upstream on lncRNA-314 and was a target gene of lncRNA-314.These results provide novel insights into
the evolution and regulatory function of lncRNAs in plants.
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3:46 pm
LEVERAGING GENETICS AND GENOMICS TO DEFINE MECHANISMS UNDERLYING FRUIT SIZE
VARIATION IN PEPPER
Hill T.A., Weir A., Visser J., Chunthawodtiporn J., Stoffel K., Van Deynze A.
Plant Sciences Department, University of California, Davis, CA
Contact: Theresa Hill, [email protected]
Fruit are an important part of the human diet and have been under strong selection during
domestication. In general, continued directed selection has led to varieties having larger fruit with
greater shape variation and tremendous increases in fruit mass. The extent to which the molecular
mechanisms underlying fruit size variation within and between crops is unknown. At least six genes
involved in fruit size and shape determination have been identified in tomato (Solanum ssp), a model
for fruit development. Our work and previous studies suggest some of these genes play a similar role
in pepper (Capsicum ssp). However, there are many QTL for pepper fruit traits that do not overlap with
those identified in tomato and the relationship between fruit size and yield differs between these
genera. This indicates there may be crop-specific mechanisms controlling fruit variation. Cultivated
pepper, used as both a vegetable and dried spice, has undergone selection leading to multiple
lineages with distinct fruit morphologies appropriate for consumers’ uses and preferences. Identifying
the molecular components contributing to fruit variation in additional Solanaceous crops, such as
pepper, will help further define common and crop-specific size and shape determinants for gynoeciumderived fruit and the evolutionary plasticity of fruit developmental pathways. We have identified
regions of the pepper genome that have been under significant selection in the lineage leading to
large fruited sweet pepper types and QTL for fruit size and shape in multiple biparental populations.
Using comparative genetics and genomics approaches we have defined both general and unique
genetic determinants of fruit size and shape variation among pepper populations and between pepper
and tomato. Annotated genes within these regions include several organ size regulators that have not
previously been associated with fruit size or shape variation in crops.
COFFEE Break (4:00 — 4:20 pm), Conference Center lobby and patio
CONCURRENT WORKSHOPS, 4:20 — 5:30 pm, Conference Center
• Sol Genomics Network workshop: New features and data in the SGN database, Ballroom A
• Government, Industry, Academics Career Panel (for students and postdocs), Ballroom B
• Collaboration for Plant Pathogen Strain Identification (CPPSI), Ballroom C
• Accelerating Plant Science with CyVerse ­— Genomics Workflows, Data Management and Training,
2nd floor, Room 2207
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CAREER PANEL WORKSHOP
Purpose: To provide information and real-life experiences
of individuals who have careers throughout fields related to
the pipeline of discovery, development, release and use of
Solanaceous plants.
Thursday, September 15, 4:20-5:30 PM
UCD Conference Center Ballroom B
PANEL PARTICIPANTS
Donna Harris PhD
Tomato Pre-Breeder, Bayer Crop Science Vegetable Seeds
Donna grew up on a small beef cattle farm near Athens, Georgia where her dad
also was a part time farmer who raised wheat and soybean and a full time
research professional at the University of Georgia in the soybean breeding
program. She developed a love for agriculture early in life. Donna attended
Georgia Tech after high school for mechanical engineering, but decided after a
year and an internship to come back home to the University of Georgia and
received a B.S. in Crop Science. She earned her M.S. and PhD at Georgia in Plant
Breeding, Genetics, and Genomics. For five years, between her masters and
doctorate, she was a corn breeder in industry. Since July of 2015, she has been
with Bayer CropScience Vegetable Seeds as a tomato pre-breeder located in
Acampo, CA. In her opinion, pre-breeding is a great combination of academia and industry because of
the opportunities to support breeding through the utilization of unadapted germplasm for gene/allele
discovery work.
Gene Miyao
Vegetable Crops Advisor, Yolo/Solano/Sacramento Counties, University of
California Cooperative Extension
Gene received his BS in Agricultural Science and Management at UC Davis in
1971 and an M.S. in Agricultural Economics from UC Davis in 1973. He was a
Farm Advisor for the UC Cooperative Extension of Yolo County in the 1980s
and of Yolo and Solano Counties in the 1990s. Currently he is the Farm
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Advisor for Yolo, Solano and Sacramento Counties. He was Director of the California Tomato Research
Institute in 1990. His specialty is tomato production management.
Rita Mumm PhD
Emerita Associate Professor in Quantitative Genetics and Plant Breeding, U.
of Illinois; Principal, GeneMax Services Urbana, Illinois
Rita Mumm has had an extensive career in crop improvement which spans
industrial seed product development, academic research, and plant breeding
education. Drawn to agriculture through organic vegetable production for her
family, she is a diligent advocate for global food and nutritional security. Dr.
Mumm was a pioneer in developing some of the first biotechnological seed
solutions in crops with DEKALB Genetics Corp, and in establishing a highthroughput molecular marker system to implement genomic information in seed
product development; she is a named inventor on four U.S. patents. She joined
the faculty at the University of Illinois to establish and direct the Illinois Plant
Breeding Center, now one of the preeminent educational centers for crop
genetic improvement in the USA at the graduate level. She led the National Association of Plant
Breeders (USA) in its fledgling years. She currently serves as Education and Training Lead for the
USAID Soybean Innovation Laboratory and on the Board of Trustees for CIMMYT. Additionally, Dr.
Mumm is Principal at GeneMax Services, a consulting firm to the seed industry. She directs the African
Plant Breeding Academy, a continuing education program for African plant breeders established as an
initiative of the African Orphan Crop Consortium.
Diane Okamura PhD
Program Direction, National Science Foundation, Plant Genome Research
Program, Directorate for Biological Sciences, Division of Integrative
Organismal Systems
Dr. Diane Jofuku Okamuro is the Program Director for the Plant Genome
Research Program (PGRP) at the National Science Foundation, Directorate for
Biological Sciences, Division of Integrative Organismal Systems. The PGRP
supports basic discovery research on a genome-wide scale in and/or relevant to
plants that are important to the U.S. economy such as maize, soybean, cotton,
wheat and rice. She is a plant molecular geneticist by training, and has broadbased experience in cutting-edge genomics technologies. She has held research
and management positions in both academia and industry prior to joining NSF in
2005.
Victor Haroldsen PhD
Senior Analyst, Office of Corporate Relations (OCR) at UC Davis, a unit
within the Technology Management and Corporate Relations Division
Victor received a Ph.D. from UC Davis in Biochemistry and Molecular Biology,
a B.Sci. in Biology from Utah State University, and is a registered patent agent
licensed to practice before the USPTO. Prior to joining OCR, Victor worked as
an intellectual property analyst for a San Francisco law firm. He also has
several years of hands-on experience working in university, industry, and
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government lab settings on projects ranging from environmental bio-remediation to crop
biotechnology. Victor works closely with UC Davis’ technology transfer office, to help identify and
generate strategic collaborations between the University and our industry partners by leveraging the
research expertise on campus, and managing and implementing special projects that promote the
integration of technology transfer opportunities.
Li Tian PhD
Associate Professor, Plant Sciences Department, University of California,
Davis
Dr. Li Tian earned her B.S. in Biochemistry at Nankai University in China,
obtained her Ph.D. in Plant Biology at Michigan State University, and was a
postdoctoral fellow in Plant Biochemistry at the Samuel Roberts Noble
Foundation. She joined UC Davis in 2008 as part of the Foods for Health
Initiative and is now an Associate Professor in the Plant Sciences
department. Her research focuses on investigating phytochemical
metabolism in plants with the goal of improving crop nutrient content and
performance in changing environments.
Moderator:
Ann Powell PhD
Emerita Researcher, Plant Sciences Department, University of California,
Davis
Ann received her Bachelor’s degree in Biological Sciences from Stanford
University and her PhD in Biochemistry from the University of Washington.
She was a postdoc with Dr. Elliott Kieff’s group at the University of Chicago
working on Epstein Barr virus before joining the Crown Gall/Agrobacterium
group of Gene Nester and Milt Gordon at the University of Washington. She
was a fellow at the Friedrich Miescher Institute in Basel, Switzerland, working
for three years with Fred Meins. She has been a member of the Plant
Sciences (formerly Vegetable Crops) Department at the UC Davis since 1990.
She has been involved with Seed Central since 2014. Her research has focused on fruit development
and interactions with pathogens and the promotion of opportunities for the next generation of
researchers.
POSTER SESSION II (5:30 — 7:00 pm) • ABSTRACTS on page 96
Appetizers and beverages served, Drinks at poster session sponsored by The Plant Cell
Welcome Center (adjacent to Conference Center)
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FRIDAY, SEPTEMBER 16
Session XIII • PLANT DEVELOPMENT AND REGULATION
Neelima Sinha and Tim Batz, Chairs
8:00 — 9:30 am, Conference Center Ballroom
8:00 am
DOMESTICATION DELAYED CIRCADIAN RHYTHMS IN TOMATO
Müller N.A.1, Wijnen C.L.1, Srinivasan A.1, Ryngajllo M.1, Ofner I2, Lin T.3,4, Ranjan A.5, West D.5, Maloof
J.N.5, Sinha N.R.5, Huang S.3,4, Zamir D2, Jiménez-Gómez J.M.1,6
1
Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany;
2
Institute of Plant Sciences, Hebrew University of Jerusalem, Rehovot 76100, Israel; 3Institute of
Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and
Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory
of Horticultural Genomics, Beijing 100081, China; 4Agricultural Genomic Institute at Shenzhen, Chinese
Academy of Agricultural Sciences, Shenzhen 518124, China; 5Department of Plant Biology, University
of California, Davis, CA 95616, USA; 6INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000
Versailles, France
Contact: Jose M Jiménez-Gómez, [email protected]
The circadian clock is an endogenous timekeeper regulating many important aspects of plant
physiology and development, including key agricultural traits in crop plants. Additionally, natural
variation in circadian rhythms is important for local adaptation. By analyzing circadian leaf movements
of a variety of wild and cultivated tomato accessions we demonstrate that the circadian clock of
cultivated tomato has been slowed down during domestication. Quantitative trait locus (QTL) analyses
revealed that two loci are responsible for this deceleration. Characterization of these two loci suggests
that light signaling has been targeted to achieve a favorable clock in cultivated tomato. We
hypothesize that slower rhythms in cultivated tomato served this species to increase its performance
specifically under the long day photoperiods where it is now commonly cultivated.
8:30 am
EXAMINING THE MOLECULAR BASIS OF SPECIATION IN PETUNIA THROUGH FLAVONOIDTINTED GLASSES
Sheehan H.1, Moser M.2, Klahre U.2, Esfeld K.2, Amrad A.2, Dell’Olivo A.2, Mandel T.2, Metzger S.3,
Vandenbussche M.4, Freitas L.5, Kuhlemeier C.2
1
Department of Plant Sciences, University of Cambridge; 2Institute of Plant Sciences, University of
Bern; 3Cologne Biocenter, University of Cologne; 4ENS de Lyon, CNRS, INRA, UCBL; 5Department of
Genetics, Universidade Federal do Rio Grande do Sul
Contact: Hester Sheehan, [email protected]
The genus Petunia comprises species that are pollinated by different animal pollinators including bees,
nocturnal hawkmoths and hummingbirds. Transitions in adaptation to these different pollinators have
helped drive speciation within the genus. Such transitions require the modification of multiple floral
traits, among them visible colour, ultra-violet (UV) absorbance, scent, nectar production and
morphology. How can such complex changes happen again and again over short periods of
evolutionary time? To answer this question, we determine the genes and mutations responsible for
transitions in floral traits using a combination of genomics, genetics and behavioural ecology.
The majority of Petunia species, such as P. inflata, have UV-reflective, purple flowers and display the
ancestral pollination syndrome of bee pollination. A clade of closely-related, derived species show
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different floral colours and display different pollination syndromes. Two classes of flavonoids are
important for Petunia floral colour: anthocyanins produce the reds, blues and purples, whilst flavonols
absorb UV light. Our data indicate that differences in anthocyanin and flavonol levels
between Petunia species are caused by a limited number of mutations of large phenotypic effect. The
R2R3-MYB transcription factor, AN2, plays a central role in determining differences in anthocyanin
levels between Petunia species. Another R2R3-MYB, MYB-FL, is responsible for gain and loss of UV
absorbance, reinforcing the prevalance of MYB transcription factors in interspecific transitions in floral
colour. Modifications to MYB-FL also cause reciprocal alterations to anthocyanin levels implying
constraint on the diversity of visible and UV colour combinations in flowers.
8:50 am
REGULATION OF TOMATO MERISTEMS IN RESPONSE TO SUBMERGENCE
Kajala K.1,2, West D.A.1, Zumstein K.1, Sinha N.R.1, Brady S.M1,2
1
Department of Plant Biology, University of California Davis, CA, USA; 2 Genome Center, University of
California Davis, CA, USA
Contact: Kaisa Kajala, [email protected]
Extreme precipitation patterns – droughts and flooding – are increasing with climate change. Plant
development is a plastic process affected by environmental cues, and different plants respond to these
water stresses differently. In order to maintain or improve agricultural yield it is critical to understand
how crop species regulate or modify their development in order to acclimate to unfavorable
environments. Here we describe how tomato root and shoot meristems respond molecularly to
flooding.
Seven-day old seedlings of cultivated Solanum lycopersicum cv. M82 and wild drought-tolerant S.
pennellii were submerged, as were Agrobacterium rhizogenes-induced M82 hairy root cultures to
determine if root-to-shoot signaling is required for the root submergence response. After two hours of
submergence, ADH2 transcript is strongly upregulated. However, not all gene expression changes in
response to abiotic stresses are regulated on the level of transcript abundance.
In order to finely dissect the molecular regulation of the submergence response in tomato meristems,
we chose to study chromatin accessibility, the nuclear transcriptome and mRNA associated with
ribosomes (the “translatome”). We optimized two molecular methods for isolating distinct regulatory
compartments in tomato: nuclei by Isolation of Nuclei Tagged in specific Cell-Types (INTACT) and
ribosomes by Translating Ribosome Affinity Purification (TRAP), and generated an atlas of 15 cell and
tissue -specific promoters for both S. lycopersicum and S. pennellii to determine the molecular nature
of stress responses at cell and tissue-resolution. We established pipelines for studying chromatin
accessibility through ATAC-seq, and the nuclear transcriptome and the translatome through RNA-seq
in tomato. This wealth of gene expression and regulatory data allows us to understand how the cellular
and developmental changes in response to two-hour flooding are regulated on genetic level.
Furthermore, in addition to S. lycopersicum cv. M82 and S. pennellii, corresponding datasets are being
generated for rice and Medicago truncatula by our collaborators, elucidating how conserved the
submergence responses are across the flowering plants.
9:05 am
THE EVOLUTION OF INFLORESCENCE DIVERSITY IN THE NIGHTSHADES AND HETEROCHRONY
DURING MERISTEM MATURATION
Lemmon Z.H.1, Park S.J.1,3, Jiang K.1,3, Van Eck J.2, Schatz M.C.1,3, Lippman Z.B.1
1
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA;2The Boyce Thompson Institute, Ithaca,
NY, USA;3Present address: Division of Biological Sciences, Wonkwang University, Republic of Korea
(SJP), Dow AgroSciences LLC, Indianapolis, Indiana, USA (KJ); Departments of Computer Science and
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Biology, Johns Hopkins University, Baltimore, MD, USA (MCS)
Contact: Z.H. Lemmon, [email protected]
One of the most remarkable manifestations of plant evolution is the diversity of floral branching
systems. These inflorescences arise from stem cell populations in shoot meristems that gradually
mature to a reproductive state. Genetic analyses in model and crop species have revealed several
pathways controlling meristem maturation and their significance for inflorescence development.
However, the basis for the continuum of inflorescence complexity observed in nature is poorly
understood. In the nightshade (Solanaceae) family, which includes the pepper and tomato crops,
inflorescences range from a solitary flower to highly elaborate branched structures that can bear
dozens or hundreds of flowers. Here we compare transcriptome profiles of meristem maturation stages
from five domesticated and wild Solanaceae species reflecting the evolutionary range of inflorescence
complexity. We find these species share hundreds of dynamically expressed genes enriched for
transcription factors. Principal component analysis shows meristem stages have distinct molecular
identities, and points to modified maturation schedules underlying architectural variation. These
modified schedules are reflected in a peak of transcriptome divergence during reproductive transition,
driven by heterochronic shifts of a small subset of dynamic genes including transcriptional regulators
with known roles in flowering. Thus, quantitative variation in Solanaceae inflorescence complexity is
determined within a critical transitional window of meristem maturation, which we propose is the
foundation for similar examples of inflorescence diversity in the plant kingdom. More broadly, our
findings resemble a recently proposed transcriptome “inverse hourglass” model for animal
embryogenesis, suggesting both plant and animal development morphological variation is driven by a
transitional period of transcriptome divergence.
9:17 am
ROOT OF POWER: LONG DISTANCE RNA MOVEMENT ASSOCIATED WITH GRAFTING-INDUCED
VIGOR
Frank M.H., Chitwood D.H.
Donald Danforth Plant Science Center, St. Louis, MO 63132
Contact: Margaret Frank, [email protected]
Grafting has been used to increase yield, especially in the context of biotic and abiotic stress for over
2000 years. Although recent experimental evidence suggests that non-cell autonomous long-distance
signals may play an important role in the mechanism through which grafting impacts plant growth and
physiology, the precise identity of these signals and the mechanisms by which they act to affect yield
remain largely unexplored. In tomato, the grafting of elite fruit producing shoots (scions) onto vigorous,
interspecific hybrid root systems significantly increases yield. Here, we present data showing that
grafting-induced vigor can be reciprocally transferred between the root and shoot systems of an
interspecific hybrid (Solanum lycopersicum x S. habrochaites) and domesticated (S. lycopersicum)
tomatoes. We combine these measurements with RNA-seq profiles from reciprocally grafted root and
shoot systems in order to identify non-cell autonomous graft-transmissible transcripts that may serve as
molecular signals through which grafting-induced vigor is conferred.
COFFEE Break (9:30 — 10:00 am), Conference Center lobby and patio
Session XIV • METABOLITES, FLAVOR AND QUALITY
Cathie Martin and Sassoum Lo, Chairs
10:00 — 11:30 am, Conference Center Ballroom
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10:00 am
THE GENETIC BLUEPRINT FOR DEVELOPING A BETTER TASTING TOMATO
Klee, H. and Tieman, D.
University of Florida, Horticultural Sciences and Plant Innovation Center, Gainesville FL 32611
Contact: Harry Klee, [email protected]
Tomato flavor is a complex food sensation involving integration of multiple sensory inputs with ~30
chemicals influencing consumer preferences, including sugars, acids and volatiles. This large number
of flavor chemicals makes the underlying genetics extremely complex. Consequently, flavor quality has
largely been ignored by breeders and modern varieties are widely perceived as being less flavorful.
Our goal is to reverse that deterioration, starting with the consumer and working back through
biochemistry to the underlying genetics. Cultivars spanning a broad range of biochemical diversity
were evaluated by consumers, generating a sensory profile of liking. The resulting statistical
preference models provide a target for genetic improvement, defining the most important chemicals
contributing to flavor. In parallel, we have developed a comprehensive understanding of the
biosynthetic pathways and rate-limiting steps for the most important volatiles. In collaboration with
Sanwen Huang’s group, we have expanded our analyses to genome-wide selections, identifying
alleles of many genes that associate with desirable alleles affecting flavor chemical composition. That
information is now being harnessed to build a toolbox for molecular breeders to restore great flavor in
elite commercial varieties.
10:30 am
COMPARATIVE BIOCHEMICAL GENOMICS OF SOLANACEAE ACYLSUGARS ILLUSTRATES THE
MECHANISMS OF EVOLUTIONARY DIVERSIFICATION IN PLANT SPECIALIZED METABOLISM
Moghe G. 1, Leong B.2, Hurney S.3, Jones D.1,3, Last R.1,2
1
Department of Biochemistry and Molecular Biology, 2Department of Plant Biology, 3Department of
Chemistry, Michigan State University, East Lansing, USA
Contact: Gaurev Moghe, [email protected]
The Solanaceae family has >2500 species, many of which produce metabolites with extensive uses in
agriculture and food, folk medicine, horticulture and cultural practices. Plants produce these
specialized metabolites for communication or defense, and characterizing the biosynthesis and
diversity of these compounds can help provide innovative solutions for diverse human endeavors. Our
lab previously dissected the biosynthesis of one class of defense-related, trichome-derived specialized
metabolites called acylsugars - typically composed of fatty acid moieties esterified to sucrose/glucose
cores – using the cultivated tomato Solanum lycopersicum and its closely related wild species. With
the tomato pathway well-characterized, we sought to understand the origins and evolutionary
diversification of this pathway across the Solanaceae family. We first characterized acylsugar diversity
across >40 species of the Solanaceae using mass spectrometry and performed de novo RNA-seq on
four species with interesting acylsugar profiles, revealing several candidate genes and trichomeenriched specialized metabolic pathways. We then chose two species - Solanum quitoense, a plant
with inositol acylsugars, and Salpiglossis sinuata, a basal species of the Solanaceae family – for
pathway characterization. An integrated approach using NMR, in vitro enzyme assays and RNAi-based
in vivo validation was used to identify multiple acylsugar biosynthetic enzymes. Phylogenetic analyses
of all characterized Solanaceae acylsugar biosynthetic enzymes further provided evidence that this
pathway has emerged and subsequently diversified via multiple paths including evolution of substrate
preference between orthologs, gene duplication and divergence, and gene loss. These findings
illustrate how a comparative biochemical approach integrating high-throughput genomics,
computational biology and molecular evolution can help discover novel enzyme activities for synthetic
biology and provide insights into the origins of the fascinating chemical diversity in the plant world.
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10:50 am
TYPE VI GLANDULAR TRICHOMES OF TOMATO SPECIES: FROM DEVELOPMENT TO
BIOSYNTHESIS OF SPECIALIZED SESQUITERPENOIDS
Bennewitz S., Bergau N., Zabel S., Balcke G., Athmer B., Tissier A.
Leibniz-Institute of plant Biochemistry, Department of Cell and Metabolic Biology, Weinberg 3, 06120,
Halle, Germany
Contact: Alain Tissier, [email protected]
Type VI trichomes of tomato are mainly involved in the biosynthesis of defense terpenoids. In the wild
tomato species, Solanum habrochaites, type VI trichomes have a distinct morphology with a large
intercellular cavity where the secreted metabolites are stored. This and the higher metabolic capacity
than in S. lycopersicum contributes to the high resistance against herbivores of S. habrochaites. To
understand the molecular basis of the morphological and metabolomics differences of type VI
trichomes and of the natural variation in sesquiterpene biosynthesis, a combination of genetics,
transcriptomics and metabolomics was applied. Using a trichome phenotype scoring on a backcross
population between S. habrochaites LA1777 and S. lycopersicum WVA106, several QTL controlling
type VI trichome morphology could be identified. The same population was also used to identify
biosynthesis genes involved in the biosynthesis of sesquiterpene carboxylic acids. Using a backcross
population between S. habrochaites LA2167 and S. lycopersicum LA4024, the biosynthesis of oxidized
derivatives of 7-epi-zingiberene could also be elucidated. In parallel, to investigate the connection
between primary and secondary metabolism in glandular trichomes, a combination of comparative
transcriptomics and metabolomics between leaves and trichomes was used. Although type VI
trichomes are photosynthetic, the energy and reducing power are primarily used to fuel the
biosynthesis of secondary metabolites rather than for CO2 fixation via the Calvin cycle. Plastidic
glycolysis and malic enzyme are overexpressed in trichomes thereby supplying precursors for the
methyl-erythritol phosphate pathway which yields the plastidic isoprenoid precursors, isopentenyl
diphosphate and dimethylallyl diphosphate. In the cytosol, overexpression of enzymes of the citratemalate shuttle including ATP-citrate lyase, ensure high levels of acetyl-CoA, the precursor of the
mevalonate pathway. Based on these, a metabolic network model of type VI glandular trichomes is
proposed.
11:10 am
COMBINED METABOLIC QUANTITATIVE TRAITS LOCI (mQTL) AND EXPRESSION QTL (eQTL)
ANALYSIS IN A RECOMBINANT INBRED LINE POPULATION
Gonda I.1, Ashrafi H.2, Strickler S.R.1, Ma Q.1, Sun H.1, Mueller, L.A.1, Sacks G.L.3, Klee H.J.4, Howe K.5,
Thannhauser T.W.5, Alseekh S.6, Fernie A.R.6, Fei Z.1,5,
Foolad M.R.7, Giovannoni J.J.1,5
1
Boyce Thompson Institute, Cornell University Campus, Ithaca, NY, USA; 2Department of Horticultural
Science, North Carolina State University, Raleigh, NC, USA; 3Department of Food Science, Stocking
Hall, Cornell University, Ithaca, NY, USA; 4Horticultural Sciences Department, University of Florida,
Gainesville, FL, USA; 5USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA;
6
Max-Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany; 7Department of Plant
Science, The Pennsylvania State University, University Park, PA, USA
Contact: Itay Gonda, [email protected]
The quality of tomato fruit is affected by the presence and composition of various metabolites
including sugars, acids, pigments and volatile compounds. While information about structural
biosynthetic genes of various important metabolites is increasing, additional genes and loci governing
their production and accumulation often remain uncharacterized. Quantitative trait loci (QTL) for these
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metabolic traits can be detected by various methods, but pinpointing them down to the causative gene
requires substantial effort. Here we used a tomato recombinant inbred line (RIL) population consisting
of 148 families from an interspecific cross between Solanum lycopersicum (NC EBR-1) and Solanum
pimpinellifolium (LA2093) to map metabolic trait loci using an ultra-high resolution genetic map of this
population. The genetic map was constructed using genotyping-by-sequencing technology followed
by SNP calling and determination of the genetic bins. Focusing on the ripe fruit pericarp, we have
quantified various chemical traits including central metabolites, untargeted specialized metabolites as
well as volatile compounds. By using model selection QTL analysis, we were able to narrow some
known metabolic quantitative trait loci (mQTL) in addition to detecting novel mQTLs. Several QTLs for
different traits were co-localized, suggesting the possibility of common regulation for these traits.
Moreover, we have measured gene expression in the entire population by RNA-seq, enabling the
simultaneous detection of expression QTL (eQTL). We have focused on known structural genes of
various volatile compounds and carotenoids, and generated eQTLs that were grouped as cis-acting or
trans-acting. Co-localization of mQTL and eQTL allowed us to detect loci controlling expression of
genes affecting the relevant traits. This work demonstrates an efficient process for increasing mapping
resolution with expression candidate discovery toward accelerated gene discovery and simultaneous
development of information applicable to molecular breeding efforts.
11:30 am - 12:00
pm
Conference Conclusion
Introduce 2017 Solananceae Conference
Toni Granell
PLEASE COMPLETE CONFERENCE EVALUATION AT
SOLGENOMICS2016.UCDAVIS.EDU/EVALUATIONS/
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CONFERENCE POSTER PRESENTATIONS
Poster Sessions I and II will be held on Tuesday and Thursday evenings at the UC Davis WELCOME
CENTER (adjacent to the Conference Center). Posters will be removed immediately after each evening
poster session. Posters will be available for general viewing at times other than the poster sessions in
conference rooms A and B, located just off of the main lobby area on the first floor of the Conference
Center.
POSTER SESSION I • TUESDAY, September 13
6:05 — 7:30 pm, UC Davis Welcome Center
DIVERSITY-TAXONOMY/CROP GERMPLASM DIVERSITY
101-TU. GETTING TO THE ROOTS OF PUNGENCY: THE TAXONOMY AND PHYLOGENY OF
LYCIANTHES AND CAPSICUM (CAPSICEAE, SOLANACEAE)
Bohs L.1, Dean E.2, Barboza G.3, Van Deynze A.2, Knapp S.4, Stoffel K.2, Hulse-Kemp A.2, Walden G.2
1
Department of Biology, University of Utah, Salt Lake City, UT, USA; 2Plant Sciences Department,
University of California, Davis, CA, USA; 3Multidisciplinary Institute of Biology (IMBIV-CONICET) and
Faculty of Chemistry, National University of Córdoba, Argentina, 4Life Sciences (Plants) Division, British
Museum of Natural History, London, UK
Contact: Ellen Dean, [email protected]
One of the major clades in the Solanaceae is the Capsiceae, consisting of the genera Capsicum and
Lycianthes. Capsicum, with about 35 exclusively Neotropical species, includes the chili and bell
peppers and their relatives. Capsicum is unique in that the fruits of most species contain pungent
capsaicinoids that deter predation by mammals and reduce microbial attack while permitting dispersal
by birds. Capsaicinoids are known only from the genus Capsicum, and their evolution, biosynthesis,
genetic control, and ecological significance are of great biological and practical importance. Lycianthes
contains 150 to 200 species, about 80% of them neotropical and 20% from tropical Asia and the
Pacific. Lycianthes fruits lack capsaicinoids and various species are eaten by humans as wild food
sources. Morphologically, Capsicum and Lycianthes share an unusual calyx structure but are
differentiated by nectary and anther structure. Capsicum anthers open by longitudinal slits, as do most
other Solanaceae, and the flowers have a nectary at the base of the ovary. Lycianthes anthers open by
terminal pores and the flowers lack a nectary. We constucted a phylogeny based on a four-gene
dataset to investigate the roots of pungency in the Capsiceae and the relationship between Lycianthes
and Capsicum. Capsicum forms a well-supported monophyletic group and Lycianthes is paraphyletic,
but resolution and support are low in the backbone of the tree. To produce a more definitive
phylogeny, we are using exome capture and sequencing to characterize the diversity in orthologous
genes across Lycianthes and Capsicum species. During year one of the project, transcriptomes
derived from the root and leaf tissue of diverse species from both genera were sequenced. Sequences
from approximately 14,000 genes represented in the transcriptomes of three Lycianthes species and
one Capsicum species were selected for probe design for exome capture. From this set, about 3000
genes were selected to represent uniform spacing across the genome and genes of interest. In
addition to phylogeny reconstruction, this project will produce online species descriptions and
taxonomic synonymy for all New World species of the two genera. Species descriptions will be posted
on our Solanaceae Source website (http://solanaceaesource.org/).
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102-TU. DEVELOPMENT OF A SOLANUM SITIENS INTROGRESSION LINE POPULATION TO
HARNESS THE POWER OF WILD GERMPLASM FOR TOMATO GENETICS
Burkart-Waco D., Moritama Y, Wills T, Huo X, Silva SJ, and Chetelat RT
Department of Plant Sciences, UC Davis, Davis, California, USA
Contact: Diana Burkart-Waco, [email protected]
Cultivated tomato (Solanum lycopersicum)is of great agronomic importance, but modern cultivars lack
certain key traits such as abiotic stress tolerance and resistances to emerging diseases. Wild relatives
are an important source of genetic diversity and have the potential to accelerate tomato improvement
for abiotic and biotic stress tolerance. The wild tomato relative Solanum sitiens, a species endemic to
the Atacama Desert of Chile, grows under conditions of extremely limited rainfall, low temperatures,
and high soil salinity. Until recently, strong breeding barriers, including hybrid inviability, sterility, and
interspecific incompatibility, prevented hybridization and introgession of S. sitiens with cultivated
tomato. We bypassed these barriers using a ‘pseudo-double cross hybrid’ breeding strategy. The main
objective of our research is to develop an introgression line (IL) population that captures the genome
of S. sitiens in the background of cultivated tomato. Approximately 75 ILs, each containing a single S.
sitiens segment and together spanning all 12 chromosomes, are being backcrossed to tomato cv. NC
84173 using approximately 150 evenly distributed cleaved amplified polymorphic sequences (CAPs)
and/or insertion/deletion markers. Next generation sequencing (NGS) will be employed to precisely
define the breakpoints of each introgression. Segregation distortion, cross compatibility, and sterility
are being assessed during backcrossing to map loci affecting these interspecific hybridization barriers.
This IL population should be a useful germplasm resource to identify causal genes affecting abiotic
stress tolerances and other traits unique to this wild nightshade, and to further tomato improvement
through the sampling of widely divergent germplasm.
103-TU. GENOTYPING-BY-SEQUENCING IN CHILE PEPPERS FROM OAXACA, MEXICO YIELDS
INSIGHTS INTO EVOLUTIONARY HISTORY OF DIFFERENT CHILE PEPPER USE-TYPES
Taitano N.1, Bernau V.2, Mercer K.2, McHale L.2, Wallace J.1, Leckie B.3, Mazourek M.4, Jardón-Barbolla
L.O.5, van der Knaap E.1
Institute for Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, USA;
Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, USA; 3School of
Agriculture, Tennessee Technological University, Cookeville, TN, USA; 4Department of Plant Breeding
and Genetics, Cornell University, Ithaca NY, USA; 5Department of Evolutionary Ecology, Universidad
Nacional Autónoma de México, Mexico City, MX
Contact: Nathan Taitano, [email protected]
1
2
Chile peppers (Capsicum spp.) have increasing economic importance worldwide. In the southern
Mexican state Oaxaca, near the C. annuum domestication center, various named chile pepper types
exhibit extensive variation, including in fruit morphological traits. Studying the distribution of genetic
diversity among these named chile pepper types may help us identify important fruit-trait loci, explore
fruit-trait evolution under domestication, and draw comparisons with the extensive knowledge
generated by fruit-trait research in tomato (Solanum lycopersicum). Our objectives in this study were to
1) determine whether the various named chile pepper types, especially fresh vs. dry use-types,
represented distinct genetic lineages, 2) identify genomic patterns consistent with selection for traits
specific to fresh vs. dry use-types, and selection for domestication traits, and 3) identify genetic
markers associated with fruit morphological traits in genome-wide scans. To accomplish these
objectives, 103 chile pepper seed accessions of 22 named types were collected in 2013 from 29
locations in Oaxaca, Mexico. From these 103 seedlots, 190 plants were grown and genotyped via
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genotyping-by-sequencing (GBS). After removal of poor quality reads, filtering for low coverage and
heterozygosity, the remaining sequences revealed a total of 32,623 single-nucleotide polymorphisms
in this population. Phylogenetic analysis indicated that the largest fresh-use (chile de Agua) and dryuse (Costeño) types clustered into separate, monophyletic clades. This separation confirms that these
two “named types” represent largely distinct lineages, with potentially distinct selective pressures.
However, some phenotypically distinct named types did not assort into separate monophyletic groups,
suggesting them as interesting accessions for further study in controlled crosses.
BARRIERS TO BREEDING
201-TU. MATING SYSTEM TRANSITIONS IN SOLANUM HABROCHAITES IMPACT INTERACTIONS
BETWEEN POPULATIONS AND SPECIES
Broz A.K.1, Randle A.M.1, Sianta S.A.1, Tovar-Méndez A.2, McClure B.A.2,Bedinger P.A.1
1
Department of Biology, Colorado State University, Fort Collins, CO, USA; 2Department of Biochemistry,
University of Missouri-Columbia, Columbia, MO, USA
Contact: Amanda Broz, [email protected]
In plants, transitions in mating system from outcrossing to self-pollinating are common; however, the
impact of these transitions on interspecific and inter-population reproductive barriers is not fully
understood. We examined the consequences of mating system transition on reproductive barriers in 19
populations of the wild tomato species Solanum habrochaites. We identified S.
habrochaitespopulations with self-incompatible (SI), self-compatible (SC) and mixed SI/SC mating
systems, and characterized pollen-pistil interactions between S. habrochaites populations, and
between S. habrochaites populations and other tomato species. Further, we determined whether
mating system or cross-compatibilities corresponded with the presence of pistil SI factors and/or floral
morphology. We documented five distinct reproductive phenotypes reflecting loss of reproductive
barriers near the northern species range-margin. Transitions from SI to mixed mating were not
associated with weakened interspecific reproductive barriers or loss of known pistil SI
factors. However, transitions to SC were accompanied by loss of S-RNase, smaller flowers, and
weakened (or absent) interspecific pollen-pistil barriers. Finally, we identified a subset of SC
populations that exhibited a partial inter-population reproductive barrier with central SI populations.
Our results support the hypothesis that shifts in mating system, followed by additional loss-of-function
mutations, impact reproductive barriers within and between species.
202-TU. THE REPRODUCTIVE BIOLOGY OF SOLANUM HABROCHAITES: A STORY OF INCIPIENT
SPECIATION?
Miller C.1, Broz A.1, Acosta-Quezada P.G.2, Riofrio T.2, Chamba D.2, Tovar-Méndez A.3, McClure B.3,
Chetelat R.4, Bedinger P1.
1
Department of Biology, Colorado State University, Fort Collins, CO, USA; 2Departamento de Ciencias
Agropecuarias y de Alimentos, Universidad Técnica Particular de Loja, Loja, Ecuador; 3Department of
Biochemistry, University of Missouri-Columbia, Columbia, MO, USA; 4Department of Plant Sciences,
University of California, Davis, One Shields Avenue, Davis, CA, USA
Contact: Chris Miller, [email protected]
Species range margins are frequently regions where local adaptation can promote speciation.
Reproductive isolation is generally considered to be a relatively late stage in the process of speciation.
The northern margin of the wild tomato species, Solanum habrochaites—located in southern/central
Ecuador—offers an opportunity to examine early speciation involving reproductive isolation. We
studied recently collected wild germplasm of Ecuadorean S. habrochaites and analyzed reproductive
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characters of these populations including the presence of a specific S-RNase allele associated with the
loss of self-incompatibility in some populations. Our data support the differentiation of four
reproductively distinct ecogeographic groups in Ecuador: the central coast (67-200m), central
mountains (1250 – 2500m), southern mountains (1600 - 2500m), and southwestern uplands (500 –
1700m). Each group is delimited by their unique assembly of reproductive features; the southwestern
uplands are self-incompatible (SI) while the other groups are all self-compatible (SC). In some SC
groups we observed differences in corolla diameter and stigma exsertion; we noted large flowers and
well-exserted stigmas in the southern mountains and small pale flowers in the central coastal region.
We hypothesize the transition from SI to SC in western Ecuador may be due to selection for
reproductive assurance according to Baker’s Law, but further analysis is required. Further, we
observed a partial reproductive barrier between populations, in that pollen from some SC populations
is rejected by pistils of the SI populations. The aggregation of these differences in reproductive biology
suggests a unique instance of early, ongoing speciation in which populations are becoming
reproductively isolated from one another.
203-TU. THE ROLE OF UNILATERAL INCOMPATIBILITY FACTOR ui1.1 (SpSLF-23) IN
GAMETOPHYTIC SELF-INCOMPATIBILTY IN SOLANUM
Qin X., Li W., Markova M., Chetelat R.T.
Plant Sciences Department, University of California, Davis, CA, USA
Contact: Xiaoqiong Qin, [email protected]
We previously showed that the pollen factor ui1.1 encodes an S-locus F-box protein, SLF-23. To
investigate whether SLF-23 also functions in SI, an RNAi construct was introduced into SC S.
pennelliiLA0716 to generate transgenic plants with reduced expression of SLF-23 in pollen. Pollen from
T0 transgenic lines were crossed onto pistils of SI S. pennellii accession LA1272. T-DNA transmission
ratios in the progeny were analyzed to determine whether SLF-23 expression is required to overcome
SI-based rejection. Two independent transgenic lines were tested as pollen donors. Both carried single
copy T-DNA insertions, as indicated by the 1:1 segregation of the T-DNAs observed in progeny of the
control crosses onto the SC accession, LA0716. When pollen of the two T0 lines was crossed onto an SI
accession, three out of five female tester plants showed elimination of T-DNA pollen in the
F1T1 progeny. Analysis of stylar S-RNase’s revealed all three individuals contain SpS1-RNase, which is
not present in the other two tester plants. This S-RNase is therefore a probably target of SpSLF23. SpS1-RNase/SpSLF-23interaction is supported by phylogenetic analysis with their related genes
in Petunia. SpS1-RNase is grouped together with PhS9, SpSLF-23is closely related to type-2 SLFs.
Interestingly, type 2 SLFs have been experimentally demonstrated to recognize S9 RNase inPetunia. In
conclusion, UI1.1/ SLF23 functions in SI as well as UI in Solanum, it is required to recognize one or more
specific S-RNases in the pistil. The conserved recognition of SpS1-RNase bySpSLF-23 and their
orthologs in Petunia (PhS9-RNase by type 2 SLFs) indicates S-RNase based SI is conserved
in Solanaceace.
204-TU. PUTATIVE SELF-INCOMPATIBILITY IN THE ROCOTO CHILI (CAPSICUM PUBESCENS):
PROGRAMIC PHASE AND STARCH MOBILIZATION
Carrizo García C.
Instituto Multidisciplinario de Biología Vegetal, University of Córdoba and CONICET, Córdoba,
Argentina
Contact: Carolina Carrizo García, [email protected]
Capsicum pubescens, the so-called ‘rocoto’, is a chili pepper native to the highlands of South America,
cultivated from Mexico to NW Argentina. As for most Capsicum species, C. pubescens is regarded as
self-compatible, but self-incompatible strains have been described in the species and even variable
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levels of self-incompatibility (SI) have been registered. The occurrence of SI in C. pubescens has been
inferred through analyses of the progamic phase and the fruit set. In addition, a relation between
pollen reserves and the timing of pollen tube abortion has been proposed as a possible explanation
for the differences in the SI level. Because SI alleles could not be retrieved so far in C.
pubescens (pers. obs.), a similar approach was followed in a small group of plants cultivated in NW
Argentina to analyze the relationship between the level of compatibility, pollen tube growth and starch
reserves. Most individuals show some level of SI (fully, mostly, partially SI vs. fully self-compatibility), as
evidenced by the fruit set after self- and cross-pollination. Fruit set after cross-pollination is highly
variable among plants and does not seem to be related to the level of self-(in)compatibility. Pollen
tubes growth was arrested at different lengths along the style when fruit set failed after self-pollination,
showing no correlation with the level of self-(in)compatibility or with pollen starch content. Starch
content in the stigma/style would not be a constraint that hampers pollen tube development during the
progamic phase. Part of the evidence indicates the occurrence of SI in C. pubescens, but many
variables have a regulatory role in the relation between pollen tubes and pistil. Starch was considered
this time, due to its key participation in pollen tube nutrition, but it does not seem to be a relevant
constraint. Further analyses are needed to understand better the irregular behavior of pollen tubes
during the progamic phase and the frequent occurrence of not fully SI in C. pubescens, including new
attempts at the molecular level.
205-TU. MUTATIONS IN TWO POLLEN SELF-INCOMPATIBILITY FACTORS REINFORCE THE
BREAKDOWN OF SELF-INCOMPATIBILITY IN SOLANUM
Markova D., Petersen J., Qin X., Chetelat R.
C.M. Rick Tomato Genetics Resource Center, Dept. of Plant Sciences, University of California, Davis, CA
95616
Contact: Dragomira Markova, [email protected]
Self-incompatibility (SI) is a genetic mechanism that prevents inbreeding in many plant species. The
mutational breakdown of SI occurs frequently in outcrossing species, yet relatively little is known about
the evolutionary steps involved in the progressive loss of pistil and pollen SI function. We used SI and
SC accessions of wild tomato species (Solanum sect. Lycopersicon) to study natural genetic variation
for two pollen factor loci, ui1.1 and ui6.1. The former encodes S-locus F-box protein (SLF-23), the latter
encodes a Cullin1 (CUL1) protein; both loci function in self- and interspecific incompatibility. In S.
habrochaites, a mostly SI species, we detected loss-of-function mutations in CUL1 and/or SLF-23 in SC
populations collected near the northern or southern geographic margins of this taxon’s natural range.
Non-marginal SC and SI accessions expressed mostly functional alleles of these pollen factors, and
several accessions contained both functional and nonfunctional alleles. That these pollen factor
mutations were found only in the northernmost and southernmost SC populations establishes that
these mutations are not required for SC and suggests they become fixed relatively late during SI to SC
transitions, and were likely preceded by loss of pistil-side SI function. Comparison of
the CUL1 sequences in these accessions identified several shared deletion mutations present in both
northern and southern margin SC biotypes, suggesting they derive from ancestral variation within more
centrally located populations. Interestingly, most other green-fruited species seem to have evolved an
SC mating system through a different evolutionary and genetic trajectory than S. habrochaites.
206-TU. ALEURAIN: ITS ROLE IN POLLEN REJECTION RESPONSE IN NICOTIANA
Rosillo-Salazar O.D.1, Cruz-González Y.1, Cruz-García F1.
1
Biochemistry Department, Faculty of Chemistry, National Autonomous University of Mexico, Mexico
City, Mexico
Contact: Oscar Daniel Rosillo Slazar, [email protected]
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Plants are capable of recognizing and rejecting self-pollen to prevent inbreeding; this is known as selfincompatibility (SI). In Nicotiana, SI is genetically controlled by the highly polymorphic S-locus that
encodes the S-RNase and SLF (S-locus F-box) proteins. Physical interaction of both proteins specifically
determines pollen rejection. Loss of function experiments suggest that HT-B (High Top Band), 120K
and NaStEP (N. alata Stigma Expressed Protein) are also essential to the SI response. During pollen
tube (PT) growth, S-RNase and 120K are endocytosed from the transmitting tissue and stored in a PT
vacuole, containing thus, the cytotoxic activity of S-RNase. HT-B and NaStEP are also incorporated into
the PT. HT-B remains stable in SI crosses and promoting the vacuole rupture and releasing S-RNase
onto cytoplasm. However, in self-compatible (SC) crosses, HT-B is degraded and the PT vacuole
remains intact, allowing PT growth. NaStEP is a Künitz-type inhibitor and regulates HT-B stability, when
absent, HT-B is degraded in PT of both SI and SC crosses. If NaStEP protects HT-B from degradation, it
is hypothesized that NaStEP also must be degraded in SC to allow PT growth. Proteases activities
seem to play a major role in SI response. However, proteases responsible of HT-B, 120K and NaStEP
degradation have not been identified yet. For this reason, an interesting candidate to consider is
aleurain, a cysteine protease that colocalizes with S-RNases and 120K in the same PT vacuole. So the
aim of this research is to determine if aleurain degrades 120K, HT-B and NaStEP. This objective will be
addressed through silencing by RNAi and in vitro assays.
GENOMES AND GENOME TECHNOLOGIES
301-TU. ANALYSIS OF A TRANSGENIC TOMATO PLANT OVEREXPRESSING A
RHAMNOGALACTURONAN LYASE GENE
Ochoa-Jiménez V.A.1, Burgara-Estrella A.2, Rivera-Domínguez M.3, Troncoso-Rojas R.1, Báez-Sañudo R.1,
Handa A.K.4, Tiznado-Hernández M.E.1
1
Cordinación de Tecnología de Alimentos de Origen Vegetal, 3Cordinación de Ciencias de Alimentos,
Centro de Investigación en Alimentación y Desarrollo A. C., Hermosillo, Sonora,
México.2Departamento de Investigación en Física, Universidad de Sonora, Hermosillo, Sonora,
México, 4Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,
IN, USA
Contact: Verónica Ochoa-Jiménez, [email protected]
The enzyme rhamnogalacturonan lyase (RGL) degrades the rhamnogalacturonan I (RGI) polymers
through cleaving the glycosidic bond between rhamnose and galacturonic acid residues by a βelimination mechanism. Although the biochemical mode of action of RGL is well known there is little
information about the physiological function of this enzyme in the plant cell wall, and in the fruit
physiology.
The coding region of the Solyc11g011300 gene was isolated with primers designed using the sequence
deposited on the database Sol Genomics Network. This gene was chosen because previous studies
had shown that it is expressed mainly during fruit development and ripening. The Solyc11g011300
cDNA was cloned into the GUS-less pCAMBIA2301 binary vector In the chimeric construct designed
(pcVRGL), the CaMV35S is driving the expression of the RGL cDNA and it was introduced into tomato
plant by Agrobacterium infection. The unaltered pCAMBIA2301 vector was used as a positive control.
The presence of the pcVRGLconstruct in the genome of the transgenic tomato plants was
demonstrated by PCR analysis.
The experiments are underway to create transgenic tomato plants homozygous for the transgene by
mendelian inheritance. The study of the transgenic tomato plants overexpressing the Solyc11g011300
gene, will help in the elucidation of the function of this enzyme in the physiology of the fruit and
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vegetative tissues.
302-TU. ISOLATION AND ANALYSIS OF A RHAMNOGALACTURONAN LYASE GENE REGULATORY
REGION BY USING TRANSGENIC TOMATO PLANTS
Berumen-Varela G.1, Burgara-Estrella A.2, Rivera-Domínguez M.3, Troncoso-Rojas R.1, Baéz-Sañudo R.1,
Handa A.K.4, Tiznado-Hernández M.E.1
1
Coordinación de Tecnología de Alimentos de Origen Vegetal, 3 Coordinación de Ciencia de los
Alimentos, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora,
Mexico; 2Departamento de Investigación en Física, Universidad de Sonora, Hermosillo, Sonora,
Mexico; 4 Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,
IN, USA
Contact: Guillermo Berumen-Varela, [email protected]
Rhamnogalacturonan lyase (RGL) recognizes and cleaves the α-1,4 glycosidic bonds located between lrhamnose and d-galacturonic acids in the main chain of the rhamnogalacturonan-I, one of the plant cell
wall pectin domain polysaccharides. Although the biochemical mode of action of RGL is well known,
there is little information about the physiological function of this enzyme in the plant cell wall and
during postharvest of fruit. Tomato is a good model to carry out fruit genetic engineering. The analysis
of specific regulatory regions using reporter genes is an important tool to study the spatial and
temporal gene expression pattern. Based on the previously mentioned, we had developed transgenic
tomato plants expressing a reporter gene under the transcriptional control of different promoter
regions isolated from the Solyc11g011300 gene, which encodes a rhamnogalacturonan lyase
isoenzyme in tomato.
The promoter region sequence located -1012 bp upstream of the tomato Solyc11g01300 gene
sequence from start codon was obtained from the Sol Genomics Network database. The regulatory
sequence was analyzed in silico for the presence of putative cis-acting elements using PlantPAN
software. Moreover, we designed two chimeric constructs in which thepromoter regions of -788 and 496 bp are transcriptionally controlling the β-glucuronidase (GUS) reporter gene using the
pCAMBIA2301 promoter-less vector. The unaltered pCAMBIA2301 vector was used as a positive
control. The RGL promoter::GUS fusions were confirmed by PCR and restriction analysis of plasmids.
Transgenic tomato plants were created by Agrobacterium tumefaciens infection.
In silico analysis of the promoter region showed responsive elements playing a role during pollen
germination and in response to ethylene, auxin and water stress.PCR analysis and histochemical GUS
assays revealed that the transgenes are stably integrated into the tomato genome and active.
303-TU. COMPREHENSIVE REPEATOME ANNOTATION REVEALS STRONG POTENTIAL IMPACT
OF REPETITIVE ELEMENTS ON TOMATO RIPENING
Jouffroy O.1, Quesneville H. 1, Maumus F.
1
URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
Contact: Ophélie Jouffroy, [email protected]
Plant genomes are populated by different types of repetitive elements including transposable
elements (TEs) and simple sequence repeats (SSRs) that can have a strong impact on genome size and
dynamic as well as on the regulation of gene transcription. At least two-thirds of the tomato genome is
composed of repeats. While their bulk impact on genome organization has been largely revealed by
whole genome assembly, their influence on tomato biology and phenotype remains largely
unaddressed. More specifically, the effects and roles of DNA repeats on the maturation of fleshy fruit,
which is a complex process of key agro-economic interest, still needs to be investigated
comprehensively and tomato is arguably an excellent model for such study.
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We have performed a comprehensive annotation of the tomato repeatome to explore its potential
impact on tomato genome composition and gene transcription. Our results show that the tomato
genome can be fractioned into three compartments with different gene and repeat density, each
compartment presenting contrasting repeat and gene composition, repeat-gene associations and
different gene transcriptional levels. In the context of fruit ripening, we found that repeats are the
support of the majority of differentially methylated regions and thousands of repeat-supported DMRs
are found in gene proximity including hundreds that are differentially regulated. Furthermore, a study
of the proximity between repeats and binding sites of the key ripening protein RIN is also underway to
target more precisely differentially expressed genes potentially influenced by proximal repeats.
304-TU. A NEW NICOTIANA TABACUM CHROMOSOME LEVEL GENOME REFERENCE SEQUENCE
ENABLES MAP-BASED CLONING
Fernandez-Pozo N.1, Edwards K.D.2, Drake-Stowe K.3, Humphry M.2, Evans A.D.2, Bombarely A.4, Allen
F.2, Hurst R.2, White B.2, Kernodle S.P.3, Bromley J.R.2, Sanchez-Tamburrino J.P.2, Lewis R.S.3, Mueller
L.A.1
1
Boyce Thompson Institute, Ithaca, NY, U.S.A. 2Plant Biotechnology Division, British American Tobacco,
Cambridge, U.K 3Crop Science Department, North Carolina State University, Raleigh, NC,
U.S.A. 4Department of Horticulture, Virginia Tech, Blacksburg, VA, U.S.A. Department
Contact: Noe Fernandez-Pozo, [email protected]
Nicotiana tabacum, is an important model plant for the study of plant diseases, development,
polyploidy, and evolution, among other biological processes. Historically, it has played a very important
role in the development of tissue culture and transformation in plants. However, the Nicotiana
tabacum genome is large and complex; 4.5Gb in size and comprised of around 70% repeats. It is a
recent allotetraploid that originated less than 0.2 million years ago by the hybridization of ancestors
from Nicotiana sylvestris and Nicotiana tomentosiformis. All of these characteristics have complicated
tobacco genome sequencing and anchoring to pseudomolecules. Here, we present a new N.
tabacum genome assembly, improved with the application of Bionano Genomics optical mapping. The
assembly has non-N sequence coverage of 4 GB (90% of the genome), an N50 size of 2.17 Mb, and 64%
of it is anchored to chromosomal locations. To analyze this new assembly, 69,500 genes were
predicted and the ancestral origin was identified for chromosomes as well as genes. The genome
sequence study showed a good separation between the parent sequences, finding that genome
reorganization after the hybridization of the parents has resulted in the preferential lost of N.
tomentosiformis sequences over N. sylvestris, but a significant gene loss was not observed from either
of the ancestors. This tobacco genome also allowed the study of nitrogen genes at the YB loci,
responsible for the chlorophyll deficienct phenotype in tobacco burley varieties, as well as affecting
nitrogen utilization efficiency and alkaloid and leaf nitrate levels in these cultivars. We now aim to
improve this genome assembly, in combination with previously published tobacco genome sequences,
to produce a tobacco genome reference for the scientific community.
305-TU. TomTILL BY SEQUENCING: USING NGS FOR IDENTIFICATION OF INDUCED MUTATIONS IN
TOMATO
Gupta P.1, Bodanapu R.1, Salava H.1, Upadhyaya P.1, Sarma S.1, Tyagi K.1, Malhotra B.1,Narayan S. 1, Kumar
R.1, Till B. J.2, Sreelakshmi Y.1, Sharma R. P.1
1
Repository of Tomato Genomics Resources, Dept. of Plant Sciences, University of
Hyderabad, Hyderabad, INDIA; 2 Plant Breeding and Genetics Laboratory, IAEA, Vienna, Austria
Contact: Prateek Gupta, [email protected]
TILLING (Targeting Induced Local Lesions in Genomes) is an efficient reverse genetics approach that
allows screening for mutations in specific gene of interest. Combined with next-generation sequencing
(NGS) technology and multidimensional pooling strategy, TILLING provides an efficient and economical
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platform for mutant identification. Tomato fruit being a good source of health promoting nutrients, has
gained both scientific and economic importance. In order to screen for mutants with enhanced
nutritional quality and its associated metabolic traits, we have developed a 120 mM ethyl methane
sulphonate (EMS) re-mutagenized tomato population combined with Illumina sequencing platform to
identify mutations in genes related to carotenoid and folate biosynthesis pathway. DNA and seed
libraries were prepared from 5000 M2 plants. DNA from 768 individual plants were pooled in a three
dimensional manner into 44 superpools. These superpools were amplified with 600 bp of target
regions and the amplicons were subjected for sequencing. By screening 768 M2 lines from the TILLING
population, two missense mutations were identified in chromoplast specific lycopene beta
cyclase (CYCB) and 9-cis epoxy-carotenoid dioxygenase (NCED), one missense and one silent
mutation in zeaxanthin epoxidase (ZEP), two silent mutations in gamma glutamyl hydrolase1 (GGH1)
and plastidial folylpolyglutamyl synthase (FPGSp) and one silent mutation in GTP cyclohydrolase 1
(GCH1). However, no mutations were detected in phytoene synthase 1 (PSY1) and carotenoid
isomerase(CrtISO) genes in the screened region. These observed SNPs were further validated by
Sanger sequencing and lines carrying the mutations were advanced to next generation to study gene
function. The overall mutation frequency was observed 1 SNP/460 kb. TILLING using NGS is an
efficient strategy to identify mutations in other biosynthetic pathways gene that could contribute
towards improved traits in tomato.
GENE EDITING AND NEW BREEDING TECHNOLOGIES
501-TU. APPLICATION OF CRISPR-Cas9 NUCLEASES ALTERED PAM SPECIFICITIES TO TOBACCO
Komatsu H.1, Ariizumi T.2, Ezura H.2
1
Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba,
Ibaraki 305-8572, Japan; 2Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1
Tennoudai, Tsukuba, Ibaraki 305-8572,Japan
Contact: Hiroki Komatsu, [email protected]
CRISPR/Cas9 system is a novel site-directed mutagenesis tool for the basic science and the crop
breeding. SpCas9, a protein discovered in Streptococcus pyogenes, recognizes PAM motif (only NGG)
in target sequence and induces DNA double strand breaks. Thus, the targeted sequence is limited to
sites containing NGG motif. To overcome this constraint, many works have been done. Recently,
Kleinstiver et al. (2015) revealed that modified SpCas9 recognize alternative PAM sequence (NGA) in
zebrafish and human cell. Here, we investigate the genome editing performance of the modified
SpCas9 in plant. The modified SpCas9 protein has three amino acid substitutions (D1135V / R1335Q /
T1337R) in PI domain, which recognizes PAM motif. In this research, the sequence of SpCas9 in
pDeCas9-kan vector (Fauser et al.2014) was directly edited by using Infusion technique. To investigate
the activity of the modified SpCas9, we used a frame-shift GUS reporter system according to Yinet
al. (2012). SpCas9-m vector used for infection to plant is based on pDeCas9-kan vector. Vectors
having GUS genes interrupted by 25-28bp inserts were constructed, causing the frame shift of GUS
gene. These frame shifted GUS genes produce non-functional GUS proteins. These inserts consist of
modified SpCas9 protein candidate PAM motif recognition sites (NGA, NGG, NGC and NGT). Tobacco
(Nicotiana tabacum) was co-infected by Agrobacterium tumefaciens strains having SpCas9-m vector
and GUS vector. GUS activity was observed in vivo by GUS staining of tobacco leaf. If GUS inserts
were cleaved by SpCas9-m, the abnormal frame of GUS gene will be corrected and the functional GUS
expression is recovered, indicating the occurrence of SpCas9-m`s PAM motif recognition activity. In
this study, GUS activity was not observed. Therefore, DNA was obtained from leaves and target
sequences were amplified. The amplified products were cloned into TA vectors and vectors from each
colony were sequenced to identify mutations. But, the mutations were not detected. Investigation of
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modified SpCas9 activity in stable condition is now ongoing in transgenic tomato.
502-TU. DEVELOPMENT OF NEW POTATO VARIETIES WITH LATE BLIGHT AND POTATO CYST
NEMATODE RESISTANCE, REDUCED BRUISING AND IMPROVED PROCESSING QUALITY
Pais M.1, Tomlinson L.1, Witek K.1, Karki H.1, Jupe F.1, Marillonnet S.2, Urwin P.E.3, Richael C.4, Jones J. D.1
1
The Sainsbury Laboratory, Norwich Research Park, Norwich, UK; 2Department of Cell and Metabolic
Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany; 3Centre for Plant Sciences, University
of Leeds, Leeds, UK; 4Simplot Plant Sciences, J. R. Simplot Company, Boise, Idaho, USA
Contact: Marina Pais, [email protected]
This project aims to address serious problems affecting the potato industry by delivering multiple GM
traits through state-of-the-art cloning methods. Late blight disease (LB), potato cyst nematodes (PCN),
tuber bruising and the cold-induced accumulation of reducing sugars (which leads to blackening and
formation of acrylamide by reaction with asparagine upon cooking at high temperature) all cause
significant losses and food wastage. Our goal is to provide solutions based on the use of 3-Resistance
to Phytophthora infestans (Rpi)-genes against LB (Rpi-vnt1 + 2 Rpi genes from Solanum americanum),
the use of two genes to control PCN and the use of silencing constructs to reduce browning, levels of
asparagine and the cold-induced accumulation of reducing sugars in tubers. The potato variety chosen
for transformation is Maris Piper, since it is grown three times more than any other variety in the UK. If
successful, this project will benefit potato farmers, processors and consumers.
The plant selectable marker used is an allele of the tomato acetolactate synthase that confers
resistance to the herbicide chlorsulfuron, and conditions for selection with this herbicide have been
optimized. To detect copy number of the T-DNA, digital droplet PCR is used. Further, we use an
optimized binary vector, which carries multiple left borders, the ipt gene in the vector backbone and a
right border with full flanking overdrive sequences. These features aim to decrease the chances of
backbone integration and to allow counter-selection of plants where such event occurs. In addition, the
binary vector contains a low-copy-number origin of replication for Agrobacterium tumefaciens, to
reduce the probability of multiple insertions. Cloning of the gene stacks is performed by the Golden
Gate technique. Although the project is not primarily about biological discovery, it will generate
extensive data on the efficiency with which large T-DNAs can transfer multiple genes simultaneously
into plants.
Finally, transient assays were performed to verify that the Rpi genes work as expected when
combined. No interference between the function of these LB R genes was detected and we aim to trial
plants carrying the Rpi genes in the field to assess their usefulness against UK blight strains.
503-TU. PRODUCTION AND CHARACTERIZATION OF A TOMATO TILLING POPULATION
Jiang J.1, Kiser J.1, Tsai, H.1, Omura C.1, Van Deynze A.2, Chetelat R.2, Comai L.1
1
Department of Plant Biology and Genome Center; 2 Plant Sciences Department, University of
California, Davis, CA, USA
Contact: Luca Comai, [email protected]
Targeting Induced Local Lesions IN Genomes (TILLING) populations are derived by chemical
mutagenesis and are suitable for forward and reverse genetics screen. TILLING alleles provide a range
of functionality and are accepted as the basis of GMO-free (i.e. non transgenic) traits. We report here
the production of a large scale TILLING population in the same processing tomato line that was used
for reference genome sequencing, Heinz 1706. The project consisted of two phases. In the first, using
funding provided by USDA, we screened several varieties for their response to mutagenesis. We found
considerable variation including recalcitrance. Variety Heinz 1706 was found satisfactory by multiple
criteria and was chosen for further development. In the second phase, funded in part by industry, we
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scaled up the Heinz 1706 population. By high throughput sequencing we have determined the
presence of mutant alleles in multiple test genes, with a rate ranging between 4 and 2 mutations/MB of
diploid DNA. The population is available for TILLING (see
"http://tilling.ucdavis.edu/index.php/Tomato_Tilling"). Around 4,500 lines are available without
restriction for any use. Around 10,000 additional lines developed using industry funding are available
for basic research with some restrictions for trait and intellectual property development. The availability
of this large population should facilitate the search for alleles informative of gene function in tomato.
GENOMICS-ASSISTED BREEDING
701-TU. INITIATING GENOMIC SELECTION IN TETRAPLOID POTATO
Sverrisdóttir E.1, Janss L.2, Byrne S.3, Asp T.3, Nielsen K.L.1
1
Aalborg University, Department of Chemistry and Bioscience, 9220 Aalborg, Denmark; 2Aarhus
University, Centre for Quantitative Genetics and Genomics, 8830 Tjele, Denmark; 3Aarhus University,
Section for Crop Genetics & Biotechnology, 4200 Slagelse, Denmark
Contact: Elsa Sverrisdóttir, [email protected]
Breeding for more space and resource efficient crops is important to feed the world’s increasing
population. Potatoes produce approximately twice the amount of calories per hectare compared to
cereals. The traditional “mate and phenotype” breeding approach is costly and time-consuming;
however, the completion of the genome sequence of potato has enabled the application of genomicsassisted breeding technologies. Genomic selection using genome-wide molecular markers is
becoming increasingly applicable to crops as the genotyping costs continue to reduce and it is thus an
attractive breeding alternative.
We have used genotyping-by-sequencing to genotype 762 individuals. The individuals were randomly
selected from a population of 5,000 individuals derived from a poly-parental cross generated from 18
tetraploid cultivars and breeding clones (MASPot population). Phenotypic data have been established
for six agronomical important traits for the entire population.
We have generated statistical models for genomic prediction and have obtained relatively high
predictive power with absolute accuracies of 74%, 56%, 54%, and 21% for starch content, chipping
quality, late blight resistance, and yield, respectively. When scaled to the trait heritability, which can
also be interpreted as the maximum variance explained by genetic factors, relative prediction
accuracies of 116%, 68%, 73%, and 49%, respectively, were obtained. As expected from the limited
population size of this study, the within-population predictive power is considerably higher than its outof-population predictive power. Nonetheless, to validate the prediction model, a test panel of 74
individuals not closely related to the training population were genotyped. Absolute prediction
accuracies for starch content, chipping quality, and yield, were 40%, 43%, and 51%, with relative
accuracies of 62%, 53%, and 109%, respectively. For late blight resistance, there was no correlation
between predicted and observed phenotypic values. This was expected because specific dominant Rgenes conferring resistance in the training population were different from the ones expected to be
present in the validation population.
We are currently expanding the training set for a better calibration of the prediction model. Taken
together, our results suggest that genomic prediction of complex traits, and hence selection of
breeding material by genomic selection, can be obtained with good prediction accuracies in tetraploid
potato.
702-TU. EXPLOITATION OF A LARGE NUMBER OF SSR AND INDEL MARKERS AND
CONSTRUCTION OF A HIGH-DENSITY GENETIC MAP OF PEPPER (CAPSICUM ANNUUM L.)
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BASED ON PEPPER GENOMIC INFORMATION
Zhang X-F., Sun H.-H., Xu Y., Chen B., Yu S-C., Geng S-S., Qian Q.
College of Agriculture and Biotechnology, China Agricultural University, Beijing, China; 2Beijing
Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
Contact: Zhang Xiaofen, [email protected]
Capsicum annuum, the most widely cultivated species of pepper, is used worldwide for its important
nutritional and medicinal values. The construction of an intraspecific high-density genetic linkage map
would be of practical value for pepper breeding. However, the numbers of PCR-based simple
sequence repeat (SSR) and Insertion/deletion (InDel) markers that are available are limited, and there is
a need to develop a saturated, intraspecific linkage map. The non-redundant Capsicum species
expressed sequence tag (EST) database from the National Center for Biotechnology Information (NCBI)
was used in this study to develop a total of 902 usable EST-SSR markers. Additionally, 177,587 SSR loci
were identified based on the pepper genomic information, including 9,182 SSR loci 500bp both
upstream and downstream of coding regions. Another 4,497 stable and reliable insertion/deletion
(InDel) loci were also developed. From 9182 SSR and 4497 InDel loci, 3,356 pairs of genomic SSR
primers and 1,400 pairs of InDel primers that were evenly distributed in 12 chromosomes were
selected. A high-density intraspecific genetic map of C. annuum was constructed using the F10generation recombinant inbred line (RIL) of parents PM702 and FS871 as the mapping population,
screening the selected 3,356 pairs of genomic SSR primers and 1,400 pairs of InDel primers and the
902 EST-SSR markers developed earlier, and 524 published SSR markers and 299 orthologous
markers (including 263 COSII markers and 36 tomato derived markers) used previously to develop an
interspecific genetic map (C. annumm × C. frutescens). Eventually, a high-density complete genetic
intraspecific linkage map of C. annuum containing 12 linkage groups and 708 molecular markers with a
length of 1260.00 cM and an average map distance of 1.78 cM was produced. This intraspecific, highdensity, complete genetic linkage map of C. annuum contains the largest number of SSR and InDel
markers and the highest amount of saturation so far, and it will be of considerable significance for the
breeding of improved cultivars of this important field crop in the future.
703-TU. Presenter opted out of program listing
SYSTEMS BIOLOGY AND NETWORKS
801-TU. Presenter opted out of program listing
802-TU. PROPOSING A GENE NETWORK MODEL OF FLOWERING IN TOMATO
Ta J., Runcie D.
Plant Sciences Department, University of California, Davis
Contact: James Ta, [email protected]
Flowering in tomato consists of complex physiological transitions that involves translation of
environmental signals into differential gene expression at the shoot apical meristem (SAM) and
sympodial meristems to drive floral maturation. The timing of flowering is critical because it influences
plant fitness and architecture, and must synchronize with favorable environmental conditions.
Consequently, flowering time is heavily regulated by multiple gene pathways. While experiments have
helped qualitatively characterize tomato flowering genes, how these genes interact to regulate
flowering time remains unanswered. A quantitative understanding through gene network modeling
could elucidate the genetic mechanisms underlying flowering and can generate hypotheses for future
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experiments. Creating an accurate tomato flowering network model can also provide a tool for plant
breeders to optimize crop yield. Because tomato shares many flowering orthologs from A. thaliana,we
adopt an earlier A. thaliana flowering network model to propose a theoretical tomato flowering
network model. We investigate various gene network topologies that attempt to predict flowering time
of the initial vegetative segment and subsequent sympodial units.
Our model is driven by these questions:
1. How do florigen (SFT) and vegetative (SP, TMF) proteins interact to regulate vegetative and
reproductive growth?
2. How does plant architecture influence florigen partitioning among inflorescence and sympodial
meristems in tomato?
803-TU. RESOURCES, TOOLS AND DATA FOR COMPARATIVE PATHWAY ANALYSIS FOR
SOLANACEAE CROPS IN PLANT REACTOME DATABASE
Naithani S.1*, Preece J.1, D'Eustachio P.2, Elser J.L.1, Gupta P.1, Fabregat A.3, Weiser J.4, McKay S.4, Stein
L.4, Ware D.5, Jaiswal P.1
1
Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR; 2NYU School of
Medicine, New York, NY; 3European Molecular Biology Laboratory - European Bioinformatics Institute,
Hinxton, United Kingdom; 4Ontario Institute of Cancer Research, Toronto, ON, Canada; 5Cold Spring
Harbor Laboratory/USDA-ARS, Cold Spring Harbor, NY
Contact: Prateek Gupta, [email protected]
Plant Reactome database (http://plantreactome.gramene.org/), a pathway and network portal of
Gramene database. It employs the structural framework of a plant cell to show metabolic, genetic,
developmental and signaling pathways for several model and crop plant species including tomato and
potato. Plant Reactome features Oryza sativa (rice) as a reference species, where we curate pathways
supported by published literature and known information about the gene functions and metabolite
roles. Plant Reactome also hosts gene homology-based pathway projections for 62 plant species. Plant
researchers can i) search and browse various components of the database; ii) compare projected
pathways with those from the reference species to identify potential gaps in projection or biological
differences; iii) visualize curated baseline and differential gene expression data in the context of
pathways; and iv) upload and analyze Omics datasets generated in their laboratories to identify
differentially expressed pathways and associated genes. The presentation will discuss development of
the Plant Reactome, curation of reference pathways, and use cases from tomato and potato. The
project is supported by the Gramene database award (NSF IOS-1127112) and the Human Reactome
award (NIH: P41 HG003751, ENFIN LSHG-CT-2005-518254, Ontario Research Fund, and EBI Industry
Programme).
ABIOTIC STRESSES
901-TU. SCREENING THE RESPONSES OF TOMATO ROOTSTOCKS TO DROUGHT AND SALINITY
STRESS UNDER IRRIGATION
Hirich A.1, Choukr-Allah R.1, Fiene G.2, Morton M.2 and Tester M.2
1
International Center for Biosaline Agriculture, Dubai, UAE; 2Center for Desert Agriculture (CDA), King
Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
Contact: Gabriele Fiene, [email protected]
Salinity and drought are major constraints limiting agricultural crop productivity in the world and water
salinity is continuously increasing due to over-extraction of groundwater. Using saline water to irrigate
crops requires selection of tolerant species, genotypes and varieties. The aim of this study was to
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screen for the most suitable tomato rootstocks that can be used for grafting under saline and drought
conditions. For this purpose, 12 commercial varieties and 2 wild species (Solanum pimpinellifolium and
Solanum cheesmanii) were tested in a field trial using four salinity levels of irrigation water (1.5, 4.0, 7.0
and 10 dS/m) and three irrigation levels (100, 50 and 25%) using fresh water (1.5 dS/m). Many
parameters, such as stem diameter, root and shoot weight and sodium contents in leaves, were
determined. The tested lines differed greatly in their responses to drought and salinity. Under the most
water-stressed treatment (25% of full irrigation), the highest root weight and root to shoot ratio was
recorded for Arazi, while the highest shoot weight and stem diameter was recorded for Empower and
DR9011TV. However, under high salinity (10 dS/m), Solanum pimpinellifolium showed the highest root
and shoot weight as well as the highest root to shoot ratio. While Arazi recorded the largest stem
diameter. In terms of tolerance index, Unifort and Solanum pimpinellifolium were the most tolerant to
water and salinity stress in terms of root and shoot weight. These preliminary screening results,
combined with measures of leaf sodium content (in progress), will enable selection of suitable
rootstocks for tomato grafting for growth in drought and salinity conditions. Based on the present
study, a greenhouse experiment will evaluate the responses to water and salinity stress of commercial
tomato varieties grafted to selected rootstocks in order to select the rootstock-variety combination that
will be most tolerant to water and salinity stresses.
902-TU. EXPLOITING NATURAL GENETIC VARIATION TO IMPROVE WATER USE EFFICIENCY AND
DROUGHT RESISTANCE IN TOMATO
Thompson A.1, Kurowski T.1, Almeida P.1, Prasanna H.2, Shirgaonkar N.2, Solomon E.1, Peres L.3, Mohareb
F.1
1
Cranfield Soil and AgriFood Institute, Cranfield University, UK; 2Division of Crop Improvement,Indian
Institute of Vegetable Research, Varanasi, India; 3Laboratory of Hormonal Control of Plant
Development, ESALQ, Universidade de São Paulo, Piracicaba, Brazil.
Contact: Andrew Thompson, [email protected]
When water is limited there are two critical crop traits that are the target of plant breeding: (i) “crop per
drop”, the ability to produce a high ratio between yield and water lost by transpiration, also known as
water use efficiency (WUE); and (ii) the ability to maintain yield during periods of low water availability
or soil drying, a trait particularly relevant to rain-fed crops that defines “drought resistance” (DR).
Tomato (Solanum lycopersicum) is a predominantly irrigated crop that makes a huge contribution to
food security and human nutrition. Our aim is to identify genetic variation that can be used by breeders
to improve WUE and DR in elite tomato varieties.
S. pennellii, S. chilense and S. sitiens are tomato wild relatives that are adapted to semi-arid areas of
South America. In S. pennellii, which has been extensively studied genetically, a 79.9 Mbp region on
chromosome 1 named "Water Economy Locus in Lycopersicon" (WELL) delayed wilting and improved
WUE when it was introgressed into tomato cultivar “Micro-Tom”. We are currently genetically mapping
WELL, aiming to identify genetic markers that will be useful for breeding and understanding the
genetic mechanisms causing delayed wilting and increased WUE. In the other species, S.
chilense and S. sitiens, there is a lack of research as well as genetic and genomic resources. For S.
chilense we are developing mapping populations that will allow WUE and DR traits to be easily studied,
and we are creating new reference genomes for both S. chilense and S. sitiens to make it easier to
identify genes that cause specific traits. We are also studying the drought physiology of S. chilense,
and will present results of studies to establish if drought resistance is associated with root vigour.
903-TU. DEVELOPMENT OF SSR MARKERS LINKED TO STRESS RESPONSIVE GENES ALONG
CHROMOSOME 3 IN TOMATO
Sadder M.S.1, Migdadi H.M.2, Brake M.H.3, Al-Qadumii L.W.4
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Department of Horticulture and Crop Science, Faculty of Agriculture, University of Jordan, Amman
11942, Jordan; 2Department of Plant Production, College of Food and Agricultural Sciences, King Saud
University, P. O. Box 2460, Riyadh 11451, Saudi Arabia; 3Science Department, Faculty of Science,
Jerash University, Jordan; 4Faculty of Science, Philadelphia University, Jerash, Jordan
Contact: Monther Sadder, [email protected]
1
This study was aimed to develop novel SSR markers in tomato. Several BAC clones along
chromosome 3 in tomato were selected based on their content. The criteria was the availability of
stress related loci, either directly or indirectly related to stress response (drought, salinity, heat) in
tomato. Nearby SSRs and their adjacent sequences were identified in silico. The developed SSR
markers were assessed using tomato landraces. A total of 29 determinate and semi-determinate
Jordanian tomato landraces collected from diverse environments were utilized. A total of 33 alleles
with mean of 1.65 alleles per locus were scored and showed 100% polymorphic patterns with mean of
0.18 polymorphism information content (PIC) values. Mean of observed and expected heterozygosity
were 0.19 and 0.24 respectively. The mean value of Jaccard similarity index was used for clustering the
landraces. Clustering was consistent with the known information regarding geographical location and
growth habit. The developed microsatellite markers showed power to assess genetic variability among
tomato landraces. The genetic distance information reported in this study can be used by breeders in
genetic improvement of tomato landrace for tolerance against diverse stresses.
904-TU. ROLE FOR PHYTOL KINASE IN RESISTANCE TO COMBINED LIGHT AND TEMPERATURE
STRESS IN TOMATO PLANTS
SPICHER L.1, Almeida J.2, vom Dorp K.3, Pipitone R.1, Dörmann P.3, Glauser G.4, Rossi M.2, Kessler F.1
1
Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland; 2Departamento
de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090,
São Paulo, Brazil; 3Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn,
D-53115 Bonn, Germany; 4Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, 2000
Neuchâtel
Contact: Felix Kessler, [email protected]
Plants have to cope with increasing temperatures often in combination with high light intensity. The
ability of the photosynthetic machinery to adapt to an ever-changing environment is crucial for plant
survival. The photosynthetic light reactions occur at the photosystems in the thylakoids of chloroplasts.
The photosystems are composed of proteins in a specific lipid environment. It includes not only
membrane lipids but also lipophilic pigments (chlorophylls, carotenoids) and prenylquinones
(plastoquinone, phylloquinone, tocopherol). Apart from their respective roles in light harvesting and
electron transport, carotenoids and prenylquinones have important antioxidant properties and protect
plant cells against ROS (reactive oxygen species). Notably, tocopherols have been described as lipid
antioxidants that protect photosystem II from photodamage under high-light stresses. The synthesis of
tocopherol requires the condensation of an aromatic ring derived from the plastidial shikimate pathway
and a prenyl side chain that can be either derived from the methyl erythrytol phosphate pathway or
from the recycling of the chlorophyll degradation-derived phytol. In the latter, phytol kinase (VTE5) is a
key enzyme for the salvation pathway that converts the phytol liberated from chlorophyll into phytyl
diphosphate. In SIVTE5 tomato plants, the content of tocopherol is significantly diminished in leaves
and fruits due to the silencing of VTE5 enzyme encoding gene. To better understand the role of
tocopherol in plant adaptation to changes in the environment, SIVTE5 tomato plants were challenged
with combined temperature and high-light stress. The results provide new insight on the ability of the
photosynthetic machinery to acclimate to the ever-changing environment.
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RESISTANCE, PATHOGENS, PESTS AND MICROBIOMES
1002-TU. ASSESSMENT OF TOMATO GENOTYPES FOR RESISTANCE TO BACTERIAL SPOT
AlBallat I.A.2, Panthee D.R.1
1
Department of Horticultural Science, Mountain Horticultural Crops Research & Extension Center,
North Carolina State University, Mills River, NC 28759, USA; 2Horticulture Department, Tanta
University, Tanta, Egypt.
Contact: Dilip R. Panthee, [email protected]
This study was aimed to assess the bacterial spot caused by Xanthomonas perforans race T4 in 33
tomato hybrid developed from a combination of different resistance sources. They were evaluated
along with 13 tomato lines as controls, in a randomized block design with two replications at MHCREC,
Mills River, NC, USA from May to September 2015. We evaluated the disease severity and transformed
the data into area under disease progress curve (AUDPC). The analysis of variance and grouping of
AUDPC means were presented. Five out of 33 hybrids including NC 25P X Fla 7060_216, NC 22L1(2008) X Fla 7060_216, NC 25P X Fla 7060_Xv4, NC 5Grape X Fla 7060_Xv4, and NC 6Grape X Fla
7060_Xv4 showed lower mean AUDPC than the controls indicating that they may show some promise
for bacterial spot resistance. In these hybrids, the source of resistance gene is contributed through
male parent. These hybrids are being further evaluated to confirm the results in 2016.
Key words: Xanthomonas spp; Solanum lycopersicon; biotic stress.
1003-TU. TOMATO–PATHOGENS INTERACTIONS UNDER ELEVATED CO2: THE ROLE OF
STOMATA
Shi K.1, Li X.1, Zhang H.1, Yu J.Q.1
Department of Horticulture, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou
310058, China
Contact: Kai Shi, [email protected]
Stomata played an active role in restricting bacterial invasion as part of the innate immune response;
nonetheless, as a passive port of entry. We found that the susceptibility of tomato plants to
Pseudomonas syringae (P. syringae) is significantly reduced under elevated CO2 conditions. Using
scanning electron microscopy, we noticed that under elevated CO2, the stomatal aperture was
constantly smaller than the ambient counterpart and did not show any evident transient changes in
response to P. syringae inoculation, thus inhibiting the entry of bacterial pathogens through the
stomata. Using diverse techniques including gene silencing and isolation of guard cells, we found that
elevated CO2-induced tomato stomatal closure did not depend on the amount of intracellular ABA
content, but was highly dependent on the production of respiratory burst oxidase 1 (RBOH1)-mediated
hydrogen peroxide (H2O2) in guard cells. Further studies involving genetic, biochemical and cytological
approaches demonstrate that H2O2 functions downstream of the CO2 receptor open stomata 1 (OST1)
to regulate the slow anion channel associated 1 (SLAC1), and the stomatal movement. Based on this
study, we proposed the OST1-H2O2-NO-SLAC1 model of stomatal movement under elevated CO2.This
work is crucial to deepen the understanding of CO2 signaling pathway in guard cells and their roles in
tomato basal defense against Pseudomonas syringae.
1004-TU. ANALYSIS OF THE INTIMATE INTERACTION BETWEEN TOMATO AND THE PARASITIC
PLANT CUSCUTA PENTAGONA
Farhi M., Sinha N.R.
1
Department of Plant Biology, University of California, Davis, CA, USA
Contact: Moran Farhi, [email protected]
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Cuscuta species (dodders) are obligate holoparasitic plants with worldwide distribution that suppress
their hosts' growth, leading to losses in Solanaceae crops. Once Cuscuta entwines itself around a host,
it invades the tissues using a specialized organ, haustorium, that serves as a conduit for host derived
nutrients and water. Successful parasitism is an interactive process between the host and parasite,
conditioned by a number of genetic and physiological factors. The molecular mechanism underlying
these processes and the mechanisms that are activated in response by tomato parasitized
by Cuscuta are unknown. We have generated extensive transcriptional data from numerous Cuscuta
pentagona tissues, including laser dissected haustoria and the surrounding tomato host tissue at
different time points. Next, we examined expression changes in the RNA-seq data using deferential
expression, clustering and gene co-expression network analysis. We find that most changes are
observed at the early stage of infection, in both haustoria and host. Genes that are up-regulated in
young haustoria are enriched for transcripts related to biotic response and cell wall and membrane
related functions. These results match reports on changes in cell wall components in the haustoria
of C. reflexa. Furthermore, it implies that in C. pentagona stress response pathways may be recruited
to regulate early infection processes. In tomato, we observe most transcriptional changes 4 days
after Cuscuta attachment. Tomato genes showing expression changes are enriched for functions
relating to biotic stimulus and carbohydrate metabolism, demonstrating that the activated defense
pathways to the parasitic plant are similar those involved in response to herbivores and pathogens.
This is also supported by an enrichment of element binding sites of ethylene response in the
promoters of genes that show expression change after attachment of C. pentagona. Similarly, elevated
ethylene emission is detected in tomato plants attacked by Cuscuta. Interestingly, we find that tomato
mutants that are blocked for ethylene perception actually enable better growth of C. pentagona. This
raises the possibility that ethylene response in the host supports C. pentagona growth on tomato. Our
work set the genetic foundation needed to further dissect the intimate interaction of tomato and the
parasite Cuscuta.
1005-TU. GENETIC MAPPING OF VERTICILLIUM DAHLIAE-INDUCED EARLY DYING AND EQTL IN
POTATO
Tai H.H.1, De Koeyer D.1, Sønderkær M.2, Hedegaard S.2, Goyer C. 1, Davidson C. 1, Nolan L.1, Lägue M. 1,
Paudel J. R. 1, Neilson J. 1, Murphy A. 1, Wang H.-Y., Xiong X., Halterman D.4,5, Nielsen K. L. 2
1
Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB,
Canada; 2Department of Life Sciences, Aalborg University, Aalborg, Denmark; 3College of Horticulture
and Landscape, Hunan Agriculture University, Hunan, Changsha, China; 4Department of Plant
Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA; 5U.S. Department of
Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, Wisconsin,
United States of America
Contact: Helen Tai, [email protected]
Verticillium wilt in Solanaceae crops is caused by one of two fungal pathogens, V. albo-atrum and V.
dahliae. Infections induce wilting and chlorosis and cause early dying that leads to reduced
yields. Verticillium fungi are hemibiotrophic, infecting live plants through the roots and completing life
cycles as a saprophyte feeding on dead plant tissue. Verticillium wilt disease severity was mapped to
the Ve2 resistance gene. However, Verticillium wilt disease severity is a complex trait and other genes
are involved. Moreover, tolerance to Verticillium can develop where the host does not develop
symptoms despite carrying high loads of pathogen. To unravel the complexities of V. dahliae-induced
early dying, a potato diploid mapping population derived from a parent that was heterozygous for the
resistance allele of the Ve2 gene, 12120-03, and a parent that had tolerance to the pathogen and did
not carry resistance alleles, 07506-01, was used to map disease severity quantitative trait loci
(QTL). QTL were mapped to chromosome 5 and 9, which included loci for the StCDF1 and Ve2 genes,
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respectively. The StCDF1 gene is involved in regulation of maturity and tuberization in
potato. Genome-wide gene expression analysis was done on the foliage of the mapping population
using DeepSAGE and Nanostring nCounter. The data was used for an eQTL analysis to find gene
networks involved in controlling disease severity. StSP6A and StSP5G genes were found to have eQTL
that were highly correlated with disease severity QTL. These genes are downstream of StCDF1 and,
StSP6A functions as the mobile peptide that signals maturity and tuberization, further suggesting a role
for StCDF1 in disease severity. Epistasis analysis was done and the StCDF1 gene was found to act
downstream of the Ve2 gene. The results provide evidence that V. dahliae triggers natural senescence
upon infection through the StCDF1 pathway. Furthermore, it is proposed that the Ve2 resistance gene
functions to reduce activation of the StCDF1 gene by the pathogen and that tolerance occurs when
StCDF1 carries a mutation rendering it insensitive to pathogen activation.
1006-TU. SEEKING THE GENETIC BASIS OF BIOCONTROL IN S. SISYMBRIIFOLIUM
Wixom A.1, Casavant C.1, Wasilczuk A.2, Kuhl J.1, Xiao F.1, Dandurand L.M.1, Caplan A.1
1
Department of Plant, Soil, and Entomological Sciences, University of Idaho, Moscow, ID,
USA; 2Department of Virology and Immunology, Maria Curie-Sklodowska University, Lublin, Poland
Contact: Alexander Wixom, [email protected]
The pale cyst nematodes, Globodera pallida, are particularly destructive parasites of potatoes. In
nature, their eggs can lie dormant for decades until triggered to hatch by exudates from a compatible
host such as potatoes and tomatoes. Solanum sisymbriifolium, also known as “Litchi Tomato” or “Sticky
Nightshade,”is a poorly analyzed plant species that also induces nematode hatching but does not
support further development and reproduction of the parasites. Many times, resistances have been
tied to “resistance genes” (R-genes) which canonically have nucleotide-binding-site and leucine-richrepeat domains. There are other cases where nematode defense genes without these domains have
been found, such as the soybean gene, Rhg1, the sweet potato gene, IbMIPS, and the upland cotton
gene, MIC-3. We have set out to characterize the anti-nematode defense in S. sisymbriifolium
beginning with the de novo development of the plant’s transcriptome followed by the identification of
responsible genes. We used single molecule real time (SMRT) sequencing, which has the advantage
over previous technologies of not needing computational assembly, but also has the disadvantage of
providing much lower coverage of each base pair compared to more conventional short read
sequencing approaches. This transcriptome was independently assessed for accuracy and
completeness by comparing it to sequences found in a cloned cDNA library of the same plant. We then
applied a series of programs that could reduce and refine the “Next-Next Generation Sequencing”
consensus isoform data into a small, but biologically relevant, reliable, and informative transcriptome.
These data files were next screened for genes homologous to R-genes. It is noteworthy that until now,
we have found no closely matching homologues to the previously mentioned nematode defense
genes. This indicates that novel nematode sensors and/or downstream response genes are being
used in this plant. In the future, RNA-seq protocols will screen for potential plant protection genes
operating here.
1007-TU. ELUCIDATING THE ROLE OF MORC1, A NEW EPIGENETIC FACTOR, DURING PLANT
IMMUNITY IN SOLANACEAE
Jackson N.1, Nam J.C. 2, Kang H.G.2, Fei Z.3, Klessig D.F.3, Manosalva P.1
1
Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, CA,
USA; 2Department of Biology, Texas State University, San Marcos, TX, USA; 3Boyce Thompson
Institute for Plant Research, Ithaca, NY, USA.
Contact: Patricia Manosalva, [email protected]
Microrchidia (MORC) proteins are a subset of the GHKL ATPase superfamily, containing GHKL and S5
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domains that form a catalytically active ATPase module. Proteins containing this GHKL ATPase motif
play roles in chromatin remodeling, heat shock responses, signal transduction, and DNA mismatch
repair. MORC proteins have been recently described as components involved in the RNA-directed
DNA methylation (RdDM) pathway and heterochromatin silencing. Previously, we reported that MORC1
and its closest homologs function in multiple layers of plant immunity in Arabidopsis and Solanaceous
plants. MORC1 regulates plant immunity and cell death in a species-specific manner behaving as a
positive regulator in Arabidopsis and potato and as a negative regulator in tomato and tobacco. This
antagonistic phenotype has been mapped to the C-terminal region of these proteins suggesting that
the MORC1 species-specific effects are mainly due to how and to whom these proteins interacts at
their C-terminal regions. In this study, we identified two proteins that differentially interact with the Cterminal region of potato and tomato MORC1 using the yeast two-hybrid system. In addition, because
of the involvement of small RNAs and MORC1 in the RdDM pathway, we sequenced small RNAs in
empty vector and MORC1-silencing tomato plants before and after bacterial pathogen infection. Our
preliminary results suggest that micro RNAs targeting hormone signaling, epigenetic factors, and
resistance components are regulated by MORC1 in tomato. Together our results suggest that the
MORC1 effect on plant immunity in Solanaceous crops might be mediated by specific host protein
interactions and regulation of resistance components and epigenetic factors.
TUBERS AND ROOT SYSTEMS
1101-TU. SILENCING TWO CYTOCHOME P450 GENES IN STEROIDAL GLYCOALKALOID
BIOSYNTHETIC PATHWAY CONTROLS TUBER SPROUTING
Umemoto N.1, Nakayasu M.2, Ohyama K.1, Mizutani M.2, Saito K.1, Muranaka T.3
1
RIKEN Center for Sustainable Resource Science, Yokohama, Japan; 2Graduate School of Agricultural
Science, Kobe University, Kobe, Japan; 3Graduate School of Engineering, Osaka University, Suita,
Japan
Contact: Naoyuki Umemoto, [email protected]
α-Solanine and α-chaconine, steroidal glycoalkaloids (SGAs) found in potato (Solanum tuberosum), are
among the best-known harmful metabolites in food crops. We had showed that potato glycoalkaloid
biosynthesis 1 and 2 (PGA1 and PGA2), two genes that encoded cytochrome P450 monooxygenases
(CYP72A208 and CYP72A188), were involved in the SGA biosynthetic pathway, respectively. The
knockdown plants of either PGA1 or PGA2 contained very little SGA, yet vegetative growth and tuber
production were not affected. Analyzing metabolites that accumulated in the plants and produced by in
vitro enzyme assays revealed that PGA1 and PGA2 catalyzed the 26- and 22-hydroxylation steps in the
SGA biosynthetic pathway, respectively. The PGA-knockdown plants had two unique phenotypic
characteristics: the plants were sterile and tubers of these knockdown plants did not sprout during
storage. Surprisingly, when planted in soil, the tubers began to sprout and grew normally, even after
storage for several years.
Sprouting reduces the quality and yield of potato tubers in storage. Suppression of tuber sprouting is
of significant benefit to the industry for the long-term storage of tubers. Thus, controlling tuber
sprouting is another important objective in potato breeding. The traits controlling both potato
glycoalkaloid biosynthesis and tuber sprouting, can significantly impact potato breeding and the
industry.
1102-TU. FUNCTIONAL ANALYSES OF A TUBERIGEN HOMOLOG IN TOMATO
Moriya C., Yamada M., Goto K.
Research Institute for Biological Sciences, Okayama Prefecture.1Present address: National Agriculture
and Food Research Organization
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Contact: Koji Goto, [email protected]
The SP6A gene of potato (S. tuberosum) is known to function as the tuberigen. Tuberigen is
synthesized in leaves under short-day conditions and transmitted long distance to the underground
stolon to function as a signal for tuber formation. SP6A gene belongs to the same clade of FT, which is
the florigen gene of Arabidopsis, but SP6A does not function as florigen in potato. Tomato (S.
lycopercicum) is closely related species of potato and also has SP6A gene homolog in the genome,
but SP6A gene of the tomato cultivar has nonsense mutation in coding region. SP6A genes of tomato
wild relatives (SP6Awild), however, do not have such mutation; therefore, it seems to have function.
Among tomato wild relatives, we took S. pennellii for further analysis. We first introducedSP6Awild gene
into Arabidopsis under constitutive promoter (35S) and found that these
transgenic Arabidopsis showed early flowering phenotype.
Many species of tomato wild relatives as well as S. pennellii show short-day flowering habit. We
examined the expression pattern of SP6A in S. pennellii. It is specifically expressed in mature leaves
and showed diurnal expression pattern under short-day conditions. This expression pattern is similar to
the tuberigen in potato, but S. pennellii does not produce tuber. In order to examine the original
function of SP6A, we introduced SP6Awild under the inducible promoter into Micro-Tom. This transgenic
Micro-Tom flowered early under inducible conditions. Using the transgenic Micro-Tom, we are now
performing gene expression analysis to find target genes of SP6A and grafting with potato stocks to
examine whether SP6Awild can induce potato tuber.
1103-TU. GENETIC ANALYSES OF TOMATO ROOT MUTANTS
Kevei Z.1, Ferreira D.1, Kurowski T.1, Mohareb F.1, Sherman T.2, Daniels S.3, Peres L.4, Thompson A.1
1
Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, MK43 0AL, UK; 2Zeraim Gedera
Ltd., M.P Shikmim, Kibutz Revadim, 7982000, Israel. 3Syngenta Crop Protection LLC, 3054 Cornwallis
Rd. Research Triangle Park, NC 27709, USA; 4Laboratory of Hormonal Control of Plant Development,
ESALQ, Universidade de São Paulo, Piracicaba, Brazil
Contact: Andrew Thompson, [email protected]
Fresh market tomatoes are predominately produced as a grafted crop using elite scion genotypes
grafted to specialized rootstock genotypes which are usually a hybrid of tomato and a wild relative
species. Rootstocks provide resistance to soil borne diseases, increase scion vigour, enhance late
season yield and have potential to give resistance to a range of abiotic stresses. In low input
agricultural systems, including those depending on variable rainfall, the acquisition of soil water and
nutrients may be limiting, and deeper more vigourous root systems may enhance yield and yield
stability. We are studying the available genetic variation in tomato root traits, including the classical
monogenic root mutants, and newly identified mutants, and hope to exploit this to underpin the
development of improved rootstock genotypes. We are currently mapping the following root mutants:
the aerial roots (aer) mutant with adventitious roots that develop on the aerial part of the stem; the
bushy root (brt) mutant that has shorter roots and delayed plant establishment; the bushy root-2 (brt-2)
mutant that shows a “kinked” root growth pattern; the branched root (bro) mutant which develops
lateral branching following root meristem death. We will report our progress in phenotyping these
mutants and in mapping the underlying genes using Illumina next generation sequencing, bulked
segregant analysis and KASP markers.
FLOWERS, FRUIT AND SEEDS
1201-TU. THE SPATIOTEMPORAL DYNAMICS OF THE TOMATO FRUIT TRANSCRIPTOME UNDER
WATER STRESS CONDITIONS
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Nicolas P.1, Fernandez-Pozo N.1, Shinozaki Y.2, Zheng Y.1, Xu Y.1, Ma, Q.1, Snyder S.I.2, Fich E.A. 2,
Vrebalov J.1, Giovannoni J.J.1-3, Fei Z.1-3, Mueller L.A.1, Rose J.K.C.2, Catalá C.1-2
1
Boyce Thompson Institute; 2 Section of Plant Biology, School of Integrative Plant Science, Cornell
University, 3U.S. Department of Agriculture/Agriculture Research Service, Robert W. Holley Centre for
Agriculture and Health, Ithaca, NY, 14853, USA
Contact: Philippe Nicolas, [email protected]
Fruit development is regulated by coordinated changes in gene expression that can be strongly
influenced by environmental stresses. For example, drought can have a profound effect on many
aspects of fruit biology and substantially reduce crop yield by suppressing reproductive development.
To date, most molecular studies of plant responses to drought have focused on vegetative organs,
such as roots and leaves, and far less is known about the molecular bases of drought responses in
fruit. There is growing evidence that in addition to abscisic acid (ABA), other hormones, including
ethylene, cytokinins, brassinosteroids, auxin and jasmonic acid, are involved in responses to water
stress in vegetative tissues. However, the role of ABA and the significance of hormone cross-talk
during water stress responses in fruit is not yet understood.
Although some studies have suggested that fleshy fruits undergo changes in gene expression and
metabolite profiles in response to water stress, such observations have yet to be supported by
comprehensive transcriptomic analyses. Fruits are complex organs with various distinct tissue types
and so, to obtain a full picture of the molecular responses governing fruit development during growth
under drought conditions, we have examined the tissue-specificity of such responses. Specifically, we
have performed a tissue-specific transcriptome analysis of tomato (Solanum lycopersicum) fruit at
stages spanning growth and ripening under moderate drought conditions. We have used the data sets
to identify and map components of phytohormone synthesis, metabolism and signaling pathways, with
particular reference to tissue and cell type-specific responses to drought stress.
1202-TU. TRANSCRIPTIONAL REGULATION OF FW2.2 BY GIBBERELLIN SIGNAL DURING EARLY
FRUIT DEVELOPMENT IN TOMATO
Ezura K.1, Shinozaki, Y.2 Ariizumi T.2, Ezura H.2
1
Graduate School of Life and Environmental Sciences University of Tsukuba, Japan; 2Faculty of Life
and Environmental Sciences, University of Tsukuba, Japan
Contact: Kentaro Ezura, [email protected]
Tomato FW2.2 is one of the important genes underlying major quantitative trait loci for fruit
weight; fw2.2 loci explains 30% of fresh fruit weight variation in interspecific populations between the
wild tomato and domesticated tomato. FW2.2 was proposed to act as a negative regulator of cell
proliferation interacting with other proteins in plasma membrane. Cell division rate preceding cell
expansion directly influences final fruit size. Therefore, it is important to understand the mechanism
that sifts the state from cell division to expansion during early fruit development, and the location of
FW2.2 in it. However, regulation mechanism of CNR/FW2.2 family genes is still largely unknown.
In the present study, we observed expression of tomato CNR/FW2.2 family genes in various organ and
cell type, identifying members expressed in the pistil. In addition, we conducted expression analysis
using our RNA-sequence data of the tomato pistil during fruit set stage in Micro-Tom and a
parthenocarpic mutant procera (sldella), which displays gibberellin (GA)-constitutive response
phenotype because of the mutation in the repressor of GA signaling. procera mutant shows high
degree of parthenocarpy efficiency, but produces small fruit because of the reduction of cell division
rate. We found that some members including FW2.2 transcriptionally responded to such fruit set
signal.Notably, transcript level of FW2.2 was increased from anthesis stage without pollination
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in procera while it was upregulated only after pollination in the WT. To confirm the relationship
between FW2.2 and fruit set signal, expression analysis was performed using unpollinated pistil of
Micro-Tom treated with synthetic gibberellin GA3. As a result, FW2.2 was upregulated by GA treatment
at 4DAA similar to expression of the GA responsive gene SlGAST1. Analysis of Cis-regulatory elements
revealed the presence of GA-related element P-box in the promoter region of FW2.2.
Our results indicated that GA signal modulates the expression of CNR/FW2.2 family genes. Although
further studies of the genetic interaction between FW2.2 and SlDELLA in controlling fruit size should
be investigated, the transcriptional regulation of FW2.2 by GA signal would associate developmental
shift from cell division phase to cell expansion phase during early fruit development.
1203-TU. INTEGRATIVE TRANSCRIPTOMIC AND FUNCTIONAL ANALYSES TO UNVEIL DISTINCT
GENETIC INFLUENCES ON FRUIT RIPENING BETWEEN PEPPER AND TOMATO
Yoo H. J.1, Lee G.M.1, Choi D.2, Lee J.M.1
1
Department of Horticultural Science, Kyungpook National University, Daegu; 2 Department of Plant
Sciences, Seoul National University, Seoul, Korea
Contact: Hee Ju Yoo, [email protected]
Pepper and tomato provide suitable models for comparisons of fruit ripening processes. We present
distinct molecular patterns of ripening between pepper and tomato by transcriptomic analysis. Our
analyses unveil potential mechanisms of non-climacteric ripening and pepper-specific pigmentation
due to defect of regulators and ethylene synthesis. Functional analysis of ripening regulators by virus
induced gene silencing in pepper fruits are in progress. The Golden-like 2 transcription factor is shown
to distinct expression pattern rationalizing differential ripening pattern. The gene silencing effect of
the Golden-like 2 in pepper fruit is analogous to the uniform mutation. The integrated analysis allows
us to better understand differential genetic factors of fruit development and ripening in pepper and
tomato.
1204-TU. CHARACTERIZATION OF NOR MUTANT ALLELES ISOLATED FROM EMS MUTAGENESIS
MICRO-TOM
Liu D., Wang N., Tanase K., Pankasem N., Chen H., Kusano M., Ezura H.
Graduate school of Life and Environmental Sciences, University of Tsukuba Tennodai 1-1-1, Tsukuba
305-8572, Japan
Contact: Ning Wang, [email protected]
Shelf-life ensure less losses during processes of food producing, transporting, retailing, and serving.
Climacteric fruits are characterized by ripening associated with increased ethylene production and a
rise in cellular respiration. Tomato as a model for studying fruit ripening is particularly in ethylene
biosynthesis and signaling pathway. So far numerous ripening genes have been reported to regulate
the ethylene biosynthesis, for instance, gene RIN and NOR code for transcription factor which is
transcriptional regulating ACS and ACO gene families. We applied TILLING, a sensitive molecular
screenings, and enable to identify a serial of novel alleles of ethylene biosynthesis related genes from
EMS-mutagenized lines. Among these novel alleles, one of the nor knock-down mutants is revealing
extremely long shelf-life, however, it was found delay in developmental phase in compare with wild
type. We confirmed segregation of monogenetic trait and nor allele is complete associate with
morphological differences in a segregating F2 population divided from nor crossed with WT Micro-Tom
(MT-J). Although nor is absent on ethylene-associated respiratory peak, seedling and mature-green
fruits are responsible to exogenous ethylene. Real-time PCR for ACS and ACO gene families
demonstrated that NOR is transcriptional regulating ethylene biosynthesis genes and thus for nonclimacteric phenomenon. We further confirmed alterations in carotenoid profiles that resulted in a less
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color change in nor in compare with that in wild type. The currently available alleles are expected for
systematic functional genomic studies but also direct utilizations in breeding programs.
1205-TU. DECIPHERING THE MECHANISM INVOLVED IN FORMATION OF HAPLOID POTATO
PROGENY IN THE SOLANUM TUBEROSUM GROUPS TUBEROSUM X PHUREJA CROSSES.
Nganga L.1, Tan E.K.1, Ordonez B.1, Amundson K.1, Santayana M.2, Khan A.2, Bonierbale, M.2, Comai L.1
1
Plant Biology and Genome center, University of California, Davis, CA, USA;
2
International Potato Center (CIP), Lima, Peru
Contact: Livingston Nganga, [email protected]
Haploid induction, a powerful tool in plant breeding, decreases the time required for obtaining
‘inbreds’, simplifies the complex genetics of polyploids, and helps overcome dosage-related
incompatibilities. Crossing certain clones of diploid Solanum tuberosum (S.t.) Group Phureja as male to
tetraploids of S.t. Group Tuberosum results in maternal Tuberosum di(haploids). The mechanism
involved is unclear: both development of an unfertilized egg (parthenogenesis) and postzygotic loss of
the paternal genome (genome elimination) have been suggested. Reports describing limited retention
of the haploid inducer genome in potato haploids are consistent with incomplete genome elimination.
To clarify the mechanism of haploid induction in different genetic crosses, we plan to investigate the
source and number of chromosomes during embryo development through the use of genome-specific
FISH and immuno staining of centromeric histone H3 (CENH3). To develop FISH probes specific to the
Tuberosum and Phureja genomes we sequenced several Phureja haploid inducers (IvP-101, IvP-48, IvP35), a non-inducer (DM 1-3), one tetraploid S.t tuberosum (Desiree), and a tetraploid S.t Andigenum
(Alca Tarma). High-copy number k-mers unique to either Tuberosum or Phureja genomes are being
characterized to develop genome-specific FISH probes. CENH3 is a histone H3 variant that specifies
centromeres and marks their position. Immunostaining of potato centromeres with anti-CENH3
antibodies was previously demonstrated in the Jiang Lab (Madison, WI). Previous work has shown that
between 5-20% of fertilized ovules result in potato haploids. By probing the presence of Phureja
genome and counting chromosomes in sufficient number of early embryos we should be able to
assess the relative contribution of parthenogenesis vs. genome elimination.
1206-TU. DDB1 LOSS OF FUNCTION INFLUENCES TOMATO FRUIT MATURATION AND RIPENING
Wang A. 1,2, Chen D.2, Ma Q. 1, Fei Z. 1, Liu Y. 2, Giovannoni J. 1,3
1
Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA; 2School of Biotechnology and
Food Engineering, Hefei University of Technology, Hefei 230009, China; 3United State Department of
Agriculture, Robert W. Holley Center, Cornell University, Ithaca, NY 14853, USA
Contact: Anquan Wang, [email protected]
Fruit ripening is a process governed by multiple external and internal cues and accompanied by
changes in color, texture, volatiles and additional quality traits. While delayed ripening and increased
phytonutrients are desired traits, delayed ripening is often accompanied by reduced nutritional value.
The tomato hp1 (ddb1) mutant has attracted attention for its phytonutrients over-accumulation. In this
study, we show that the hp1 mutant also exhibits delayed fruit maturation and ripening initiation.
Furthermore, mutation in the DDB1 gene impedes fruit softening. Ethylene and transcriptome analysis
ofhp1/hp1 fruits through development reveals that loss of tomato DDB1 function inhibits ethylene
production, primarily through ACS1a, ACS1b, ACO1, ACO3 and ACO6 expression. The DDB1 mutation
also reduces expression of ethylene signaling components, including ETRs, EILs, EBFs and ERFs, at the
Immature Green stage, further suggesting that altered ethylene perception in hp1/hp1 fruits contributes
to maturation differences. Loss of DDB1 function elevates expression of photosynthesis associated
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genes at all stages tested and light/dark treatment of wild type fruits suggests a role for light in
ethylene biosynthesis. Expression patterns of several known ripening transcription factors, including
RIN (RIPENING-INHIBITOR) are altered in hp1 fruit. Hypergeometric test shows that RIN’s targets are
enriched among Differentially Expressed Genes at Breaker + 7 day stage in hp1 fruit, suggesting DDB1
influences ripening through RIN. Finally, DDB1 loss of function influences ABA (abscisic acid)
biosynthesis, as ABA content and NCED1 expression in Breaker stage hp1 fruit were lower than those
in wild type. Together these results suggest DDB1 partners with other ripening-related regulators to
modulate plant hormones and influence ripening activities.
PLANT DEVELOPMENT AND REGULATION
1301-TU. CHANGES IN THE EXPRESSION OF GENES ENCODING ISOZYMES OF
RHAMNOGALACTURONAN LYASE DURING THE ONTOGENY OF TOMATO FRUIT (Solanum
lycopersicum L.)
Trillo-Hernández, E.A.
Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en
Alimentación y Desarrollo, A. C., Hermosillo, Sonora, México
Contact: Eduardo Antonio Trillo Hernández, [email protected]
Tomato is a good model to study the physiological function of the plant cell wall in fruits mainly
because the genome is available, it produces a fleshy fruit and the life cycle is relatively short. The
plant cell wall is made of three domains: cellulose, hemicellulose and pectin. The pectin is the most
complex domain and consists of the polymers homogalacturonan, rhamnogalacturonan-I (RG-I) and
rhamnogalacturonan- lI. The RG-I can be degraded by the rhamnogalacturonan lyase enzyme
(RGlyase). Although the biochemical changes induced by RGlyase in the RG-I polymer are well known,
the physiological role is not well understood. The objective of the present work was to evaluate the
expression of genes encoding different isoenzymes of RGlyase during tomato fruit ontogeny. Tomato
fruits cultivar `Rutgers´ with 5, 10, 30 and 40 days after anthesis (DAA) were obtained by tagging
unpollinated tomato flowers. Further, tomato fruits at the stages of development mature green (MG),
turning (TUR) and red ripe (RR) were harvested. In the tomato fruits with the last three stages of
development, it was recorded the respiration rate and ethylene production. The changes in
expression of the genes Solyc04g076660.2.1, Solyc07g046630.2 and Solyc11g011300.1.1 were
evaluated by quantitative PCR using oligonucleotides designed against not conserved regions of the
mentioned genes. It was found a large expression level of the gene Solyc04g076660.2.1 at 10 DAA
and MG stage. The gene Solyc04g076630.2 showed a slight increase in expression at 30 DAA and RR
stage. Moreover, the highest expression was observed at MG. The expression of the gene
Solyc11g011300.1.1 showed low levels during the tomato fruit development and increasing levels from
MG until RR stages. At this last stage, this gene showed the highest expression level. It was concluded
that the expression pattern of the genes Solyc04g076660.2.1 and Solyc07g046630.2 correlates with
the stage of development in which the fruit is growing by cell expansion. Also, the increased
expression of the gene Solyc11g011300.1.1 correlates with the stage of development in which it is taking
place the loss of fruit firmness and large ethylene production during fruit ripening. With the data
generated in the present work and obtained from the literature, it was created a model describing the
regulation of expression of the Solyc11g011300.1.1 gene. It was concluded that different isoenzymes of
the RGlyase enzyme plays different roles during tomato fruit development.
1302-TU. ISOLATION OF A NEW GENE RESPONSIBLE FOR GAMETOGENESIS DEVELOPMENT IN
TOMATO
Hao S.1, Ariizumi T.2, Ezura H.2
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Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba,
Ibaraki 305-8572, Japan; 2Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1
Tennoudai, Tsukuba, Ibaraki 305-8572,Japan
Contact: Shuhei Hao, [email protected]
1
Angiosperm form reproductive organs such as anther and pistil that bear pollen grains and ovules,
respectively. Gametogenesis is a key step to produce ovules or pollen in higher plants and its
regulatory molecular mechanism has been well analysed in Arabidopsis, whereas little is known in
tomato. In this study, we characterized a tomato (Solanum lycopersicum cv. ‘Micro-Tom’) ?-ray
mutant,sexual sterility (slses), that showed both male and female sterility. Morphological analysis
showed the slses mutant formed incomplete ovules and wilted anther structure at anthesis stages.
There were no pollen grains in the anther of the slses mutant. Moreover, we could not observe
development of ovule integument, and pollen mother cell (PMC) in the developing ovary and anther of
the slses mutant, respectively. Genetic analysis indicated that the responsible gene for
the slses mutant was monogenic recessive. Further, map based positional cloning lead us to the
identification of the locus of candidate genes on Chr. 7. Then, sequencing analysis showed
the slses mutant has a 13 base pair deletion in 1st exon of a homologue of SPOROCYTELESS/NOZZLE
(SPL/NZZ) which is required for gametogenesis development in Arabidopsis. The putative SlSES amino
acid (a.a.) sequence was shortened from 353 a.a. to 57 a.a. due to the flame shift. Complementation
experiment demonstrated that introduction of SlSES genomic region including upstream and
downstream region of SlSES CDS into the slses mutant fully restored normal phenotypes. Expression
levels of SlSES, WUSCHEL(WUS) and INNER NO OUTER (INO), required for ovule development, were
dramatically reduced in the early stages of pistils of the slses mutant. Our result indicate that SlSES is a
key gene for both male and female sterility in tomato.
1303-TU. INCREASED BRANCHING, AN INTRIGUING PHENOTYPE OF TOMATO (SOLANUM
LYCOPERSICUM CV MICRO-TOM) PLANTS OVEREXPRESSING ATCKX2
Pino L.E.1, Lima J.E.2, Schumülling T.3, Werner T.3, Figueira A.1, Peres L.E.P.4
1
Laboratório de Melhoramento de Plantas, CENA, Universidade de São Paulo; 2 Departamento de
Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; 3 Institute of
Biology/Applied Genetics, Freie Universität Berlin, Berlin,Germany; 4Departamento de Ciências
Biológicas, ESALQ, Universidade de São Paulo, Brazil.
Contact: Lilian Ellen Pino, [email protected]
Plant architecture is modulated by numerous endogenous, developmental and environmental factors
integrated over the post-embryonic developmental phase. Shoot branching, a major component of
plant architecture, results from a complex spatio-temporal regulation of axillary bud outgrowth. The
coordination of shoot branching, according to environmental cues, relayed through the action of the
plant hormones auxin, cytokinins and strigolactones. In particular, cytokinins directly promote bud
outgrowth and therefore, inactivation of cytokinins is supposed to reduce shoot branching. It is
however unknown how the integration of a cytokinin oxidase/dehydrogenase gene from Arabidopsis
(AtCKX2) acts on tomato development, mainly in the control of branching. Transgenic Solanum
lycopersiconcv. Micro-Tom overexpressing AtCKX2, which is responsible for irreversible degradation
of cytokinins, present around 2-fold more branching than control plants. We investigated some
parameters that could interfere in that phenotype. In the transgenic plants, the tZeatin metabolites
were much more abundant than iP derivates in both shoots and roots, reaching levels around 300-fold
greater, comparing those tissues. In shoots, the content of tZeatin and iP was reduced only in one of
three transgenic events tested, compared to the wildtype. High AtCKX2 expression levels resulted in
extended vegetative phase, as 35S:AtCKX2 plants showed delayed flowering and produced about
25% more leaves than MT. Overexpression of AtCKX2 also led to alterations in the development of
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primary, lateral and adventitious roots. Nonetheless, the endogenous content of cytokinin, associated
with the delayed vegetative and altered root pattern of development, were not enough to explain the
more branched phenotype of transgenic tomato overexpressing AtCKX2. We then investigated the
cytokinin and strigolactone interaction in the control of branching using double-transgenic tomato
lines, obtained by crossing 35S:AtCKX2 plants with 35S:asCCD7 plants (silenced in a key gene of the
strigolactone biosynthesis pathway). Branching was increased in the double-transgenic compared to
both parents, which suggests an additive interaction. Expression analysis of genes of strigolactone
biosynthesis and response confirmed the addictive interaction in the control of branching. Further
analysis exploring cytokinin-auxin interaction and other mechanisms that could be associated with the
increased branching phenotype of tomato overexpressing AtCKX2 is underway.
1304-TU. THE ISOLATION AND CHARACTERIZATION OF A NEW della ALLELE OF TOMATO
Takahara M.1, Shinozaki Y.1, Bénard C.2, Prodhomme D.2, Gibon Y.2, Ezura H.1, Ariizumi T.1
1
Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki,
Japan; 2INRA, UMR1332, Biologie du Fruit et Pathologie, 71 av Edouard Bourlaux, 33140 Villenave
d’Ornon, France
Contact: Masaru Takahara, [email protected]
GA responses are triggered by down regulation of a negative regulatory protein DELLA through 26S
proteasome. Thus, loss of function allele of DELLA results in constitute GA responses including
increased stem elongation and induction of seedless fruits, also termed parthenocarpy. Such allele in
tomato, procera, is a naturally found della mutant which shows increased GA sensitivity thus showing
pollination-independent parthenocarpic fruit growth. From a comprehensive mutant populations of
Micro-Tom, a dwarf cultivar of tomato, a new allele of della mutant (procera- 2) was isolated. Genetic
analysis confirmed that the procera-2 mutation was monogenic recessive, similar to procera, and these
two mutants were allelic. It appeared that procera-2 showed intermediate stem elongation, indicating
that this was a weaker allele than procera. Both alleles showed improved yield due to higher fruit set
efficiency even under heat stress condition, indicating that improvement of heat stress would be
feasible by the enhancement of GA singling. Ripe red fruits of both procera alleles accumulated higher
sugar contents compared with those of WT, while procera accumulated less carotenoids than procera2. These results suggested procera-2 mutant allele may be useful for improving yield and quality of
tomato breeding.
1305-TU. IDENTIFICATION OF MUTATION IN SILVERY FIR TREE, A HEIRLOOM TOMATO SHOWING
HIGHLY COMPLEX LEAVES
Nakayama H., Rowland S., Zumstein K., Sinha N.
Department of Plant Biology, University of California, Davis
Contact: Hokuto Nakayama, [email protected]
Plants display amazing morphological diversity, and leaves are among the most diverse organs in
plants because leaf development is highly flexible. Thus, it is indispensable to reveal the basic
molecular mechanism of leaf development to understand morphological diversity in plants. Recent
studies have revealed the molecular mechanisms underlying variation in leaf morphology with some
model plant species and their relatives. Solanum lycoperisicum (tomato; Solanaceae) is an excellent
model to study the variation in leaf morphology in compound leaves. Compound leaves, such as seen
in tomato, are composed of multiple units termed leaflets and are characterized by an extended
morphogenetic activity. Some studies have demonstrated that this activity is enabled by the transient
maintenance of a meristematic state at the leaf margin, termed marginal blastozone. Tomato leaves
are thought to have a long morphogenetic activity, hence, they show a wide range of sizes, shapes,
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and complexities. It is known that leaf complexity affects efficiency of gas exchange, thermoregulation,
and water availability in plants. Leaf complexity is different among species, however, the molecular
mechanisms regulating leaf complexity is not fully understood. To elucidate the mechanisms, which
regulate leaf complexity, we focused on a heirloom tomato, Silvery Fir Tree (SFT). SFT shows highly a
complex leaf phenotype compared to that of commercial tomatoes (M82). We first investigated the
anatomy and development of leaves of SFT and M82. We then measured the morphology of terminal
leaflets and calculated their complexity. The result confirmed that there is a significant difference
between SFT and M82 regarding leaf complexity. To identify the genes responsible for the difference
in the leaf complexity, we are performing a quantitative trait locus (QTL) analysis with around 200
F2 plants derived from a cross between SFT and M82. We obtained an overview of the transcriptional
difference between SFT and M82 by mRNA-seq. Based on these results, we will discuss the regulatory
mechanism on leaf complexity in S. lycoperisicum.
1305b-TU. A TALE OF TWO TOMATOES: CELL FATE PLASTICITY IN THE SHOOT APICAL
MERISTEM DURING WATER STRESSES
WEST D.A., Kajala K., Brady S., Sinha N.
Department of Plant Biology, UC Davis, Davis, California, USA
Contact: Donnelly A. West, [email protected]
All plants have to respond quickly to environmental conditions or perish. However, domesticated plant
species lack some of the response vigor seen in their close wild relatives. In order to investigate the
responses to water stress in tolerant and susceptible species of tomato (Solanum lycopersicum and
Solanum pennellii), we couple the comparison of classic anatomy and morphology with comparative
genetics. To parse out the genetics of specific cell populations in the shoot apical meristem,
differentiating leaf tissue, and leaf vascular tissue, we use cell-type specific isolation techniques for
nuclei (Isolation of Nuclei TAgged in specific Cell Types - INTACT) and ribosomes (Translating
Ribosome Affinity Purification - TRAP). The INTACT and TRAP methods allow isolation of
transcriptional, translational, and chromosomal regulation information in morphologically
indistinguishable, yet genetically distinct cell populations. Responses in developmental genetics to
waterlogging or insufficient-watering conditions result in significant morphological responses to water
stresses. The networks involved in these processes can help illuminate desirable gene candidates
involved in cellular fate, tissue-type commitment, and water-stress response, enabling us to breed
more robust crop plants.
METABOLITES, FLAVOR AND QUALITY
1401-TU. CAN TOMATOES TOUGHEN SKIN? EXPLORING STILBENES IN HEALTHY AGING OF
HUMAN SKIN
Hawkins E.1, Martin C.1, Butelli E.1, Gavrilovic J.2, Bevan D.2
1
Department of Metabolic Biology, John Innes Centre, Norwich, UK ; 2 School of Biological Sciences,
University of East Anglia, Norwich, UK
Contact: [email protected]
The skin is the body’s largest organ, and is constantly exposed to many environmental stresses, which
are involved in the pathogenesis of many skin disorders including pigment abnormalities, skin cancers
and photo-ageing. Therefore, research into novel approaches to prevent and protect against the many
environmental stresses that act on skin has become very important.
The stilbene resveratrol and its derivative pterostilbene are secondary metabolites found in grapes,
peanuts and spruce-pine. In plants these compounds protect against environmental stresses;
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preventing decay by micro-organisms, fungal infections and damage via ultra-violet radiation. In
addition, resveratrol and pterostilbene have multiple pharmacological properties applicable to humans,
including anti-inflammatory, anti-aging and anti-cancer activities. Therefore, these compounds have
potential to be used in protective or preventive skin care treatments.
Tomatoes represent excellent bio factories for the production of secondary metabolites. However,
tomatoes lack the enzymes required to synthesise stilbenes. We aim to engineer resveratrol and
pterostilbene in tomatoes. A high resveratrol tomato has already been developed utilising grapevine
stilbene synthase (VvStSy) under the control of the 35S promoter, however the expression of StSy
throughout the whole plant and the resveratrol produced causes detrimental effects to the overall
health of the plant. Therefore, a new high resveratrol tomato is being developed utilising the E8 fruit
specific promoter. For production of pterostilbene a grapevine reverse-o-methyltransferase (VvROMT)
under the control of the E8 promoter is required in addition to the VvStSy gene. The Arabidopsis
transcription factor AtMyb12 will also be utilised in both tomato lines to enhance resveratrol and
pterostilbene production. From the transformed tomatoes, juice extracts will be obtained, and analysed
for skin health promoting functionalities.
The tomato juices will firstly be tested on the human keratinocyte skin cell line HaCaT, before
progressing onto human skin explants. Initial experiments have been performed to determine the
effect of resveratrol on inflammation, by stimulating cells with known inflammatory mediators and
observing the change in expression of 3 inflammatory genes, matrix metalloproteinase 1 and 9, and
tissue necrosis factor-α.
In addition, the effects of resveratrol in tomato extract on cell migration has been determined using a
scratch wound assay. Future experiments will be conducted using pterostilbene rich tomato extracts.
1402-TU. THEME AND VARIATION IN TRICHOME DEFENSIVE CHEMISTRIES: SOLANUM
QUITOENSE INOSITOL ESTERS
Leong B. 1, Moghe G.D.2, Hurney S.3, Jones A.D.2,3, Last R.L.1,2
1
Department of Plant Biology, 2Department of Biochemistry and Molecular Biology, 3Department of
Chemistry Michigan State University, East Lansing, MI, 48824, USA
Contact: Bryan Leong, [email protected]
Acylsugars are insect-defensive specialized metabolites produced in the glandular trichomes of
species throughout the Solanaceae family.Our previous work showed that these acylated molecules
are produced through the action of a class of enzymes known as BAHD acyltransferases.They utilize
acyl-CoAs and sugar molecules such as isovaleryl-CoA and sucrose as substrates to produce
acylsugars of enormously varied structures, typically built on a sucrose core. One such example is in
the Andean fruit crop Solanum quitoense — also known as Naranjilla. This plant is of great interest
because it produces acylsugars built on inositol cores rather than sucrose or glucose. Using an RNAseq driven approach, we identified the putative first and second steps of acyl-inositol biosynthesis inS.
quitoense. Ongoing work is focused on identifying and characterizing the enzymes responsible for
acyl-inositol biosynthesis in addition to examining roles of the homologs of these enzymes.
1403-TU. THE DEVELOPMENT OF TOMATO GENOTYPES WITH ENHANCED XANTHOPHYLL
CONTENT IN RIPE FRUIT
Rapacz E.1, Nogueira M.1, Enfissi E.M.A.1, Fraser P.D.1
1
School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
Contact: Elzbieta Rapacz, [email protected]
Ripe tomato fruit contain acyclic carotenes, most notably lycopene which is responsible for the
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characteristic red colour of ripe fruit. The nutritional benefits of carotenoids are well documented. The
carotenoids β-carotene (provitamin A) and lycopene are essential components of the human diet.
Recently, the xanthophylls lutein and zeaxanthin have gained attention as oxygenated carotenoids
that, when dietary acquired, can reduce the onset of Age-related Macular Degeneration (AMD). This is
the fourth most common cause of vision loss globally and the leading cause of blindness in the elderly.
The prevalence of AMD is predicted to increase following population ageing.
In the present study, natural variation has been exploited and transgenic genotypes created that
contain ripe fruit with varying levels and amounts of xanthophylls. The xanthophylls include zeaxanthin,
lutein and violaxanthin. These xanthophylls containing ripe fruit have been created from high βcarotene lines introgressed into transgenic varieties expressing different carotenoid hydroxylase
enzymes. These lines have been characterised to ascertain the levels and abundance of zeaxanthin
present, gene expression within the pathway, the effect on the metabolome as well as sequestration
mechanisms that operate to ensure chemically diverse carotenoids can accumulate in chromoplasts.
1404-TU. UNDERSTANDING THE TRANSCRIPTIONAL REGULATION OF VITAMIN E SYNTHESIS IN
TOMATO FRUIT
Fearnley E., Martin C.R.
John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR47UH, United Kingdom
Contact: Eleanor Fearnley, [email protected]
Vitamin E (VTE) describes a group of compounds, also known as tocopherols and tocotrienols.
Tocopherols are plastidial, lipophilic antioxidants, which are synthesised only in photosynthetic
organisms. Within the human diet, tocopherols are the most abundant type of VTE, which comprises 4
forms: alpha (α), beta (β), gamma (γ), delta (δ). As α-tocopherol is the most bioactive form in humans,
several studies have correlated its increased dietary intake with a plethora of health benefits, including:
anti-inflammatory responses, reduced cardio-vascular risk in patients with diabetes and an additional
role in improved plasma membrane repair. Thus, increased consumption of VTE is beneficial to prevent
diet related diseases.
We are using tomato (Solanum lycopersicum) as a model to increase total VTE to beneficial levels.
Previous studies in Arabidopsis thaliana have failed to improve VTE levels, and rather, have used VTE
pathway gene knockouts to alter VTE composition to less bioactive forms. Therefore, we are using a
different approach to understand transcriptional regulation of the VTE pathway and ultimately to
improve VTE levels in tomato. Studies have shown transcriptional regulation of VTE occurs spatially
and temporally across tomato fruit development, however, there was no significant change in total
tocopherol levels. We have completed a comprehensive S.lycopersicum and Solanumpennellii VTE
time course in fruit and tomato plant tissues. Within S.lycopersicum fruit, more tocopherol accumulates
in the epidermis compared to the pericarp, which suggests that VTE is differentially controlled between
the two tissues. Furthermore, using the RNA seq from the S.lycopersicum x S.pennellii introgression
line population, we have identified expression quantitative trait loci (eQTLs) that contain putative
regulators of VTE synthesis. We have identified candidate genes within these eQTL regions, which
have been tested using viral induced gene silencing (VIGS) to determine their role in VTE regulation.
We are confident that these findings will provide an understanding of the transcriptional control of VTE
synthesis, and will potentially allow the production of nutritionally enriched tomatoes.
1405-TU. COLOR-FLESHED POTATOES INHIBITS ALDOSE REDUCTASE ACTIVITY
Kalita D1, Holm D.G1, Petrash M.J2, Jayanty S.S1
1
Department of Horticulture and Landscape Architecture, San Luis Valley Research Center Colorado
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State University, Fort Collins, CO-80523, USA; 2Department of Ophthalmology, School of Medicine,
University of Colorado, Anschutz Medical Campus, Aurora, Co 80045, USA
Contact: Sastry Jayanty, [email protected]
Purple and red potato cultivars have been receiving considerable attraction from the consumers and
growers due to the presence of high level of polyphenolic compounds and its potential antioxidant
activities. In this study, we have isolated and analyzed the phenolic and anthocyanin compounds in
selected potato cultivars and advanced selections with distinct flesh colors (purple, red, yellow and
white). Among these tubers purple and red potato, cultivars had higher levels of total phenolics (TP),
total flavonoids (TF) and total anthocyanins (TA) than yellow and white ones. The TP, TF, and TA of
Purple Majesty were found to be 4482.1 ± 154.7 µg GAE/g, 140.3 ± 20.1 µg QE/g, and 2043.9 ± 22.7 µg
C3GE/g respectively. Among phenolic acids predominant, one is chlorogenic acid. Major anthocyanins
composed of derivatives malvidin and pelargonidin. The antioxidant activities of purple majesty were
found to be 84.69 ± 5.3, 301.02 ± 39.9 µmol TE/g in ABTS and ORAC assay respectively. We tested the
potential inhibitory effect of methanolic extracts of these potato tubers in the activity of aldose
reductase (AR), a key enzyme that catalyzes the reduction of glucose to sorbitol in polyol pathway
which leads to locally hyperosmotic conditions responsible for the loss of clarity in the lens of the eyes.
Purple-fleshed tubers showed most effective inhibition of AR activity, for example, 50 µg/ml of an
extract of Purple Majesty inhibited 66%. Kinetic studies showed that fraction of phenolic acids inhibited
the aldose reductase activity in a non-competitive manner.
OTHER TOPICS
1501-TU. EFFICIENT SELECTION OF ANTIBODY FRAGMENTS USING PHAGE DISPLAY AND
EXHAUSTIVE YEAST TWO-HYBRID SCREENING
Tafelmeyer P.1, Moutel S.2, Djander S.2&3, Collura V.3, Arrial A.3, Jupin I.4, Olichon A.5, Perez F.6, Rain J.C.3
1
Hybrigenics Corp, Cambridge, MA, USA, 2 Translational Research Department, Institut Curie, Paris,
France, 3Hybrigenics Services SAS, Paris, France, 4 Institut Jacques Monod, Paris, France, 5INSERM,
CRCT, Toulouse, France, 6CNRS UMR144, Institut Curie, Paris, France,
Contact: Petra Tafelmeyer, [email protected]
Antibodies represent central tools in most biological studies to analyze protein localization and
function. One of the remaining limitations is the challenge to make them work inside a living cell. For
this purpose intrabodies can be selected as powerful tools to answer complex biological questions, as
has been shown for example with a conformational intrabody recognizing specifically the GTP-bound
form of the small GTPase Rab6, GTP-tubulin, or farnesylated PSD95.
So far, the access to intrabodies was limited to highly trained lab specialists in this field. We have
therefore set up a new platform for intrabody screening and designed for this purpose a fully synthetic
humanized naïve Llama VHH library containing 3x10exp9 antibodies, based on a unique scaffold with
random complementary determining regions (CDRs). We use a combination of phage display and
subsequent yeast two-hybrid (Y2H) screening to identify antibodies against native antigens and
eventually intrabodies. The VHH clones are directly accessible and the recombinant antibodies can be
produced as fusions to either a human, mouse or rabbit Fc domain.
We successfully selected from this library VHH against a variety of antigens including large proteins,
haptens and receptors directly selected from cell surface expression. The affinity of our VHH is similar
to the affinity of antibodies selected after animal immunization.
Using only a single round of phage display followed by one round of Y2H screening we were able to
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significantly enrich the selection in intrabodies. In addition, we took advantage of yeast genetics to
further study and characterize the selected intrabodies. Here this technique will be exemplified with
the selection of intrabodies against USP7, HER2 and a plant-virus protein.
1502-TU. DEVELOPMENT OF TOMATO BIORESOURCES BASED ON MICRO-TOM AS A MODEL
PLANT FOR FRUITS BIOLOGY
Hoshikawa K.1, Shikata M.1, 2, Ariizumi T.1, Fukuda N.1, Kanayama Y.3, Kubo Y.4, Aoki K.5, Ezura H.1
1
University of Tsukuba, Tsukuba, 305-8572, Japan; 2Institute of Agrobiological Sciences, NARO,
Tsukuba, 305-8602, Japan; 3Tohoku University, Sendai, 981-8555, Japan; 4Okayama University,
Okayama, 700-8530, Japan; 5Osaka Prefecture University, Sakai, 599-8531, Japan
Contact: Hoshikawa K., [email protected]; Ezura H., [email protected]
Tomato is an excellent model plant for fruit biology research and for genomic studies of
the Solanaceae family, which is consisting of potato, eggplant, pepper and so on. For facilitation of
breeding and functional genomics research of tomato, we launched on the tomato bioresource
program in 2007 within the framework of the National BioResource Project (NBRP) in Japan (NBRP
tomato; http://tomato.nbrp.jp/). The major purpose of the NBRP-tomato is to collect, preserve and
provide tomato bioresources including major experimental lines (Micro-Tom, Moneymaker, Ailsa Craig,
M82 etc.), wild tomato species (S. pennellii, S. peruvianum, S. pimpinellifolium, etc.), introgression lines,
mutant lines and full-length cDNA collections derived from Micro-Tom, a small and rapid growth variety
of tomato. Our activity mainly focuses on the development of mutant lines since they can greatly
facilitate as functional genomic tools. We have so far produced over 15,000 mutagenized M3
populations that were generated with ethylmethanesulfonate (EMS) treatment or gamma-ray irradiation
and about 2,000 individual mutants were identified. All of the visible phenotyping data and other
associated data of individual mutants were recorded within the database ‘TOMATOMA’
(http://tomatoma.nbrp.jp/), and these mutant seeds are available via this database. For enhancement of
the quality of the mutant resources registered, we are also accumulating metabolic profiles of the
tomato mutants, such as carotenoid contents and Brix values. In addition to the Micro-Tom mutants, we
have started providing T-DNA tag lines of Micro-Tom recently. On the other hand, as DNA resources,
the sequence information of Micro-Tom full-length cDNA and EST is available from database ‘KaFTom
(http://www.pgb.kazusa.or.jp/kaftom/) and EST database ‘MiBASE’
(http://www.pgb.kazusa.or.jp/mibase/), respectively. A reference genome sequence of Micro-Tom will
be available through ‘TOMATOMICS’ (http://bioinf.mind.meiji.ac.jp/tomatomics/). These tomato
resources will seed up research and development of tomato and fleshy fruits.
1503-TU. EPISTASIS FOR POST MATING PRE-ZYGOTIC ISOLATION
Hamlin J., Sherman N.A., Moyle L.C.
Department of Biology, Indiana University, 1001 E. Third St. Bloomington IN 47405, USA
Contact: Jenna Hamlin, [email protected]
Because the formation of new species involves the evolution of reproductive isolating barriers,
understanding the genetic basis of these barriers can provide insight into mechanisms of speciation.
The genetics of postzygotic reproductive isolation has been examined in several plant groups, but
postmating prezygotic barriers—that occur after pollen transfer but before fertilization--have received
comparatively little attention. Unilateral incompatibility (UI) is one such postmating prezygotic barrier in
which pollen rejection in the female reproductive tract (pistil) occurs in only one direction of an
interspecific cross. We investigated the genetic basis of pistil-side UI among Solanum species, with the
specific goal of understanding the role and strength of epistasis between UI QTL. Using Solanum
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pennellii introgression lines (ILs), we assessed the individual and pairwise effects of three
chromosomal regions (ui1.1, ui3.1, and ui12.1) previously associated with UI among Solanum species.
Specifically, we pyramided ui12.1 with each of ui1.1 and ui3.1, and assessed the strength of UI pollen
rejection (of domesticated tomato pollen LA3475) in pyramided lines, compared to individual IL
genotypes. We found that none of the three QTL individually showed UI rejection phenotypes, but
lines combining ui3.1 and ui12.1 showed significant pistil-side UI rejection. Furthermore, we observed
variation between pyramid lines that combined different chromosomal regions overlapping ui3.1,
indicating at least two genetic factors on chromosome three contribute to the strength of interspecific
pollen rejection. Our data indicate that loci on both chromosomes 3 and 12 are jointly required for the
expression of UI between S. pennellii and S. lycopersicum, emphasizing the importance of epistasis
among loci in the expression of postmating prezygotic reproductive isolating barriers between species.
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POSTER Session II • THURSDAY, September 15
5:30 — 7:00 pm, UC Davis Welcome Center
*Poster introduction will be presented at the ONE-MINUTE ORAL POSTER PRESENTATIONS
session: Wednesday 11:25 am, Conference Center Ballroom
DIVERSITY-TAXONOMY/CROP GERMPLASM DIVERSITY
*104-TH. UTILIZING WILD CAPSICUM ANNUUM (CHILE PEPPER) FOR BREEDING BEET CURLY TOP
VIRUS RESISTANCE IN CULTIVATED HOT PEPPERS
Jimenez R.C.1, Chen L.F.2, Gilbertson R.L.2, Hill T.H. 1, Van Deynze A.E.1
1
Plant Sciences Department; 2 Department of Plant Pathology, University of California, Davis, CA, USA
Contact: Randi Jimenez, [email protected]
Geminiviruses are the largest family of viruses threatening global vegetable production. Additionally,
Beet curly top virus (BCTV) is one of the most damaging geminivirus of chili pepper (Capsicum
annuum) in the United States that can result in yield losses ranging from 20-80%. BCTV is transmitted
by leafhoppers (Circulifer tenellus) and infect a wide range of plants, such as pepper, bean, sugar beet,
tomato, cucurbits and spinach. Both the virus and the insect vector continue to be difficult to control.
Our goal is to investigate germplasm sources from landraces collected in Mexico, where virus is
prevalent, as well as 10 lines from the literature for resistance to BCTV. To identify sources of
resistance, we utilize a rapid Agrobacterium-mediated inoculation assay. Interestingly, 20% of the
accessions from the literature were susceptible to BCTV, while only 26% of the wild accessions
appeared to be susceptible. Resistance has been confirmed using a leafhopper assay for some of the
wild accessions.
Several accessions identified as resistant have been crossed into a cultivated, susceptible jalapeño
variety to generate and test populations segregating for BCTV resistance and favorable agronomic
traits. Wild accessions were preferentially selected based on traits such as seed production, fruit type,
and the ability to cross with other C. annuum. These populations are being used to determine the
genetics of BCTV resistance in pepper. Our long-term goals are to develop and release pepper
breeding lines that combine resistance from wild pepper germplasm to BCTV, as well as to determine
the genetic basis of this resistance. Identifying genetic resistance from multiple sources is the key to
integrated management programs to protect yield and quality in pepper and other crops.
*105-TH. ANALYSIS OF SEQUNCE DIVERISTY IN SOLANUM SECT. PETOTA SPECIES IDENTIFIES
LOCI UNDER SELECTION DURING DOMESTICATION OF CULTIVATED SOLANUM TUBEROSUM
Hardigan M.A.1, Crisovan E.1, Wiegert-Rininger K. 1, Laimbeer P.2, Douches D.S.3, Veilleux R.E.2, Buell
C.R.1
1
Department of Plant Biology, Michigan State University, East Lansing MI 48824; 2Department of
Horticulture, Virginia Tech, Blacksburg VA 24061; 3Department of Plant, Soil, and Microbial Sciences,
Michigan State University, East Lansing MI 48824 USA
Contact: Michael Hardigan, [email protected]
The cultivated potato (Solanum tuberosum L.) was domesticated from wild diploid (2n=2x=24) species
approximately 8,000 years ago by South Americans native to the Andes Mountains of southern Peru.
Potatoes were subsequently adopted and grown across the Andean highlands of Peru, Bolivia, and
Ecuador, becoming a keystone of its cultural heritage, later spreading beyond the central Andes to the
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equatorial region of modern Colombia and Venezuela, and to the coastal lowlands of southern Chile,
where they were collected by Europeans in the 16th century. From these ancient origins, cultivated
potato has since been widely adopted into the global diet, becoming the third most important food
crop worldwide in terms of human consumption, and providing food security in the developing world.
In the era of genomics-enabled breeding, evaluating the available pool of genetic diversity within tuber
bearing Solanum, and the impacts of domestication and past breeding efforts on this diversity are
critical to support future food security through effective breeding and germplasm utilization.
Domestication and improvement of potatoes from their primitive South American relatives involved
selection on a wide variety of processes, above- and below-ground. Modification for human
consumption required loss of toxic glycoalkaloids, and increased synthesis and transport of
carbohydrates to the tuber. Cells were enlarged in the tubers of cultivated varieties due to altered cell
cycle regulation, and aboveground responses to day-length required adjustment for proper timing of
maturity across a broad altitudinal and latitudinal range. To understand the impacts of potato’s
domestication on its genetic diversity and identify key loci having undergone selection to produce
high-yielding varieties, we have re-sequenced a diversity panel of 63 genotypes including 20 wild
South American diploid species, 20 landrace populations, and 23 North American cultivars.
Comparison of these populations has yielded a subset of candidate domestication and improvement
genes most likely critical to potato’s agricultural performance and adaptation to growth in the Northern
hemisphere.
*106-TH. A COMPARATIVE BIOCHEMICAL ANALYSIS OF SOLANUM VEGETABLE SPECIES IN
UGANDA
Kabod, P.N.1, Namutebi, A.N.2, Kasharu, A.K.3, Jagwe, J.N.4, Rees,D.5, Kizito, E.B.1
1
Uganda Christian University Mukono, Uganda; 2 Makerere University, Kampala, Uganda; 3 Chain
Uganda Limited; 4 Farmgain Africa Limited; 5 NRI, University of Greenwich, UK
Contact: Pamela Nahamya Kabod, [email protected]
Variability was characterized bio-chemically by comparing relative total anti-oxidant active and
selected micro-nutrients across 12 leafy vegetable species in Uganda. Micro-nutrients and vitamins are
essential in the absorption and metabolism of ingested food thereby combating under-nourishment.
Total vitamin c, total anti-oxidant capacity, trans β carotene, iron and zinc were determined. Total antioxidant capacity ranged from7.2 to 53.1% DPPH, highest in Solanum aethiopicum, Gilo; vitamin c
ranged from0.6 to 5.2mg/100g, highest in Solanum aethiopicum, Shum. Trans β carotene ranged from
376.5 to 85710μg/100g and highest in Solanum aethiopicum, Shum. Iron ranged from 1381.4 to
4989mg/kg and zinc from 30.6 to 135.9mg/kg. Solanum aethiopicum,Gilo and Solanum nigrum had the
highest content of iron and zinc respectively. the data was further subjected to principal component
analysis to establish the proximate character accounting for the most variation observed across
the Solanum leafy vegetables. Trans β carotene accounted for 98.78% of the total variation at
principal component (PCA) 1. Cluster analysis resulted in 7 clusters groups: cluster 1 consisting of
accessions 168 (7596.5μg/100g) and accession 157 (7557.9μg/100g) accounted for the highest
variability. This variability analysis affords breeders a means for selecting parental stock for use in crop
improvement. The richness of diversity for micro-nutrients in indigenous vegetables is a ready and
cheap source in the staple diets and enriches promotional and awareness programs in a country
where micro-nutrient deficiency plagues millions.
Key words: variability, leafy vegetable, micro-nutrients, principal component analysis
*107-TH. ARGENTINEAN TOMATO LANDRACES, VALUABLE SOURCES FOR FRUIT QUALITY
TRAITS
Peralta I.E.1,2, Asprelli P.D.1,3, Sance M.1, Valle E4, Carrari F.5, Asis R.6
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Agronomy Faculty, National University of Cuyo; 2CCT CONICET Mendoza; 3INTA La Consulta
Experimental Station; 4Molecular Biology Institute of Rosario, CONICET; 5Biotechnological Institute,
INTA Castelar, Buenos Aires; 6Chemical Sciences Faculty-CIBICI, National University of Córdoba,
Argentina
Contact: Iris Edith Peralta, iperalta@fca,uncu,edu,ar
1
Local tomato landraces have been recently recovered from Andean areas of Cuyo and Nortwestern
Argentina, and maintained in the Germplasm Bank of INTA La Consulta Experimental Station in
Mendoza. These landraces have been selected by local farmers mainly for their environmental
adaptation and fruit quality. Our goal was to establish associations among agronomic traits, fruit
nutritional qualities and commercial characteristics of this Andean tomato collection. For this purpose,
32 tomato accessions and the wild species Solanum pimpinellifolium as contrasting control were
evaluated. Tomato plants were grown at the Experimental Station INTA La Consulta and at the Institute
of Horticulture (National University of Cuyo), using a randomized design with three replicates. For the
morpho-agronomic characterization 19 traits were recorded. Mature red fruits were harvested,
immediately freezed with liquid nitrogen, and maintained in ultra-freezer until analyses. Metabolite
contents were evaluated by different methods (GC- and LC-MS and H-MNR). Volatile organic
compounds were evaluated using headspace solid phase microextraction (HS-SPME) and gas
chromatography-mass spectrometry (GC-MS). Antioxidant metabolites were measured by HPLC–DAD–
MS/MS, and their biological activities were assessed by in vitro and in vivo methods. These
approaches allowed to detect 175 different compounds and 101 volatile metabolites, among them 21
new compounds never informed in S. lycopersicum. As a complement of the biochemical analysis, fruit
organoleptic characteristics were also evaluated. All data were integrated using multiple variable
analyses. Agronomic and morphological traits, fruit nutritional and organoleptic characteristics are
associated with a broad spectrum of metabolites in an Andean tomato germplasm collection. A
different and original metabolic volatile composition was found in fruits of Andean tomatoes, in
comparison with commercial cultivars. A similar pattern was also revealed by the antioxidant properties
and organoleptic characteristics of traditional tomatoes. Natural environmental adaptation,
domestication and independent artificial selection events would have generated different genetic
constitutions, confirming that traditional agricultural habitats are important reservoirs of genetic
diversity. These results revealed a promising breeding perspective, since the incorporation of Andean
tomato accessions could reinforce genetic variability, as a source of valuable new compounds to
improve fruit quality and incorporate interesting bioactive molecules in cultivated tomatoes.
*108-TH. VARIATIONS IN MORPHOLOGICAL AND AGRONOMIC TRAITS AMONG AFRICAN
EGGPLANT ACCESSIONS
Owino W.O.1, Lagat S.2, Ambuko J.2, Chemining’wa G.2
1
Department of Food Science & Technology, Jomo Kenyatta University of Agric. and Technology;
2
Department of Plant Science &Crop Protection, University of Nairobi, P.O. Box 29053, Nairobi
Contact: Willis Owino, [email protected]
This study characterized the morphological and agronomic traits of 72 accessions from four species of
African eggplant namely Solanum aethiopicum (50), Solanum macrocarpon (1), Solanum anguivi(6)
and Solanum sp (15). Data was collected on nine quantitative and eight qualitative morpho-agronomic
traits measured at flowering and fruit maturity stages. The analysis of variance indicated significant
differences (P<0.05) for most of the accessions grown in the field and greenhouse. Fruit length was
significantly (P<0.05) and positively correlated with fruit breadth % (r = 0.59 and 0.60), fruit weight % (r
=0.72 and 0.73) and leaf blade width % (r =0.34 and 0.28) for field and glasshouse grown accessions,
respectively. However, fruit length correlated negatively but highly significantly with number of fruits
per plant (r = -0.32and -0.31) for field and greenhouse grown accessions, respectively. On the other
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hand, fruit length was positively correlated to leaf blade length (r = 0.09 and 0.09) and plant height % (r
= 0.15 and 0.16) while days to flowering had a positive correlation to SPAD value % (r = 0.08 and 0.06),
respectively, for field and greenhouse grown accessions. Cluster analysis used placed the accessions
into two cluster groups with cluster one having 51 accessions and cluster two having 21 accessions.
Qualitative characters evaluated included size and shape of the fruit, fruit prickles, leaf hairs, leaf
length and leaf width, flower colour and plant growth habit. Both at the field and in the greenhouse
87.5%of the accessions showed an upright growth, intermediate growth habit (9.7%)and prostrate
growth habit (2.8%) while those with leaf prickles were 68.1% and 31.9% did not have leaf prickles. It
was also observed that 70.8% of the accessions had leaf hairs while those without were 29.2%.
Estimates of Shannon-Weaver diversity index (H’) for the qualitative characters assessed in the field
and greenhouse were generally high (H?>0.500). Principal component analysis showed that fruit and
leaf parameters were important traits with a large coefficient of variation (> 50%), which distinctively
separated the eggplant accessions. A phenetic relationship between S.aethiopicum, S.anguivi, S.
macrocarpon and Solanum sp was generated for accuracy in classifying the accessions.
BARRIERS TO BREEDING
*207-TH. CHALLENGE OF BREEDING WITH THE DISEASE RESISTANCE: INTROGRESSION
OF PHYTOPHTHORA CAPSICI RESISTANCE AND HORTICULTURAL-TRATIED QTL ANALYSES IN
BELL PEPPER
Chunthawodtiporn J., Hill T., Stoffel K., Van Deynze A.
Plant Sciences Department, University of California, Davis, CA, USA
Contact: Jareerat Chunthawodtiporn, [email protected]
To be successful in a breeding program for disease resistance, integrating the genetic resistance while
maintaining favorable horticultural traits is essential. This study used QTL analyses in a recombinant
inbred line (RIL) population to understand the genetic basis of Phytophthora capsici resistance and
important horticultural traits while limit the unfavorable traits from the resistant parent in a bell pepper
breeding program. Genetic map was generated using the genotype-by-sequencing method aligning to
the pepper reference genome. Stepwiseqtl function in R/QTL generated the QTL models with the
percentage of phenotypic variation explained as a model and the epistatic interactions. For P.
capsici resistant study, four isolates were tested and found a major QTL on chromosome 5 along with
isolate-specific QTL on chromosome 4, 7, 8, 10 and 11. The isolate-specific QTL from PWB-53 on
chromosome 10 had high percentage of phenotypic variance that was close to the phenotypic variance
explained by the major QTL on chromosome 5 from the same isolate. Additionally, three strong
interactions were detected between the major QTL on chromosome 5 and the isolate-specific QTL on
chromosome 8, 10 and 11. For the horticultural traits, fruits and leaves were imaged and analyzed in
Tomato Analyzer Software. Most of the fruit and leaf-related QTL were located on chromosome 1, 2
and 3. Unfavorable traits for bell pepper such as stem pubescence and anthocyanin stripes on the
young pepper fruits were scored in the field. With QTL analyses and correlation studies found the
significant correlations among organ-sized, unfavorable and P. capsici resistant traits. For example, the
stem pubescence showed the negative correlation to the susceptibility from PWB-53 but not to the
others. This was explained from the tight linkage between the stem pubescence and the isolatespecific resistant QTL on chromosome 10. To integrate the genetic resistant components into a bell
pepper cultivar, RIL population were screened for both resistance and favorable traits and used as a
resistant parent to recover the fruit size in the bell pepper breeding program.
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*208-TH. TESTING SI X SC RULE IN THE TOMATO CLADE (SOLANUM SECTION LYCOPERSICON)
AND THE ROLE OF A LOW ACTIVITY S-RNASE IN INTERSPECIFIC REPRODUCTIVE BARRIERS
Baek Y.³, Tovar-Méndez A. ², Covey P.A.³, Chetelat R.T.¹, McClure B. ², Bedinger P.A.³
¹Department of Plant Sciences, University of California, Davis; 2Department of Biochemistry, University
of Missouri; 3Department of Biology, Colorado State University
Contact: Yoo Soon Baek, [email protected]
Studying the nature of interspecific reproductive barriers (IRBs) among close relatives can provide
insight into how species maintain their integrity. Interspecific pollen rejection frequently displays the SI
x SC rule, in which crosses between self-incompatible (SI) species and self-compatible species (SC) are
successful in one direction but not the other, resulting in unilateral incompatibility (UI). This implies that
SI mechanisms may be involved in IRB systems. Pollen-pistil interactions were assessed in interspecific
crosses designed to test the constancy of the SI x SC rule in the tomato clade
(Solanum sect. Lycopersicon). Generally, the SI x SC rule was followed in crosses at the species level,
but there were exceptions with more recently evolved SC populations. In addition, I investigated
whether S-RNase protein (SI pistil factor) is involved in IRBs in the SC wild species Solanum
neorickii. S. neorickii populations located at the species northern and southern margins reject
interspecific pollen and express a low activity S-RNase protein. In contrast, S. neorickii in the middle of
the species range does not reject interspecific pollen and lacks expression of the S-RNase. In F2 plants
of inter-population hybrids, it was observed that individuals that reject pollen tubes also express SRNase. However, we also observed individuals that express S-RNase but do not reject interspecific
pollen tubes. These findings suggest that a low activity S-RNase, although insufficient for SI, can act in
IRBs, and further that S-RNase is necessary but not sufficient to reject interspecific pollen tubes in S.
neorickii.
GENOMES AND GENOME TECHNOLOGIES
306-TH. SEQUENCING THE GENOME OF THE PATHOGEN RESISTANT SOLANUM
LYCOPERSICOIDES
Vogel A., Schmidt M.H-W., Denton A.K., Bolger A.M., Usadel B.
1
Institute of Biology and Molecular Genetics, RWTH-Aachen University, Aachen, Germany
Contact: Alisandra Denton, [email protected]
Solanum lycopersicoides is a wild tomato species native to Chile that shows much stronger nectropic
fungi resistance than cultivated tomato. It belongs to the Solanum section Lycopersicoides, which is
sister to the section with cultivated tomato (Lycopersicon). We’ve performed Illumina sequencing on
paired end, mate pair and fosmid libraries to achieve a draft genome with a N50 of 1.2 Mb. PacBio
data, provided from collaborators at the Boyce Thompson Institute, will be incorporated to further
improve the assembly. The genome—in combination with available public genomic resources on other
wild tomato species—will be used to elucidate the genetic basis of the pathogen resistance. This
understanding will help to jump-start breeding efforts to improve pathogen resistance in cultivated
tomato.
307-TH. GENOME DOSAGE CHARACTERIZATION OF SOLANUM TUBEROSUM HAPLOIDS
Amundson K.R.1, Tan E.H.1, Ordoñez B.1, Santayana M.2, Bonierbale M.2, Khan A.2, Comai L.1
1
Plant Biology and Genome Center, University of California, Davis, CA, USA; 2International Potato
Center (CIP), Lima, Peru
Contact: Kirk Amundson, [email protected]
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Haploid induction can be used to rapidly introduce novel genetic combinations into crop varieties. We
have previously demonstrated that haploid induction via uniparental genome elimination in
Arabidopsis is able to create a range of novel karyotypes such as truncations, deletions,
rearrangements, or minichromosomes derived from the haploid inducer genome. In the potato haploid
induction system, residual fragments of Solanum tuberosum Group Phureja haploid inducer genome
have been reported in haploid progeny, but these introgression events have not been characterized
with genome sequencing approaches. Therefore, we plan to explore the extent of dosage variation
produced by potato haploid induction crosses using whole-genome sequencing. We will test the
hypothesis that some of the haploid progeny from the haploid inducing cross in potato will exhibit
novel genome dosage variation, or may contain DNA fragments from the haploid inducer genome.
Here, we report a pilot-scale chromosome dosage analysis of F1 haploids (n=6) produced from a S.
tuberosum Group Andigena × S. tuberosum Group Phureja haploid induction cross. We found that one
of the six analyzed lines exhibited a truncated chromosome 4, which suggests that chromosome
remodeling can occur during in vivo haploid induction in potato. In order to characterize a broader
range of chromosome dosage variation, including potential introgressions from the Phureja haploid
inducer, we plan to generate and sequence 400 additional putative haploid lines.
308-TH. GENOME WIDE ASSOCIATION STUDIES CORRECTING POPULATION STRATIFICATION IN
PEPPER CORE COLLECTION
Lee H-Y.1, Han K.1, Hur O-S.2, Go H-C.2, Kwon J-K.1, Sung J-S.2, Kang B-C.1
1
Department of Plant Science and Vegetable Breeding Research Center CALS, Seoul National
University, Seoul 151-921, Korea; 2National Academy of Agricultural Science, Rural Development
Administration, Jeonju 560-500, Korea
Contact: Tel: +82-2-880-4563, E-mail: [email protected]
Genome-wide association study (GWAS) is an effective approach for identifying genetic variants
associated to useful agronomic traits. GWAS has emerged as a powerful approach for identifying
genes underlying complex diseases or morphological traits at an unprecedented rate. In such studies,
it is very important to correct for population stratification, which refers to allele frequency differences
between cases and controls due to systematic ancestry differences. Population stratification can cause
false positive findings if not adjusted properly. As we are performing GWAS for various agronomic
traits in pepper, a genotyping-by-sequencing (GBS) approach was used to provide dense genomewide marker coverage (>33,000 SNPs) for a 250 pepper core collection. Using GBS platform, a high
density haplotype map was constructed and various stratification methods, including distance based
phylogenetic methods, principal component analysis (PCA), and bayesian phylogenetic methods
(STRUCTURE) were performed to show the genetic diversity and population stratification. MLM using Q
values combined with kinship matrix estimated from stratification methods were used to identify
quantitative trait loci controlling the variation of ten agronomic traits. These results will help to
understand associations between phenotype and genotype and also will be used for validation of the
candidate genes or quantitative trait loci previously identified in pepper.
309-TH. IDENTIFYING NOVEL SMALL PEPTIDES IN TOMATO USING RIBOSOME PROFILING
Hsu P.Y.1, Calviello L.2, Wu H.L.3, Li F.W.1,4, Rothfels C.4, Ohler U.2, Benfey P.N.1,5
1
Duke University, Durham, NC, USA; 2Max Delbrück Center, Berlin, Germany; 3North Carolina State
University, Raleigh, NC, USA; 4University of California, Berkeley, Berkeley, CA, USA; 5Howard Hughes
Medical Institute, Durham, NC, USA
Contact: Polly Hsu, [email protected]
Small peptides play important roles in short and long distance signaling in plants. They regulate plant
growth and development, interactions between plants and the environment, as well as interactions
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between plants and pathogens or symbiotic microorganisms. Despite their importance on diverse
functions, only a small number of peptides have been identified so far, and they are often missed in the
genome annotation. Previously we have exploited ribosome profiling (deep sequencing of ribosome
footprints) and a computational pipeline to define translated open reading frames in Arabidopsis
transcriptome and successfully identified 50 novel small proteins/peptides. A significant number of the
novel peptides are conserved in multiple Brassicaceae species, but not outside of the clade,
suggesting some peptides are specific to certain plant families. To directly identify novel peptides in
tomato, we are applying ribosome profiling to Solanum lycopersicum (cv. ‘Heinz-1706’) root and shoot.
The resulting data are expected to reveal novel translation events including new peptides, and to
improve genome annotation.
310-TH. CHALLENGING SPECIATION AND DOMESTICATION TO ENHANCE THE RESPONSE OF
POTATO AGAINST BACTERIAL WILT.
Dalla-Rizza M.1, Boschi F.2, Murchio S.1, Ferreira V.3, Siri M.I.3, Galván G.4, Zipfel C.5, Vilaró F.1
1
Biotechnology Unit-INIA; 2INASE; 3Microbiology Department, Chemistry School-Universidad de la
República; 4Plant Production Department, CRS, Agronomy School-Universidad de la República,
Uruguay; 5The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
Contact: Marco Dalla-Rizza, [email protected]
During evolution of plant-microbe interactions, plants have developed a complex network of defensive
strategies. Perception at the cell surface of pathogen-associated molecular patterns (PAMPs) by
pattern-recognition receptors (PRRs) leads to the activation of plant basal defenses often sufficient to
resist most pathogens. A second, intracellular, layer of plant defense involves cytoplasmic nucleotide
binding site-leucine-rich repeat (NBS-LRR) proteins (often called R proteins). Different plant genotypes
vary in the presence or efficacy of particular such immune receptors, which often underline resistance
versus susceptibility to a given pathogen. In this work, we tested the use of the Brassicaceae-specific
PRR EFR (as a transgene) against Ralstonia solanacearum (Bacterial Wilt-BW) in different potato
genetic backgrounds showing partial resistance to this pathogen. Introgression of BW resistance from
Solanum commersonii (cmm)to cultivated potatoes has been achieved through sexual polyploidization
(2n gametes) and utilization of bridge species (Phureja) followed by some back crosses (BC) to
Tuberosum, at INIA potato breeding program. Disease resistance screening was performed under
controlled experimental conditions, using an aggressive pathogen strain and root damaging. Stem
latency evaluation in asymptomatic plants was performed through high sensitivity PCR test. Transgenic
events of the susceptible cultivar ‘INIA Iporá’-EFR and of the BC2 resistant clone 09509.6-EFR were
developed at The Sainsbury Lab. EFR transgenic genotypes showed higher levels of resistance to R.
solanacearum infection compared to the untransformed genotypes. Several transformed genotypes of
this BC2 cmm derived clone, achieved the highest level of resistance and reduced stem latency.
Notably, EFR seems to act into the potato germplasm as an enhancer of the defense response,
complementing the BW resistance introgressed from cmm. Studies of pathogen latency on potato
tubers are currently being performed with promising results. Among other characteristics, copy number
of the events was determined and the more responsive to BW clones of 09509-EFR are being used for
crossing into the potato breeding program.
*311-TH. IDENTIFYING CAUSATIVE MUTATION IN GENOMES WITHOUT A REFERENCE SEQUENCE
OR GENETIC RESOURCES, USING BULK SEGREGANT SEQUENCING
Rallapalli G.1, Corredor-Moreno P.1,§, Chalstrey E.1,€, MacLean D.1
1
The Sainsbury Laboratory, Norwich Research Park, Colney, Norwich, UK, NR4 7UH. Present
address: §The Genome Analysis Centre, Norwich Research Park, Colney, Norwich, UK, NR4
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7UH. €WallStreetDocs, 1 Fore Street, London, UK, EC2Y 5EJ
Contact: Ghanasyam Rallapalli, [email protected]
Forward genetic screens are essential to identify target genes behind desirable traits and their
beneficial application. Traditional map-based cloning approaches require establishment of genetic
resources, are extremely labour intensive and years can elapse between the mutagenesis and the
detection of the polymorphism responsible for the phenotype. Mapping-by-sequencing (MBS), high
throughput sequencing (HTS) based mutation mapping approach, has shortened it to a single step by
calculating allele frequency from bulks and the identification of causal mutations at single-nucleotide
resolution. However, application of MBS requires a complete chromosomal order of the genome
assembly and cannot be used with fragmented draft genomes. Most plant species lack genetic and
genomic resources to carry out such mapping studies. Hence, there is a need for computational tools
to identify mutations from plant species with a draft or pre-draft genome assembly.
We have developed a method called Computing Homozygosity Enriched Regions In genomes to
Prioritize Identification of Candidate variants (CHERIPIC). CHERIPIC makes use of fragmented genome
assemblies resulting from HTS and bulk segregant sequencing (BSS) data to call variants and identifies
a causative mutation or a few closely linked variants that help narrow down the region harbouring the
trait of interest. CHERIPIC has been successfully implemented using both simulated fragmented
assemblies and assemblies made from BSS data for Arabidopsis (backcross and outcross) and rice
(backcross). Using backcross bulk data, we could identify causative mutations in the 20 candidates
selected by CHERIPIC; with an outcross data causative mutation in the 60 candidate variants, due to
additional polymorphisms expected between selected parent and mapping parent. In addition, we
have successfully applied CHERIPIC using bulked RNA-seq data from maize and transcriptome
assembly resulting from bulk data. Seven out of ten candidate maize genes selected by CHERPIC are
very closely linked to the location of the causative mutation. Application of CHERIPIC using exome data
of barley BSS has shown that ~65% of selected variants are very closely linked to the region of the
causative mutation. We are currently testing CHERIPIC on a tetraploid wheat RNA-seq bulk data and
developing a web interface for ease of use and selection of candidate variants.
*312-TH. CHARACTERIZATION OF ANKYRIN GENE FAMILY AND OTHER GENES INVOLVED IN
PEPPER FRUIT SIZE AND CAPSAICIN CONTENT
Yadav L K, Saminathan T, Nimmakayala P, Reddy U
West Virginia State University, INSTITUTE, WV
Contact: Lav Kumar Yadav, [email protected]
Ankyrin repeat (ANK) protein domain is found in a wide range of organisms from plants, humans to the
microorganisms. It is a motif that consists of 33-residue which has two alpha helices that are separated
by a loop from each other. Our previous GWAS showed that ANK proteins were mapped for fruit size
and capsaicin in pepper and the current study aims to investigate it further. Selected Ankyrin repeats
will be analyzed using three pepper species (Capsicum annum, C. chinense, and C. baccatum) having
variation in fruit size. Current genome mining using Arabidopsis and rice ankyrin genes as homologue
search indicates that there are nearly 110 Ankyrin-repeat genes in pepper. Finally, the phylogenetic
relationship will be presented using proteins coded by these genes. This research also identified the
mutations showing non-synonymous SNPs (single nucleotide polymorphisms) and InDels in ankyrin
gene family across three species. Through this investigation, we can track down the evolution of
ankyrin gene family in pepper. In addition to that, this study will provide a list of candidates for further
improvement of fruit size and capsaicin content in various pepper species.
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*313-TH. REVERSE GENETIC TOOLS FOR CROPS PLANTS: STUDY CASE AT THE IPS2 INSTITUTE
Gomez-Roldan M.V., Marcel F., Lefeuvre E., Mania B., Bendahmane A.
Institute of Plant Sciences Paris Saclay (IPS2), Translational Research Platform, Bâtiment 630, rue de
Noetzlin, 91190 - Gif-sur-Yvette (France)
Contact: Fabien Marcel, [email protected]
Advances in whole genome sequencing technologies are providing sufficient information about the
structure, position and type of genes containing in a plant genome. However, a new challenge is to
understand the link between gene – function association and decipher their implication in biological
processes. Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to
directly identify point mutations in specific genes of interest in genomic DNA from a large chemically
mutagenized population. Classical TILLING processes, based on enzymatic detection of mutations in
heteroduplex PCR amplicons, are slow and labor intensive. In the Institute of Plant-Science Paris-Saclay
(IPS2) we have implemented a new TILLING strategy using direct next generation sequencing (NGS) to
screen and accurately identify mutant alleles in specific genes of agronomical important crops.
Genomic DNA from M2 families of an ethyl methanesulphonate (EMS) mutagenized population are
extracted in 1 week using the Biomek FX robot (5.000 M2 families). A 2D DNA pooling design is used
as template to generate amplicons (500 bp) that will serve to generate the DNA libraries. Each pool
has a unique Illumina dual-barcoding combination, and sequencing using Miseq technology generate
250 base-pair overlapping paired-end reads, that are then analyses using our in-house pipeline
(SENTINEL) to identify mutations. The whole process from DNA extraction to mutant validation is now
possible in 1 month for 8 amplicons (10 months using the Endo1 enzyme).
We have generated an EMS saturated population for tomato (50.000 M2 families var. 4131), in
collaboration with five private companies, and a population in pepper (5.000 M2 families, var.
California Wonder). Other EMS populations are also available for cucurbits species. Accurate and
efficiently results have been obtained reducing cost and time for functional genomics studies in crops
species.
*314-TH. IMPROVED TOMATO GENOME REFERENCE USING FULL-LENGTH BACs, BIONANO
GENOME MAPS AND SGN COMMUNITY RESOURCES
Saha S.1, Hosmani P.1, Flores M.1, van de Geest H.2, Sanchez-Perez G.F.2, Mueller L.A.1
1
Boyce Thompson Institute, Ithaca, NY, USA; 2Plant Research International, Wageningen University,
Netherlands
Contact: Surya Saha, [email protected]
The Solanum lycopersicum cultivar Heinz 1706 genome is the primary reference model organism for
many solanaceous species. The previous genome build SL2.50 contained 23,640 contig gaps and 79
scaffold gaps where the size was an approximation and the bases were unknown. The total size of gap
regions varied from 7.23% to 14.61% per chromosome for 10.36% over all the chromosomes.
We have integrated 1,069 full-length phase htgs3 BACs into the tomato genome to cover gap regions
and replace shorter whole genome shotgun contigs which removed 11,699,806 bases (11Mb) of contig
gaps. The reduction in contig gaps varied from 3.17% to 49.07% per chromosome. BioNano genome
maps were generated for Heinz 1706 that largely confirmed the correctness of the current build.
Chromosome 0 contains scaffolds that could not be localized in the genome build. In the new build, we
were able to integrate 2 additional scaffolds from chr 0 into chrs 2 and 9, fix 2 inversions in chr 12 and
resize 19 gaps accurately using CMaps from the BioNano assembly.
Tomato optimized annotation pipelines were run using RNAseq data kindly provided by members of
the Solanaceae community. Gene identifiers were transferred from ITAG2.4 to corresponding ITAG3.0
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models to maintain backward compatibility. In cases where a gene was modified, its version number
was updated to reflect the change. Corrections submitted by the SGN user community for ITAG 2.4
gene models and build SL2.50 have also been incorporated into ITAG3.0 and SL3.0. All data are
available through the SOL Genomics Network website (SGN, https://solgenomics.net) and FTP site
(ftp://ftp.solgenomics.net/tomato_genome/).
GENE EDITING AND NEW BREEDING TECHNOLOGIES
*504-TH. A VECTOR DESIGN STRATEGY FOR PLANT SYNTHETIC BIOLOGY IMPLEMENTED IN
GENOCAD
Coll A.1, Wilson M.L.2, Gruden K.1 and Peccoud J.3,4
1
Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana,
Slovenia; 2Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA; 3Department of Chemical &
Biological Engineering, Colorado State University, Fort Collins, CO, USA; 4GenoFAB, LLC, San
Francisco CA, USA
Contact: Anna Coll, [email protected]
Plant synthetic biology requires software tools to assist on the design of complex multi-genic
expression plasmids. Here a vector design strategy to express genes in plants is formalized and
implemented as a grammar in GenoCAD, a Computer-Aided Design software for synthetic biology. It
consists of a set of rules that define the design strategy for a specific type of application. Specifically,
we developed rules to design constructs for three categories of experiments frequently used in the
plant biology community: protein localization, promoter analysis and protein-protein studies. The plant
grammar includes a library of basic parts associated with the grammar, where each part is categorized
into functional groups allowing the user to easily manage and identify suitable biological parts. The
GenoCAD plant grammar guides the user through the design while allowing users to customize
vectors according to their needs. Therefore, the plant grammar implemented in GenoCAD will help
plant biologists take advantage of methods from synthetic biology to design expression vectors
supporting their research projects.
*505-TH. OPTIMIZING TISSUE CULTURE METHODS IN DIVERSE SOLANACEAE SPECIES
Rajewski A.1, Maheepala D.C.1, Henry A.2, Baghaei A.1, Litt A.J.1
1
Department of Botany and Plant Science, University of California, Riverside, CA, USA; 2Department of
Biology, Truman State University, Kirksville, MO, USA
Contact: Alex Rajewski, [email protected]
In vitro propagation and plant regeneration are essential for many advanced genomic techniques such
as the generation of stable transgenic plant lines as well as for propagation of lines that are sterile or
that have desirable traits. Although many solanaceous species have well-established traditional
propagation protocols, in vitro propagation methods have only been developed for a few select
species. We have adapted a tomato (Solanum lycopersicum) in vitro tissue culture and transformation
protocol developed at the Boyce Thompson Institute for use in a diverse group of Solanaceae species
with useful phylogenetic placement. These species include wild tomato (Solanum pimpinellifolium),
desert tobacco (Nicotiana obtusifolia), synthetic tobacco (N. tabacum) hybrids, jimson weed (Datura
stramonium), night-blooming jasmine (Cestrum nocturnum) and Schizanthus grahamii. Desert tobacco
is a diploid congener of N. tabacum more amenable to greenhouse growth conditions, which flowers
rapidly and copiously and can be maintained at a relatively small size. Jimson weed is a species which
lies in the fleshy-fruited Solanoideae clade but has reverted back to a dry capsule, while night
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blooming jasmine in contrast lies in the dry-fruited grade but has independently evolved a fleshy fruit.
Finally, Schizanthus grahamii is one of the most basal taxa in Solanaceae. The results of these
optimization experiments represent an important first step toward generation of stable knock out lines
for future genetic studies, the clonal preservation of important varieties, and the propagation of sterile
hybrid lines.
*506-TH. DEVELOPMENT OF A PROTOPLAST SYSTEM FOR NON-TRANSGENIC, TARGETED
GENOME EDITING IN SOLANUM TUBEROSUM
Fossi M.M.1,2,3, Amundson K.R.1,2, Jinata S.N.1, Comai L.1,2
1
Genome center and 2Plant Biology Department, University of California, Davis, CA, USA; 3HM Clause,
Davis, CA
Contact: Michelle Fossi, [email protected]
Genome editing technologies based on the CRISPR-Cas9 programmable nuclease are emerging as
invaluable tools for research and plant breeding. Crops modified using this technology have recently
been deemed non-regulated by U.S. regulatory agencies, provided that any transgenes used during
editing are removed from the final product. For clonally propagated crops such as potato (Solanum
tuberosum Group Tuberosum), transgene removal remains particularly challenging and timeconsuming. Non-transgenic genome editing by transfecting protoplasts with preassembled Cas9
ribonucleoprotein complexes offers a strategy for efficiently editing clonally propagated crops.
To knock-out selected genes and to modify others in loco, we have established a protoplast
regeneration platform in Solanum tuberosum.This system should provide a rapid method of testing
new guide RNAs and ability to quickly and easily introduce multiple edits in a crop genome at a single
time. Here, we report on our protoplast isolation and plant regeneration from two potato clones: S.
tuberosum Group Tuberosum cv. Desiree and S. tuberosum Group Phureja cv. DM1-3, as well as our
gene target design strategy. We observe efficient protoplast isolation frequencies in both S.
tuberosum Group Tuberosum cv. Desiree and in S. tuberosum Group Phureja cv. DM1-3. Contrary to
DM1-3, Desiree successfully regenerates callus and plant shoots, making it an ideal candidate to
further explore the potential of this genome editing technology for crop modification. We anticipate
that edited lines produced from our pipeline will provide useful material for potato functional
genomics.
GENOMIC-ASSISTED BREEDING
*704-TH. GENOMIC LOCI RESPONSIBLE FOR LOW-LIGHT FRUITING TRAIT OF MICRO-TOM
Chiba N.1, Shirasawa, K.2, Aoki K.1
1
Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai,
Japan; 2Kazusa DNA Research Institute, Kisarazu, Japan
Contact: Koh Aoki, [email protected]
Light condition is an important environmental factor for plant growth. Especially fruiting plants, they
need abundant light to flower and to bear fruits. The tomato is regarded as a model plant not only the
Solanaceae but also for other fruiting plants. A dwarf cultivar, Micro-Tom, has drawn attention as a
model tomato line because of its small plant size, short life cycle and easy to transformation. MicroTom also has ability to bearing fruits in low light intensity condition in which other cultivated tomatoes
cannot bear fruits. However the genes contribute to the ability of Micro-Tom have not been identified.
In this study, we attempt to identify genes which are responsible for this low light-requirement trait.
First, we evaluated fruiting behavior of several S. lycopersicum cultivars quantitatively under low light
intensity. We confirmed that Micro-Tom, a dwarf ornamental cultivar, indeed showed early fruiting in
low-light-intensity condition. To identify genomic loci responsible for low-light fruiting, we generated
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mapping population by crossing Ailsa Craig, which exhibited late fruiting phenotype under low light
intensity, with Micro-Tom, and obtained F1, F2 and F3 progenies. The light requirement of the progenies
was evaluated by measuring the leaf number under first inflorescence and ratio of fruiting. In parallel
with light-requirement evaluation, 40 F3 plants were genotyped by using RAD-Seq. RAD-Seq combined
with genome-wide association study using 593 SNPs implied that low-light fruiting trait is under
polygenic control. The association analysis allowed us to prioritize four genomic regions associated
with low-light fruiting trait; 34 Mbp-50 Mbp region of chromosome 2, 56 Mbp-65 Mbp of chromosome
8, 1 Mbp-1.4 Mbp of chromosome 9 and 67.4 Mbp-67.9 Mbp of chromosome 9. We attempt to narrow
down the region further by using SSR markers. Implication to low-light fruiting from genes located on
these regions will be also discussed.
*705-TH. GENERATING GENOMIC TOOLS FOR MORE EFFICIENT BREEDING OF THE AFRICAN
EGGPLANT
Masika B.F.1,2, Kamenya S.1, Eldridge T.2, Njuguna J.N.2, Stomeo F.2, Asami P.2, Kizito E.B.1, Odeny D.A.3
1
Department of Agriculture and Biological Sciences Uganda Christian University; 2Biosciences eastern
and central Africa-International Livestock Research Institute Hub; 3The International Crops Research
Institute for the Semi-Arid Tropics
Contact: Fred Bwayo Masika, [email protected]
In Africa, Solanum aethiopicum is underexploited and underutilized partly due to lack of improved
varieties and traditional breeding approaches. Complimenting the current conventional breeding
activities with genomics-assisted selection is a more efficient approach towards the development of
superior cultivars. This is because the crop is a potential income earner not only in Uganda but all over
Africa. However, there are currently no genomic resources developed for S. aethiopicum. There is no
genetic linkage map, no known mapping populations and no association studies reported. To generate
these tools, one intra-specific (Sa303 x Sa307) and one inter-specific (S. aethiopicum x S. anguivi)
mapping populations are currently being developed at the Biosciences eastern and central Africa International Livestock Research Institute (BecA-ILRI) Hub. Genome-wide Single Nucleotide
Polymorphism (SNP) marker discovery is also being carried out using both transcript and genomic
sequences. To identify genic SNPs, we used previously generated transcript reads from developmental
tissues of Shum and Gilo types. All the transcripts were assembled to form a reference transcriptome.
Reads from each cultivar group were aligned separately to the reference transcriptome before
generating SNP calls. To identify SNP markers from genomic sequences, genomic DNA was isolated
from young leaves of the parents of the intra-specific mapping population, enzyme digested,
sequencing libraries prepared and sequenced with the Miseq (Illumina, San Diego, CA). Processed
sequencing data was used for SNP discovery. Our results show higher levels of diversity across
different S. aethiopicum groups (between Shum and Gilo) and significantly less numbers of SNPs within
each group. The frequency of SNPs within genomic sequences was also higher than those observed
within genic sequences. Future studies will continue to discover SNPs across different species,
generate both inter- and intra-specific linkage maps and map agronomically important traits like yield,
pest and disease resistance in S. aethiopicum for improved production, food and nutrition security in
developing countries.
*706-TH. SNP MARKER DISCOVERY FOR RESISTANCE TO COLUMBIAN ROOT KNOT NEMATODE
IN POTATO
Bali S.1, Vining K.2, 4, Brown C.3, Sathuvalli V.1, 4
1
Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, Oregon
97838; 2Department of Horticulture, Oregon State University, Corvallis, Oregon 97331; 3USDA-ARS
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Vegetable and Forage Crops Research Unit, Prosser, Washington 99350; 4Center for Genome
Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
Contact: Sapinder Bali, [email protected]
Columbian Root Knot Nematode (CRKN) is one of the severe pests of potato production in the
Columbia basin of the Pacific Northwest. CRKN invades roots and growing tubers, affecting both tuber
yield and quality. Fumigation is the best way to control CRKN. Because of the environmental concerns
using fumigants and high cost incurred in its applications, host genetic resistance is viewed as best
alternative to control this pest. We aim to identify single nucleotide polymorphisms (SNPs) linked to
tuber resistance using high throughput sequencing technology and bulked segregant analysis. CRKN
resistance from wild diploid species Solanum bulbocastanum accession SB22 was introgressed into
tetraploid potato breeding material, and screening identified selection PA99N82-4, to be resistant to
CRKN. The resistance trait has also been mapped on chromosome 11. PA99N82-4 was crossed with a
susceptible selection to produce a progeny population segregating for resistance. Five resistant and
five susceptible seedlings segregating for resistance from PA99N82-4 were sequenced using Illumina
HiSeq 2000 and pooled in silico to perform Bulk Segregant Analysis for SNP discovery. Approximately,
32,510 genome contigs containing 161,775 high-quality SNPs that differentiated the susceptible pool
from the resistant pool and the SB22 reference genome have been identified. We are currently
validating SNPs coming from chromosome 11 for identifying markers linked to CRKN resistance in S.
bulbocastanum.
*707-TH. THE PERFECT MATCH: COMBINING ROOTSTOCKS THAT CONFER OROBANCHE
RESISTANCE AND HETEROTIC SFT HYBRID SCION OF PROCESSING TOMATO
Koch A.1, Hirschberg J.2, Zamir D.1
1
Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of
Jerusalem, Rehovot 7610001, Israel; 2Department of Genetics, The Hebrew University of Jerusalem,
Givat Ram, Israel
Contact: Amit Koch, [email protected]
Orobanche, (Broorape) is a root holoparasitic plant that causes severe damage to tomato crops
worldwide with yield losses of up to 100%. A key step in the Broomrape life-cycle is seed germination
which is followed by radicle growth to the host root, haustorium formation and attachment followed by
the establishment of an active connection with the conductive tissues of the host. The plants trigger
the germination of broomrape seed by the secretion of strigolactones from the host roots. The
objective of our research is to implement a genetic solution to the pest, which would be economically
viable in agricultural fields. Based on the study of Koltai et al. (2010) we screened a mutant collection of
the tomato variety M82 and identified seven mutants that showed a phenotype similar to strigolatone
deficient mutants and one of them n4129 had a recessive mutation in the ccd7 gene (which we call ST1).
Because strigolactones deficiency had a reducing effect on yield we used ST1 as a rootstock in
combination with the heterotic scion which was heterozygote for the single flower truss (SFT) mutation
(Krieger et al 2010). The advantage of the SFT hybrids is that they can be planted in the field at half the
density of regular tomato hybrids and produce comparable yield since the plants as much larger. Thus,
the combination of ST1 rootstock and SFT scion requires less grafted plants per unit area thus reducing
the costs of the seedlings in the field. Results will be presented of field trials in broomrape-infested
areas showing that the match of ST1 and SFT could be perfect for processing and fresh market tomato
hybrids in areas of Orobanche.
*708-TH. NEXT-GENERATION GENOTYPING OF SOLANUM TUBEROSUM GROUP PHUREJA
Juyó-Rojas D.1, De Koeyer D.2, Duitama J.3, Mosquera-Vasquez T.1
1
Universidad Nacional de Colombia, Bogotá, Colombia; 2Agricultural and Agri-Food Canada,
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Fredericton, NB, Canadá; 3International Center for Tropical Agriculture, Cali, Colombia
Contact: Teresa Mosquera, [email protected]
Next-generation genotyping offers several approaches which main objective is to discover,
sequencing and genotyping hundreds to thousands of markers across almost any genome of interest
in a single step. The next-generation sequence (NGS) approaches use methods depending on
restriction enzymes to fragment the DNA and to achieve a reduced genome complexity. Inside these
approaches are genotyping by sequencing (GBS) with two restriction enzymes and restriction site–
associated DNA (2b-RAD) with fragments produced by endonucleases type IIB. GBS involves the
digestion of genomic DNA with a frequent and a rare enzyme to obtain fragments with uniform size (90
to 100 bp) for subsequent sequencing.
Differently, in 2b-RAD type II, enzymes cut the DNA at precise positions close to or within their
recognition sites and short sequences with a length of 36 bp are produced. GBS and 2b-RAD
approaches use the advantages offered by NGS technology to discover and characterize a high
number of molecular polymorphisms. Here, we use these technologies to characterize genetically 150
accessions of Solanum tuberosum Group Phureja and discover single nucleotide polymorphism (SNP)
with the aim to establish the genetic diversity and the population structure analysis and lead to a better
understanding of the genetic architecture of complex traits and its application in genome wide
association studies (GWAS). We discovered 4,216 and 313 high quality SNPs with GBS and 2b-RAD
respectively. This result indicated that GBS technology was more cost-effective than 2b-RAD.
Additionally, with these SNPs were possible to identify that the population analyzed of Group Phureja
lacks of population structure and has a high diversity due to a higher number of heterozygotes and the
differentiation between individuals. Finally, the SNPs from GBS and 2b-RAD will have broad application
in genomics-assisted plant breeding programs.
ABIOTIC STRESSES
*905-TH. EFFECT OF WATER STRESS ON GROWTH, YIELD AND NUTRITIONAL QUALITY OF
SELECTED AFRICAN TOMATO ACCESSIONS
Ambuko J.,1 Tembe K1, Chemining’wa G1., Owino W.O.2
1
Department of Plant Science &Crop Protection, University of Nairobi, P.O Box 29053, Nairobi;
2
Department of Food Science & Technology, Jomo Kenyatta University of Agric. and Technology
Contact: Jane Ambuko, [email protected]
One of the limiting factors to the realization of Tomato (Solanum lycopersicum) crop’s yield potential in
developing countries such as Kenya is water stress. This study was undertaken with the objective of
determining the effect of water stress on selected growth, yield and nutritional quality attributes of
selected African tomato landraces. Twenty tomato accessions which were used in the study were
selected for their desirable agronomic traits from an initial population of 69 sourced from the World
Vegetable Centre (AVRDC). The greenhouse study was conducted at the University of Nairobi’s field
station in 2015. Two weeks after transplanting, the tomato plants were subjected to four watering
levels namely: 100%, 80%, 60% and 40% of the field capacity. Just before flowering, growth parameters
including plant height, single leaf area, and stem girth were measured. The total number and weight of
fruits per plant was determined at the end of the growing period. Fruits harvested at the full-ripe were
used to determine quality attributes including βeta-carotene, vitamin C, total phenolics and total
antioxidant activity. Results showed that the highest reduction in growth was < 30% for the lowest
watering level (40%). However significant (p<0.05) yield loss of 13 – 50% and 20 – 88% was observed
in the 60 and 40% watering levels respectively. On the other hand, the 60% watering level resulted in
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higher levels of total phenolics which ranged from 3.2 – 11.3Garlic acid equivalent (GAE)/100g in water
stressed tomatoes compared to 1.5 – 4. 9 GAE/100g in unstressed plants. Similarly total antioxidant
activity was higher in water-stressed plants (17.9 – 38.3% inhibition) compared to 13.25 – 29.3 %
inhibition in unstressed plants. On the contrary, water stress resulted in a significant reduction in
vitamin C and beta-carotene levels in all the accessions. The study revealed that some of the tomato
accessions can tolerate up to 40% reduction in water supply without significantly affecting growth and
yield. This stress level had a significant positive effect on some quality attributes of the accessions,
which is desirable is selection for tomato crop improvement.
*906-TH. GENETIC ARCHITECTURE OF FRUIT QUALITY AND GENE EXPRESSION IN CULTIVATED
TOMATO STRESSED BY WATER LIMITATION
Albert E.1, Duboscq R.1, Gricourt J.1, Duberos M.1, Latreille M.2, Santoni S.2, Gautier V.3, Poncet C.3,
Sauvage C.1, Causse M.1
1
INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Montfavet, France; 2UMR Diversité et
Adaptation des Plantes Cultivées, Montpellier SupAgro-INRA-IRD-UMII, Montpellier, France; 3INRA,
UMR1095 Génétique, Diversité et Écophysiologie des Céréales, Clermont-Ferrand, France
Contact: Elise Albert, [email protected]
Water scarcity will constitute a crucial constraint for agricultural productivity in the future. Advanced
irrigation strategies and development of drought-adapted crops are among the solutions to maintain a
reasonable productivity. Conjointly, deficit irrigation practices may constitute a way to meet consumer
needs of high quality fruits by exploiting the morphological, physiological and molecular changes
occurring in water stressed plants. Nevertheless, the genetic basis of response to drought remains
poorly understood in fleshy fruit crops. To elucidate the underlying genetic determinants in cultivated
tomato (S. lycopersicum), we studied two populations, one composed of recombinant inbreed lines
(RILs) and a second composed of unrelated ‘cherry type’ accessions, grown in greenhouse under two
watering regimes, in France and Morocco. Plants were phenotyped for a large set of yield and fruit
quality traits, including sugars, acids and vitamin C content in fruits. Taking advantage of high density
genotyping data available in both populations, QTLs and QTL by watering regime interactions were
mapped through linkage and association mapping. Besides, gene expression was measured through
RNAseq in leaves and green fruits of the RIL parents grown under both watering regimes. On the basis
of the differentially expressed genes in the parental accessions and the knowledge available in
literature, a hundred genes of interest were selected in the five main genomic regions carrying the
phenotypic QTLs. For those genes, expression was measured in the full RIL population by high
throughput microfluidigm qPCR approach and eQTLs were mapped. The results gathered will
contribute to tomato quality improvement under deficit irrigation.
*907-TH. ROLE OF THE MYB33, MYB101 AND THE MYB65 TRANSCRIPTION FACTORS IN PLANT
RESPONSE TO WATER DEFICIENCY
Wyrzykowska A., Pieczynski M., Jarmolowski A., Szweykowska-Kulinska Z.
Adam Mickiewicz University in Poznan, Institute of Molecular Biology and Biotechnology, Department
of Gene Expression, Poland
Contact: Anna Wyrzykowska, [email protected]
The goal of the project is to explain the role of the MYB33, MYB101 and the MYB65 transcription
factors in then Arabidopsis thaliana and Solanum tuberosum var. Desiree plants response to drought
stress. We rise a research hypothesis that among factors responsible for the increased plant tolerance
to water deficiency is the upregulated expression level of several MYBs genes. In our previous studies
we silenced expression of the CBP80/ABH1 gene that is involved in the ABA signaling pathway. In the
transgenic S.tuberosum amiR80.2-14 line, with no induction of the microRNA159 expression we
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observed the increased level of the MYB33 and the MYB101 genes expression, of which mRNAs are
targets of the miR159-mediated cleavage. The CBP80/ABH1 - silenced plants revealed the increased
tolerance to drought and show both physiological and phenotypical changes such as ABAhypersensitive stomatal closing, an increase in leaf stomata and trichome density, and compact cuticle
structures with a lower number of microchannels. We identified null Arabidopsis mutants of
the MYB101 and the MYB33 genes that are oversensitive to drought conditions in comparison to the
wild type plants. We observed changes in those mutants such as cuticle thickness, ABA induced
stomatal closing, leaf stomata and trichome density in comparison to WT. This result confirms our
hypothesis on the role of the MYB TFs studied in response to water deficiency. In this project we
obtained transgenic Arabidopsis and potato lines over-expressing MYB33, MYB65, and MYB101genes
under CaMV 35S promoter. Since we encountered trouble with plants transformation with construct
containing the MYB65 gene derived from potato, in both Arabidopsis as well as in S.tuberosum, we
plan to use ethanol induced promoter to overcome eventual toxic side effects of the MYB65 TF
overexpression during development of plants. The introduced MYB TF genes are mutated to be
resistant to miR159-guided cleavage. Wild type and mutant plants, cultivated in control and water
deficiency conditions will be compared (their phenotypes and selected physiological traits). We expect
that our results will help to better understand the connections and relationships between the various
genes studied and to determine their impact on water deficiency tolerance in plants.
*908-TH. NEW POTATO GENETIC ELEMENTS INVOLVED IN RESPONSE TO DROUGHT STRESS
Pieczynski M.1, Wyrzykowska A.1, Boguszewska-Mankowska D.2, Milanowska K.1, Hornyik C.3,
Jarmolowski A.1, Zagdanska B.4, Szweykowska-Kulinska Z.1
1
Adam Mickiewicz University in Poznan, Institute of Molecular Biology and Biotechnology, Department
of Gene Expression, Poland; 2The Plant Breeding and Acclimatization Institute (IHAR) - National
Research Institute, Division Jadwisin, Poland; 3The James Hutton Institute, Cell & Molecular Sciences,
Invergowrie, United Kingdom; 4 Warsaw University of Life Sciences, Department of Biochemistry,
Warsaw, Poland
Contact: Szweykowska-Kulinska Zofia, [email protected]
Two pairs of Polish closely related potato varieties (common one parent), differing strongly in tolerance
to water deficiency were selected. In each pair there is a cultivar sensitive to drought whereas the
other one is drought tolerant. Despite close relation within each pair, there is no close relation
between the pairs. Pairs differ greatly between each other in their strategy of drought toleration, they
differ in wilting behavior, dehydration avoidance and reductions in leaf assimilation area during
drought. Additionally, detailed morphological and physiological analysis showed differences between
the varieties with benefit for drought tolerant varieties in: stomatal and trichomes density, ABAdependent stomatal closing, cuticle thickness and relative water content.
Drought experiment and transcriptome sequencing at different time points upon drought and in control
conditions were carried out. Differentially expressed genes in drought-tolerant varieties in comparison
to drought-sensitive varieties were identified (47 and 174 upregulated, 64 and 142 downregulated
genes in each pair, respectively). We found well-known drought responsive genes as well as unknown
ones. Identified genes differ between the pairs of varieties confirming two different mechanisms of
drought tolerance. The results were validated by RT-PCR analysis. Within the group of the stringent
selected genes, most differing between varieties in each pair, nearly half were also identified as
drought related in rice during research by other group.
Additionally, genes with stable expression upon drought in all four cultivars studied were selected and
confirmed by RT-qPCR. New drought responsive potato microRNAs and their target genes were
identified and analysed. Some of these microRNAs differ in their expression levels between the
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cultivars that are drought sensitive and tolerant.
For the 7 selected genes (three upregulated and four downregulated), most differing between varieties
in each pair and with unknown function in drought toleration, Arabidopsis homozygous T-DNA
insertion mutants were selected. Drought experiment, together with relative water content analyses,
was carried out. We found that most of selected Arabidopsis mutant were much more tolerant to
drought in comparison to wild type plants. The results provide evidence that selected genes play
important role in plant response to drought.
*909-TH. XYLEM VASCULAR BUNDLE FUNCTIONALITY AND DEVELOPMENT IN RELATION WITH
THE SUSCEPTIBILITY OF DIFFERENT TOMATO CULTIVARS TO BLOSSOM-END ROT
Moalla R.1, Matsukura C.2, Ezura H.2, Fukuda N.2
1
Graduate School of Life and Environmental Sciences; 2Faculty of Life and Environmental Sciences,
University of Tsukuba, Tsukuba, Ibaraki, Japan
Contact: Rached Moalla, [email protected]
A reduction of calcium movement in plant body is one of the crucial factors to induce blossom end rot
(BER) symptom in tomato fruits. The increased ability of xylem bundles to uptake Safranine-O- from the
peduncle, known as xylem functionality, has been found to improve calcium movement toward the
fruit’s distal part, possibly causing an observed reduction in BER incidence. Namely, there is a
possibility that the difference of BER susceptibility among tomato cultivars, especially under salinity
stress, may be explained by their differences in xylem bundle functionality. In our previous study, -BER
resistant- Dutch tomato cultivar ‘Managua RZ’ showed an improved calcium content in its distal
pericarp under salinity stress condition in comparison with the control condition. On the other hand, BER susceptible- Japanese cultivar ‘Reiyoh’, showed drastically decreased calcium contents in its distal
pericarp under salt stress condition. From those results, we hypothesized that the functionality of xylem
bundle may be different among those cultivars, in its development levels, such as the number and size
of vessels. In this study, to make the relationship between fruit calcium uptake and xylem bundle
functionality clear, we evaluated the xylem bundle development under salinity stress condition in these
two cultivars. Xylem bundle density increased in the proximal and distal parts of ‘Managua RZ’ fruits
under salinity stress, while it only increased in the proximal part of ‘Reiyoh’ fruits. Furthermore,
although there was no difference in xylem bundle density between the proximal and distal part of
‘Managua RZ’ fruits, it was significantly lower in the distal part of ‘Reiyoh’ fruits as compared with the
proximal part. The proportion of functional xylem bundles out of the total number of bundles was of
71.6% and 28.9% in the proximal and distal part respectively, in ‘Managua RZ’ fruits, while it was less
than 2% in both fruit parts of ‘Reiyoh. This high ability to maintain the bundle density and functionality
in both the proximal and distal part of fruits, may explain the higher calcium contents and lower BER
incidence under salinity stress in ‘Managua RZ’ cultivar.
*910-TH. PROFILING NOVEL ROOT-SPECIFIC SALINITY BIOMARKERS IN TOMATO
Sadder M.S.1,2, Alsadon A.A.2, Wahb-Allah M.A.2, Ali A.A.2, Alshomali I.1
1
Department of Horticulture and Crop Science, Faculty of Agriculture, University of Jordan, Amman
11942, Jordan; 2Department of Plant Production, College of Food and Agricultural Sciences, King Saud
University, P. O. Box 2460, Riyadh 11451, Saudi Arabia
Contact: Ibrahim Alshomali, [email protected]
This study was conducted to investigate the influence of salinity stress on tomato root system. Seeds
of three advanced breeding lines (L45, L56 and L66) along with one check (tolerant accession BL 1076)
were germinated in Jiffy-7 peat pellets. Seedling were then grown in pots with soil mix (1:1:1 of
sand:peat moss:perlite). They were irrigated and fertigated as necessary for 40 days. The salinity
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treatment was conducted by irrigating with NaCl solution (EC = 7.2 dS m-1) for three times along one
week. Roots were collected and cleaned. Total RNA was isolated form roots and cDNA was
synthesized using reverse transcriptase. Eleven salinity stress biomarkers (Including calciumdependent protein kinase, universal stress protein family protein and Myb family transcription factor)
were assessed in stressed roots compared to the control. All gene expression leveled were calibrated
to the expression of actin. Quantitative real-time PCR was used to measure differential gene
expressions. The data showed slight increase in expression level of the salinity biomarker
serine/threonine-protein kinase receptor. On the other hand, the salinity biomarker WRKY transcription
factor 2 showed tangible fold increase in expression for all tomato lines, however, it was more
prominent in both tolerant line L56 and tolerant check BL 1076. Tomato root system revealed unique
profile of salinity biomarkers, which can be potentially applied in tomato breeding programs.
911-TH. BASAL ROOTS DO NOT INFLUENCE TUBER YIELD UNDER DROUGHT IN POTATO
Guardia-Velarde L., Farfán, E., Lozano, F., De Souza, J., Vega, J., Khan, A.
Genetic and Crop Improvement Division, International Potato Center, Perú
Contact: Lorena Guardia-Velarde, [email protected]
Potato, which is among the top five produced crops globally is also the most drought sensitive among
roots and tuber crops. Development of potato cultivars tolerant to drought has potential contribution
towards food security for the growing population in light of climate change. The objective of the study
was to identify important traits for adaptation to drought. Fifty-six contrasting clones developed at the
International Potato Center were evaluated for performance under drought. The clones were evaluated
in five environments around Peru under two treatments: i) normal irrigation and ii) terminal drought.
Root traits (basal root fresh and dry weight), above ground biomass traits (plant height, number of
leaves and fresh weight of above-ground biomass), tuber yield and yield component traits (number of
tubers, tuber fresh weight, harvest index and dry matter content of tubers) were measured. The data
was subjected to analysis of variance (ANOVA) and the relationship between clones, traits and
environments was established using GGE biplot analysis. Correlation among traits was examined
based on the predicted genotypic means across environments. The association between basal root
weight and harvest index was highly significant and negative whereas tuber fresh weight was
independent of basal root weight under terminal drought. Under normal irrigation, basal root weight,
above ground biomass, and tuber traits were all significantly and positively correlated. Dry matter
content of tubers was not associated with any other trait under normal irrigation conditions but was
moderately and negatively correlated with harvest index and tuber fresh weight under terminal
drought. Dry matter content was also moderately and positively correlated with basal root weight and
above ground biomass under terminal drought. These results indicate that basal roots are not
important for water uptake to the tubers but to above ground biomass. Other root classes not
measured in this study may be responsible for water uptake to the tubers. Dry matter content
increases under drought because basal roots may have a comparative advantage for depth and length
as compared to root classes responsible for the tubers thereby leading to less water being available
for the tubers. Selecting for genotypes with longer and steeper stolon roots may be important for
adapting genotypes to drought conditions on potato.
RESISTANCE, PATHOGENS, PESTS AND MICROBIOMES
1008-TH. GENETIC VARIABILITY OF PEPPER VEIN YELLOWS VIRUS (PVYV) FROM NATURALLY
INFECTED PEPPER FIELDS IN TURKEY
Buzkan N.1, Arpaci B.B.2, Yildiz A.G.1, Isikber A.A.1, Moury B.3
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Kahramanmaras Sutcuimam University, Agriculture Faculty, Plant Protection Department,
Kahramanmaras, Turkey; 2Kilis Yedi Aralik University, Agriculture Faculty, Horticulture Department,
Kilis, Turkey; 3INRA VR 407, Pathologie Vegetale, 84140 Montfavet , France
Contact: Nihal Buzkan,[email protected]
1
Pepper vein yellows virus (Polerovirus) was first described in peppers grown in open fields in Turkey by
Buzkan et al., (2013). The disease syndrome includes interveinal yellowing accompanied by fruit
discoloration. Due to its high prevalence respect to potyviruses and CMV widespread in Mediterranean
Basin, the genetic structure of PVYV populations was investigated in naturally-infected greenhouse
and open fields. DAS-ELISA was used to detect PVYV with CABYV polyclonal antiserum because of
the lack of specific antibodies to PVYV and presence of serological cross-reactions between these
viruses. Characterization of the viral populations was done by RT-PCR with samples that reacted
positively to CABYV in DAS-ELISA using primers Pol-G-F and Pol-G-R designed to hybridize to
conserved regions in the polerovirus genome. Sequences of pepper poleroviruses were aligned with
sequences representing the other species in the genus Polerovirus. Positions of the sequence
alignment corresponding to gaps were removed, providing a 485-nucleotide-long alignment,
corresponding to the 3’ end of the RNA-dependent RNA polymerase coding region. Then, phylogenies
were generated by neighbor-joining method in MEGA5, and 500 bootstrap resamplings were used to
assess the robustness of branches. The Turkish (TK) isolates were grouped in different branches in
phylogenetic tree. The isolate TK1173 had nucleotide homology with from PYLCV-Israel (HM439608),
CaYV-Turkey (FN600344) and some Tunisian isolates while TK 834 was only related to the Turkish
isolate reported from the same location previously (HE978265). Some PVYV-like isolates had high
nucleotide identity with Chinese isolates of TVDV.
*This research was granted by TUBITAK (113 O 423).
1009-TH. GENETIC VARIABILITY OF BEET WESTERN YELLOWS VIRUS (BWYV) FROM NATURALLY
INFECTED PEPPER FIELDS IN TURKEY
Buzkan N.1, Arpaci B.B.2, Yildiz A.G.1, Isikber A.A.1, Moury B.3
1
Kahramanmaras Sutcuimam University, Agriculture Faculty, Plant Protection Department,
Kahramanmaras, Turkey; 2Kilis Yedi Aralik University, Agriculture Faculty, Horticulture Department,
Kilis, Turkey; 3INRA VR 407, Pathologie Vegetale, 84140 Montfavet , France
Contact: Nihal Buzkan, [email protected]
Beet western yellows virus (BWYV), a species of the genus Polerovirus (family Luteoviridae), is an
agriculturally important virus infecting over 150 plant species in 23 dicotyledonous families worldwide.
An isolate of this virus was first described in Turkey, the first polerovirus reported to infect cultivated
pepper naturally and to cause a severe disease (Buzkan et al., 2013). The genetic structure of BWYV
populations was investigated in naturally-infected greenhouse and open fields. DAS-ELISA was used to
detect BWYV with CABYV polyclonal antiserum because of the lack of specific antibodies to the virus
and presence of serological cross-reactions among the viruses in the genus Polerovirus.
Characterization of the viral populations was done by RT-PCR with samples that reacted positively to
CABYV in DAS-ELISA using primers Pol-G-F and Pol-G-R designed to hybridize to conserved regions in
the polerovirus genome. Sequences of pepper poleroviruses were aligned with sequences
representing the other species in the genus Polerovirus. Positions of the sequence alignment
corresponding to gaps were removed, providing a 537-nucleotide-long alignment, corresponding to
the 3’ end of the RNA-dependent RNA polymerase coding region. Then, phylogenies were generated
by neighbor-joining method in MEGA5, and 500 bootstrap resamplings were used to assess the
robustness of branches. The Turkish (TK) isolates were grouped in different branches in phylogenetic
tree. The isolate TK926 from southeast Anatolia had nucleotide homology with the isolates
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(HE978258,HE978260, HE978257) reported by Buzkan et al., (2013). Four isolates of different pepper
genotypes in two regions had nucleotide identity with Tunisian (HE978253, HE978254) and American
(HM804471) isolates.
*This research was granted by TUBITAK (113 O 423).
1010-TH. PREVALANCE OF TOBACCO ETCH VIRUS (TEV) FROM NATURALLY INFECTED PEPPER
FIELDS IN TURKEY AND POPULATION GENETICS OF HATAY ISOLATES
Buzkan N.1, Yildiz A.G.1, Arpaci B.B.2
1
Kahramanmaras Sutcuimam University, Agriculture Faculty, Plant Protection Department,
Kahramanmaras, Turkey; 2Kilis Yedi Aralik University, Agriculture Faculty, Horticulture Department,
Kilis, Turkey
Contact: Nihal Buzkan, [email protected]
The prevalance and genetic structure of Tobacco etch virus (TEV) (Potyvirus) was investigated in
naturally-infected pepper (Capsicum annuum) fields in eleven pepper growing locations (Samsun,
Bursa, Çanakkale, Balikesir, Izmir, Manisa, Antalya, Mersin, Hatay, Kilis, Sanliurfa) in Turkey. Total of
1747 pepper plants were evaluated for symptoms, such as leaf mottles, mosaic pattern, vein banding,
leaf curling, plant stunting in open-field and greenhouse. Leaves and fruit samples were tested by
DAS-ELISA using TEV polyclonal antiserum (Agdia). Samples resulting positive in ELISA were subjected
to total nucleic acid isolation to test in RT-PCR. Approx. 15,91% of plants were positive for TEV in ELISA
test. The highest number of virus infected samples was from Bursa (40,98%) in northwest and the least
was from Sanliurfa (3,39%) in southeast Anatolia regions. Population genetics of TEV was evaluated
with 26 isolates from Hatay (Eastern Mediterranean) according to coat protein coding region and
blasted with other isolates in GeneBank. The most isolates from Hatay except five isolates created
three distinct groups and they were phylogenetically related to Chinese isolates
*This research was granted by Scientific Research Projects Comission at KSU (2015/1-7YLS).
1011-TH. TRICHOME CHARACTERIZATION OF CULTIVATED POTATO, SOLANUM
TUBEROSUM AND ITS WILD REALTIVE CLONES
Cho K-S.1, Kwon M.1, Cho J-H.1, Im J-S.1, Jin Y-I.1, Jang D-C.1, Hong S-Y.1, Hwang I-T.2, Kang J-H.2
1
Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development
Administration, Pyeongchang 25342, Republic of Korea; 2Lab. of Seed Biotechnology, Institute of
Green Bio Science and Technology, Seoul National University, Pyeonngchang 25354, Republic of
Korea
Contact: Kwang-Soo Cho, [email protected]
Structural characterization of trichome in cultivated potato and 17 wild relative potato was examined
with FESEM (Field Emission Scanning Electron Microscopy). Four main trichome types were identified
by their morphology (glandular type A and B, non-glandular type II and III). Potato glandular type A
(tomato trichome type VI) characterized by short multi-cellular stalk with four-celled globular heads and
glandular type B (tomato trichome type VII) characterized by a very short stalk with irregularly shaped
heads (4 to 8). And non-glandular type II and type III have long multi-cellular stalk with multi-cellular
base and multi-cellular stalk with unicellular base, respectively. Based on the trichome density, we
could classified wild relative potato clones into six groups. First group including S. mochiquense,
S.raphanifolium, S. vernei have high density only non-glandular type in abaxial side. Second group, S.
berthaultii have high density of glandular type A. Third group, S. hugasii have high density of glandular
type B. Fourth group, S. microdontum have non-glandular type II and glandular type A. Fifth group, S.
tuberosum, S. acaule S. brevicaule, S. chacoense, S. pinnatisectum have low density in glandular and
non-glandular trichomes. And the other 7 species, S. cardiophyllum, S. hjertingii, S. iopetalum, S.
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jamesii, S. kurtzianum, S. stoloniferum, S. verrucosum, have very little number of trcihomes. We will
investigate metablome and transcriptom of six categories of wild relatives compared with cultivated
potato. And the response to insects including sucking pest, Aphid and chewing pest, larger potato lady
beetle will be analyzed.
1012-TH. EMERGENCE AND GENETIC DIVERSITY OF TOMATO YELLOW LEAF CURL
VIRUS (TYLCV) INFECTING SOLANACEOUS CROPS IN SOUTH AND SOUTHEAST ASIA
Arunothayanan H., Struss D.
East-West Seed, Chiang Mai, Thailand
Contact: Hatthaya Arunothayanan, [email protected]
Whitefly-transmitted geminiviruses (begomoviruses) have emerged in many tropical and subtropical
regions of the world as an important constraint to the production of solanaceous crops, particularly
tomato (Solanum lycopersicum) and peppers (Capsicum spp.). Tomato yellow leaf curl virus (TYLCV) is
one of tomato-infecting begomoviruses causing the tomato yellow leaf curl disease (TYLCD) in tomato
worldwide. TYLCV induces the most obvious symptoms in tomato such as the severe plant growth
reduction and typical yellowing and curling of the leaves. TYLCV is transmitted by B-biotype
whitefly Bemisia tabaci in a persistent, circulative manner. South and Southeast Asia seem likely to be
a major center of diversity for begomoviruses and some species may have spread across the region
and displaced local species due to the intensively grown vegetable production in this region. Genetic
diversity analysis of the nucleotide and amino acid sequences of the viral coat protein gene (AV1) of
begomovirus in the symptomatic tomato and eggplant samples revealed that Tomato yellow leaf curl
Thailand virus (TYLCTHV) is the cause of leaf curling and yellowing of tomato plants in India and
Thailand. Despite of tomato-infection by TYLCTHV, the distinct Tomato yellow leaf curl Kanchanaburi
virus (TYLCKaV) was detected not only in tomato plants with leaf curl and yellowing, but also in
eggplant with yellow-mosaic symptom collected in Thailand. While TYLCV has only a single DNA-A-like
genome component (monopartite), TYLCTHV and TYLCKaV have bipartite genome (DNA-A and DNAB) which are distinct from other monopartite old world begomoviruses. Not only were the infections of
TYLCTHV and TYLCKaV found in tomato and eggplant, but TYLCTHV was also detected in the
suspected geminivius-infected pumpkin whereas TYLCKaV was detected in the symptomatic
cucumber collected in Thailand. The detection of TYLCTHV and TYLCKaV in cucurbit crops could be
the result of recombination between strains, which is important in virus evolution, causing the greater
spread of viruses from native vegetation into, and within, exotic crop species.
1013-TH. ALLELIC DIVERSITY IN EFFECTORS GENES OF Phytophthora infestans sensu lato
Gómez S.Y.1, Morales J.G.1, Muñoz M.1, Franco B.1,3, Restrepo S.2, Birch P.B.J.3
1
Laboratorio de Fitotecnia Tropical, Departamento de Ciencias Agronómicas, Facultad de Ciencias
Agrarias. Universidad Nacional de Colombia sede Medellín., Medellín, Antioquia, Colombia; 2Facultad
de Ciencias, Universidad de Los Andes, Bogotá, D.C, Colombia; 3Cell and Molecular Sciences, James
Hutton Institute, Invergowrie, Dundee, UK
Contact: [email protected], [email protected]
The potato late blight pathogen Phytophthora infestans sensu lato secretes a wide array of effector
proteins which are thought to act in its hosts by disarming defences and promoting an environment
conducive to pathogen colonisation. In this work, 12 of these effector genes were selected from
previous work to determine if there is allelic variation within the Colombian population. Effector
sequences were amplified from isolates obtained from cultivated and non-cultivated hosts such as
potato (S. tuberosum), tree tomato (S. betaceum), lulo (S. quitoense), S. muricatum and other Solanum
sp. Synonym and non-synonym substitution analyses suggested that some genes are under positive
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selection. Implications of these findings for P. infestans pathogenicity evolution and late blight disease
management are discussed.
*1014-TH. HYPERSENSITIVE RESPONSE OF SOLANACEOUS HOSTS TO EFFECTOR PROTEINS
OF Phytophthora infestans sensu lato
Gómez S.Y.1, Morales J.G. 1, Gaviria A.E.1, Hein I.2, Birch P.B.J.2
1
Laboratorio de Fitotecnia Tropical, Departamento de Ciencias Agronómicas, Facultad de Ciencias
Agrarias. Universidad Nacional de Colombia sede Medellín., Medellín, Antioquia, Colombia.; 2Cell and
Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, UK
Contact: [email protected], [email protected]
The plant pathogen Phytophthora infestans sensu lato causes late blight not only in potato but in a
number of Solanaceous cultivated and wild hosts worldwide. To introduce resistance to the late blight
disease into cultivated plants, classical breeding based on genetic crossing with ancestral species
like S. demisum and S. bulbocastanum was the most employed tool used in the past. But due to the
ability of the pathogen to overcome the host defence mechanisms, new techniques to find resistance
genes are needed. Effectoromics has recently emerged as a powerful tool to identify resistance (R)
genes and matching avirulence (Avr) genes of plant pathogens. In this work, the response induced by
ten genes coding for effector proteins in P. infestans were determined in a group of
Solanaceous plants including crop plants such as S. tuberosum, S. phureja, S. betaceum and wild
hosts such as S. sibundoyensis and S. huilensis. Effector genes were agro-infiltrated, using a binary
PVX-Agrobacterium tumefaciens vector. HR process was verified by histological staining confirming
the response. Tolerant accessions of potato to late blight were able to recognize most of the RXLR
genes tested as well as S. sibundoyensis and S. huilensis, the wild relatives of S. betaceum.
Implications for Solanaceous crops breeding are discussed.
*1015-TH. TOMATO PEPR1 ORTHOLOGUE RECEPTOR-LIKE KINASE1 (PORK1) REGULATES
RESPONSES TO FUNGAL INFECTION AND WOUNDING THROUGH INTERACTION WITH TPK1B
Xu S.1, Liao C.J.1, Lee S.1, Carrillo J.2, Garvey M.2, Yoon G.M.1, Kaplan I.2, Mengiste T.1
1
Department of Botany and Plant Pathology; 2Department of Entomology, Purdue University, West
Lafayette, IN, USA
Contact: Siming Xu, [email protected]
Damage-Associated Molecular Pattern (DAMP) Triggered Immunity (DTI) has emerged as an important
component in plant defense responses to pathogens and herbivorous pests. In Arabidopsis, two
closely related receptor-like kinases Pep1 Receptor1 (PEPR1) and PEPR2 recognize Pep1, a 23-amino
acid endogenous peptide, which triggers DTI to oomycete, bacterial and fungal pathogens. The
PEPR1/2 Orthologue Receptor-like Kinase1, PORK1, was identified in tomato and studied for its
molecular and biological functions and biochemical links to other components of tomato immune
regulators. The SlPORK1 expression was induced by mechanical wounding and pathogen infection.
Suppression of SlPORK1 through Virus-induced gene silencing (VIGS) showed increased susceptibility
to the necrotrophic fungus Botrytis cinerea accompanied by reduced expression of PROTEINASE
INHIBITOR II (PI-II), a known defense marker in tomato. Notably, expression of PI-II in responses to both
mechanical wounding and systemin, an 18-amino acid endogenous peptide of tomato, were
compromised in SlPORK1-silenced plants. We found interaction between SlPORK and Tomato Protein
Kinase 1 (TPK1b), which is required for defense responses to B. cinerea and larvae of tobacco
hornworm (Manduca sexta). SlPORK1 and TPK1b were phosphorylated in response to wounding and
systemin following Agrobacterium-mediated transient expression in Nicotiana benthamiana.
Interestingly, in transgenic tomato overexpressing TPK1b, phosphorylation of TPK1b in response to
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wounding and systemin were dramatically compromised when SlPORK1 is suppressed. SlPORK1 is a
functional kinase with autophosphorylation and phosphorylation of TPK1b. In summary, we
demonstrate that Tomato PORK regulates fungal resistance and responses to wounding through
interaction with TPK1b.
*1016-TH. ASSESSMENT OF TOMATO GENOTYPES FOR RESISTANCE TO BACTERIAL SPOT
AlBallat I. A.2, Panthee D.R.1
1
Department of Horticultural Science, Mountain Horticultural Crops Research &Extension Center, North
Carolina State University, Mills River, NC 28759, USA; 2Horticulture Department, Tanta University,
Tanta, Egypt
Contact: Ibrahim A. Alballat, [email protected]
This study was aimed to assess the bacterial spot caused by Xanthomonas perforans race T4 in 33
tomato hybrid developed from a combination of different resistance sources. They were evaluated
along with 13 tomato lines as controls, in a randomized block design with two replications at MHCREC,
Mills River, NC, USA from May to September 2015. We evaluated the disease severity and transformed
the data into area under disease progress curve (AUDPC). The analysis of variance and grouping of
AUDPC means were presented. Five out of 33 hybrids including NC 25P X Fla 7060_216, NC 22L1(2008) X Fla 7060_216, NC 25P X Fla 7060_Xv4, NC 5Grape X Fla 7060_Xv4, and NC 6Grape X Fla
7060_Xv4 showed lower mean AUDPC than the controls indicating that they may show some promise
for bacterial spot resistance. In these hybrids, the source of resistance gene is contributed
through male parent. These hybrids are being further evaluated to confirm the results in 2016.
Key words: Xanthomonas perforans; Solanum lycopersicon; biotic stress; AUDPC.
PLANT DEVELOPMENT AND REGULATION
1306-TH. A HAIRY STORY: HOW IS TRICHOME DEVELOPMENT CONTROLLED IN TOMATO
Galdon-Armero. J.1, Zhou, J.2, Martin, C.1
1
John Innes Centre, Norwich Research Park, Norwich, United Kingdom; 2The Genome Analysis Centre,
Norwich Research Park, Norwich, United Kingdom
Contact: Javier Galdon-Armero, [email protected]
Trichomes are epidermal outgrowths or hairs that cover the surface of aerial plant tissues. In cultivated
tomato (Solanum lycopersicum), trichomes produce a wide range of interesting secondary metabolites
and play important roles in defense against herbivores. In spite of agricultural and commercial interest
in trichomes, research on their initiation and development has been carried out mainly in Arabidopsis
thaliana. Studies in tobacco and tomato have shown that the regulatory pathways identified
in Arabidopsis are not shared by species outside the Rosid clade. Moreover, eight different types of
trichomes have been described in Solanum, including both glandular and non-glandular trichomes, in
contrast to Arabidopsis, where only one type of non-glandular trichome is present. The lack of a model
to explain the initiation, development, identity and spatial distribution of trichomes in tomato limits
realising the full exploitation of trichome engineering for crop improvement.
In order to gain insights into trichome development and its relationship to the development of other
epidermal cell types (stomata and pavement cells), we screened a population of 76 S.lycopersicum cv.
M82 x Solanum pennellii introgression lines (IL) to search for quantitative trait loci (QTLs). By scanning
electron microscopy (cryo-SEM) screening of mature leaf surfaces, we evaluated the outer epidermis of
the ILs and characterised their trichome phenotypes. Using machine-learning image analysis tools we
identified 6 QTLs involved in determination of trichome density. We observed an inverse association
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between the density of trichomes and the density of stomata, suggesting an early commitment step in
the determination of these alternative specialized cell types. The alternative choices in epidermal cell
fate determination are likely to have profound effects on the tolerance of tomato to abiotic stresses
such as drought. By assessment of aberrant trichomes present in specific ILs, we also identified
genomic regions responsible for correct growth and development of multicellular trichomes
in Solanum species. Finally, we observed an absence of specific types of trichomes in some ILs,
pointing towards the existence of genes regulating trichome identity. The IL screening has improved
our understanding of the development of epidermal cell types, and has established a foundation for
further characterisation of the identified loci at a gene-level resolution.
1307-TH. TOMATO AtORE1 ORTHOLOG SILENCING IMPACTS LEAF PHOTOSYNTHESIS AND FRUIT
METABOLISM.
Lira B.S.1, Gramegna G.1, Trench, B.1, Alves F.R.R.1, Silva E.M.2, Silva G.F.F.2, Nogueira F.T.S.2, Freschi L.1,
Rossi M.1
1
Botany Department, Biosciences Institute, University of São Paulo (USP), São Paulo, Brazil; 2Biological
Sciences Department, College of Agriculture “Luiz de Queiroz” (ESALQ), University of São Paulo (USP),
Piracicaba, Brazil
Contact: B.S. Lira, [email protected] (http://www.ib.usp.br/botanica/gmp/en/)
The NAC (NAM/ATAF/CUC) transcription factors (TF) comprise an extensive family involved in the
regulation of a wide spectrum of processes. In particular, the Arabidopsis thaliana AtORE1 is known to
be a key trigger for leaf senescence initiation, additionally, this protein physically interacts with GLK
TFs, which are essential for chloroplast development and maintenance, preventing their activity of
target upregulation. Thus, AtORE1shifts the signal from chloroplast maintenance towards deterioration.
Up to date, only 5 out of 101 tomato (Solanum lycopersicum) putative NAC TFs were studied.
Additionally, the knowledge regarding the impact of leaf senescence regulation over freshly fruit
development and ripening is also scarce. In this context, we aimed to gain further insight into how leaf
senescence affects tomato fruit growth and metabolism by identifying and modulating tomato AtORE1
ortholog. The search for AtORE1 ortholog in tomato genome led to the identification of three
candidates, namely SlORE1S02, SlORE1S03 and SlORE1S06. By in silico sequence analysis, transcript
sequencing and in vivo mRNA profile of tomato transgenic lines overexpressing miR164, we verified
that SlORE1S03 and SlORE1S06 were miR164 targets, but not SlORE1S02, possibly by an insertion that
disrupted the binding site. Additionally, the three putative orthologs are capable of physically interact
with both SlGLKs. Since all three candidates are similarly regulated except for SlORE1S02, we have
generated tomato knockdown lines for this gene. The transgenic lines had, at least, 54% less
transcripts in non-senescent leaves, which also displayed an increase in SlGLK1 mRNA levels and
enhanced carbon assimilation. Maintaining detached leaves in dark induced senescence in nontransgenic lines, but not in SlORE1S02-knockdown lines. Collectively, these data indicate that the
manipulation of SlORE1S02 altered the leaf senescence process, so we addressed the impacts over
fruit development and metabolism. As major sinks, it would be reasonable to hypothesize that the
above described alterations would enhance fruit metabolism. Indeed, for instance, the pericarp of ripe
fruits had an increase in soluble solid (Brix) content. In summary, we have characterized the regulation
of a still unknown tomato NAC TF that is involved in leaf senescence initiation and addressed its
physiological role in vegetative and fruit development.
1308-TH. PHYTOCHROME INTERACTING FACTORS IN TOMATO: DIVERSITY, EVOLUTIONARY
HISTORY AND EXPRESSION PROFILING DURING DIFFERENT DEVELOPMENTAL PROCESSES
Rosado D.1, Granegba G.1, Cruz A.1, Freschi L.1, de Setta N.2, Rossi M.1
1
Botany Department, Biosciences Institute, University of São Paulo (USP), São Paulo, Brazil; 2Center for
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Natural and Human Sciences, Federal University of ABC, Santo André, SP, Brazil
Contact: Giovanna Gramegna, [email protected] (http://www.ib.usp.br/botanica/gmp/en/)
Light signals are fundamental for plant physiology, providing not only energy for photosynthesis, but
also environmental cues for the maintenance of daily rhythms and developmental progression through
the life cycle. Phytochrome-interacting factors (PIFs) are basic helix-loop-helix (bHLH) transcription
factors that play a key role in light signal transduction being part of the regulatory network of a wide
range of developmental processes. After germination, PIF proteins accumulate in the dark inducing
hypocotyl elongation and inhibiting chlorophyll biosynthesis and chloroplast development. When
exposed to light, as PIF levels decrease, seedlings turn green and photomorphogenic growth begins.
In adult plants, PIFs induce nocturnal daily growth and regulate dark-induced leaf senescence,
activating many senescence associated genes and leading to chlorophyll breakdown and plastid
degradation. Chloroplast maintenance in source leaves and chloroplast to chromoplast transition
during fruit ripening are important to determine crop yield and quality of fleshy fruits. In this context
and considering the poorly available knowledge about PIF genes in tomato, we performed a
comprehensive characterization of this gene family in S. lycopersicum. In particular, we identified eight
PIF loci in the tomato genome. The phylogenetic and evolutionary analysis allowed us to reconstruct
the evolutionary history of PIF genes in S. lycopersicum and closely related Solanaceae species, the
wild tomato S. pennellii and S. tuberosum. To evaluate the functional diversity of tomato PIF genes, we
further explored the transcriptional profile in different physiological contexts, such as deetiolation,
dark-induced senescence, daily cycle and fruit ripening. Interestingly, PIF genes displayed oscillation in
the mRNA accumulation pattern at least along one of the analyzed experimental conditions and the
expression profiles identified suggest that they have undergone functional specification.
1309-TH. EXPRESSION PATTERN OF SHOOT REGENERATION-RELATED GENES IN THREE NEAR
ISOGENIC LINES OF TOMATO (Solanum lycopersicum CV. MICRO-TOM) WITH HIGH
ORGANOGENIC CAPACITY
Pinto M.S.1, Abeyratne C.R.2, Benedito V.A.2, Peres L.E.P.1
1
Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences, Escola
Superior de Agricultura ‘Luiz de Queiroz’ (ESALQ), University of São Paulo (USP) Piracicaba, SP, Brazil;
2
Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
Contact: Vagner A. Benedito, [email protected]
The use of tomato (Solanum lycopersicum) as A model to study natural genetic variations affecting in
vitro organogenesis is attractive due to the existence of several tomato wild relatives with enhanced
organogenic capacity. Among them, we highlight the species S. pennellii. Near isogenic lines (NILs)
were created by introgressing S. pennellii alleles conferring high organogenic capacity into the tomato
genetic model cv. Micro-Tom (MT). The NILs MT-Rg3C, MT-Rg7H and MT-Rg8F were evaluated for their
capacity to regenerate shoots and roots in vitro. All three NILs has enhanced shoot and root
regeneration in the MT background. We also evaluated the expression of genes known to be involved
in shoot regeneration to better characterize the involvement of these alleles in this developmental
pathway. We monitored the expression patterns of SHOOT MERISTEMLESS (STM), CUP-SHAPED
COTYLEDON 2 (CUC2), WUSCHEL (WUS), and MONOPTEROS (MP) in important points of shoot
regeneration: before exposing explants to the medium (day 0), one and two days after incubation on
shoot induction medium (SIM) (acquisition of competence), six days after incubation on SIM (shoot
induction) and at the end of the incubation period (day 21). The expression patterns of the genes
analyzed in the three NILs were dissimilar, suggesting that these loci affect regeneration capacity
through distinct pathways. A large increase of GOB expression in MT-Rg3C explants, compared to MT,
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was observed after six days of incubation on SIM, suggesting that the allele Rg3C and GOB may be
acting in the same pathway enhancing the acquisition of competence. Amongst all genotypes studied,
WUS expression was significantly higher on day 1 in MT-Rg7H explants, which may indicate that
meristem formation in MT-Rg7H started earlier than in the other genotypes. Also, the high expression
of STM and MP in the day two of incubation in MT-Rg7H explants corroborates the idea that shoot
induction in this NIL started earlier than in the other introgressed lines. Regarding MT-Rg8F, the main
difference in expression compared to MT was that GOB was already expressing in the explant before
incubation (day 0), which may be related to its slight difference of lobe formation in its leaves.
*1310-TH. CHARACTERIZATION OF THE TOMATO ODORLESS-2 MUTANT
St. Aubin B.1,2, Kang J.-H.2, Howe G.2,3
1
Department of Plant Biology, 2Department of Energy-Plant Research Laboratory, and 3Department of
Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
Contact: Brian St. Aubin, [email protected]
Glandular trichomes on tomato produce a variety of secondary metabolites that are implicated in
defense against insects. The recessive odorless-2 (od-2) mutation impairs trichome development and
also disrupts the production of secondary metabolites within gland cells. As a consequence, od-2
mutant plants are compromised in resistance against insect herbivores. Genetic mapping and wholegenome sequencing of the mutant revealed a nucleotide polymorphism that is predicted to disrupt a
gene involved in lipid metabolism. The roles of these lipids in trichome development and function
remain unclear. RNA-seq analysis and genetic complementation experiments are currently being used
to address this question. Our studies of the od-2 mutant support the growing understanding of
glandular trichomes as chemical factories for the production of specialized plant metabolites.
*1311-TH. CHARACTERISATION OF CANDIDATE GENES DOWNSTREAM OF THE MASTER
REGULATOR RIN IN TOMATO SOLANUM LYCOPERSICUM
Gillan J.C.1, Eugenia E.M.A.1, Seymour G.B.2, Rickett D.V.3, Hodgman C.2, Fraser P.D.1
1
School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK; 2Plant
Sciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK; 3Syngenta Jealott's
Hill, Bracknell, West Berkshire, UK
Contact: Jack Gillan, [email protected]
Tomato (Solanum lycopersicum) is one of the most extensively consumed fruit crops worldwide.
Therefore, the identification of genes central to fruit development and ripening, which influence both
the quality and nutritional content of the fruit, remains an important objective. Previous work revealed
that RIN (ripening-inhibitor) is a master regulator for normal fruit ripening; influencing fruit softening,
carotenoid accumulation and aroma formation. The rin mutation significantly delayed fruit softening,
potentially extending the shelf life of the fruits; however, it negatively impacted many other important
quality traits. Therefore, downstream targets of RIN have been identified for a more targeted approach
for tomato improvement using; Systems Biology outputs derived from transcriptomics performed over
fruit ripening and development. Three transcription factors downstream of RIN were identified and
knocked out using constructs under constitutive control. Combined phenotypic, metabolite and
expression analysis aims to characterise the function of these candidate genes. The results indicate
that the transcription factors are important to normal fruit ripening; as the constructs have similar
affects to the fruit of the RIN mutants by altering the pigment content and reducing the rate of
softening. However, the constructs improve other commercially important quality traits by increasing
the rapidity of ripening whilst showing the potential to increase total fruit yield. The project aims to
elucidate how these transcription factors influence fruit ripening, and how further manipulation can
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create varieties with improved physiological and quality traits.
*1312-TH. THE DELAYED FRUIT DETERIORATION (DFD) GENOTYPE AS A MODEL TO STUDY THE
RELATIONSHIP BETWEEN TOMATO FRUIT CUTICLE PROPERTIES AND SOFTENING, AND THE
HISTORY OF TOMATO DOMESTICATION
Romero P.1, Fernandez-Pozo N.2, Strickler S.R.2, Mueller L.A.2, Rose J.K.C. 1
1
Section of Plant Biology, School of Integrative Plant Science, Cornell University, NY, USA; 2Boyce
Thompson Institute, Ithaca, NY, USA
Contact: Paco Romero, [email protected]
Fruit softening is a complex process that involves substantial cell wall metabolism and changes in
cellular water status, although the relative contributions of these phenomena, and the molecular bases
of their control are not well understood. Fruit of the tomato genotype delayed fruit deterioration (dfd)
exhibit remarkable shelf life and maintain external quality for many months after ripening, thus
providing an excellent model to study textural changes during ripening. dfd fruit show an exceptionally
slow decrease in firmness, high desiccation resistance and low susceptibility to microbial infection and
these traits have been correlated with high levels of cutin, a structurally complex polyester that
constitutes the main component of the cuticle. We have been using a broad range of approaches to
investigate how the composition of cutin and cuticular waxes affect cuticle properties and how these,
in turn influence fruit quality, using dfd as an experimental model. This multidisciplinary approach
allows us to correlate biochemical, molecular and biomechanical data with physiological characteristics
and elucidate the molecular basis of fruit softening. In addition, we have sequenced the dfdgenome
and performed a survey of heterozygosity in comparison with a range of other tomato cultivars and
wild tomato species, to address the hypothesis that the dfd genotype is ancestral to most modern
cultivars. A deeper study of this genomic information will suggest candidate genes involved in fruit
quality and highly extended shelf life.
*1313-TH. ISOLATION AND CHARACTERIZATION OF CURLY LEAF TOMATO MUTANTS
Pulungan S.I., Ariizumi T., Ezura H.
Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
Contact: Sri Imriani Pulungan, [email protected]
Tomato (Solanum lycopersicum L.) is an economically important crop in either tropical or temperate
region. As a model plant, research in tomato has received much interest including organ and fruit
development researches. Formation of a normal leaf is a complex process that involves the initiation
and differentiation of leaf primordia from the shoot apical meristem (SAM), specification of leaf identity,
the establishment of leaf polarity, the control of cell division and expansion, and vascular pattern
formation. Any imbalance of these developmental processes results in altered leaf shape. The division
of abaxial and adaxial is also the key of growth of the lamina. However, how the polarity is maintained
remains unclear. Our research group has developed tomato mutant population generated by gamma
ray irradiation and EMS treatment in Micro-Tom tomato cultivar background. Here, we are
characterizing curly leaf (curl) tomato mutants which dorsoventrally impaired of leaf flatness, exhibiting
severe upward bend on transverse axis. The objectives of this study are (1) to characterize morphology,
hormone, and cytology of the curl mutants, (2) to investigate the responsible gene controlling the
mutant phenotype and to characterize its function in leaf morphogenesis. Segregation analysis and
allelism test had proved that occurred mutation was monogenic recessive and all mutants were allelic.
Map-based cloning had demonstrated that mutation is located in short arm of chromosome 9.
The curl produced impaired leaf curvature, along transverse axis with high extent. By contrast,
longitudinal axis remained flat. The upward curvature was initiated from the tip of leaf, followed by the
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middle and the basal area. In the mature leaves, all leaf had turned to curve, the highest extent was
observed in the middle of leaves. In addition, the curl mutants showed narrower leaf and shorter
petiole. Furthermore, mutants showed greener and glossy leaf. What is gene mutated, cell division,
adaxial-abaxial polarity, and auxin response will be investigated to dissect the complicated process of
leaf morphogenesis of the curl mutants.
*1314-TH. RESOURCES OF GENETIC DIVERSITY TO IMPROVE FRUIT QUALITY: HEIRLOOM
VARIETIES
Tang Y.P.1,2, Powell A.L.T.1, Yu Q.H.1,2, Yang S.B.1,2, An Y.1,3, Wang B.K.2, Li N.2, Vincenti-Martinez E.1,
Blanco-Ulate B.1, Yu Q.H. ,2, Bennett A.1
1
Plant Sciences Department, University of California, Davis 95616, 2Xinjiang Academy of Agricultural
Science, Urumqi Xinjiang, P. R. China, 3Beijing Forestry University, Beijing, P.R. China
Contact: Yaping Tang, [email protected]
Tomato (Solanum lycopersicum) fruit are regarded as sinks of photosynthate carbon fixed by leaf
chloroplasts. However, the chloroplasts in unripe green fruit significantly contribute to the
accumulation of sugar and metabolites and therefore, the quality and favor of ripe fruit. Traditional and
heirloom tomato varieties differ in the color and size of their fruit and they have genetic diversity which
could be appropriate germplasm resources for improving the quality of fruit. The Golden 2-like
transcription factor (SlGLK2) has an important role in regulating chlorophyll and plastid development in
unripe fruit. Genomic and promoter sequences of SlGLK2 in 19 heirloom species showed that those
varieties with SlGLK2/U coding sequences have fruit with different dark green shoulder phenotypes
and some have dark green stripes. 21 SNPs in the SlGLK2 gene intron and promoter regions and 3
coding region SNPs were identified. Some of the SNPs correlate with the amount of chlorophyll in the
green fruit shoulders and stripes. Expression profiling of genes regulating SlGLK2
expression, including, Arabidopsis Pseudo Response Regulator 2-like (SlAPPR2-like), Class I Knotted 1like Homeobox (KNOX) genes, TKN4 and TKN2, and the expression of SlGLK1 in unripe green heirloom
fruit showed that the TKN2, TKN4 and SlGLK2 gene expression is greater in the shoulders than at the
blossom end of fruit. Expression of these genes is not correlated with SlGLK2 exon SNPs but sequence
variation in SlGLK2 promoters may provide insights for use of diverse alleles to improve tomato fruit
quality.
*1315-TH. UNRAVELLING MYC2-DIRECTED TRANSCRIPTION NETWORK DURING JASMONATESIGNALED PLANT DEFENSE IN TOMATO
Du M.1,2, Lei Deng2, Ming Zhou1, Hailong Feng 1,2, Changbao Li1, Chuanyou Li2
Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of
Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing
100097, China; 2State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research
(Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing
100101, China
Contact: Minmin Du, [email protected]
1
It is believed that the activation of the jasmonate (JA) signaling pathway is required for resistance
against necrotrophic pathogens. We report here the bHLH transcription factor SlMYC2-directed
transcriptional network underlies JA-signaled tomato (Solanum lycopersicum) defense against the
necrotrophic pathogen Botrytis cinerea. We found COI1- and SlMYC2-dependent JA-responsive genes
expression is required for defense to B. cinerea. SlMYC2 plays an essential role in JA-signaled plant
defense to B. cinerea, which is quite different from its Arabidopsis ortholog AtMYC2. The combination
of ChIP-seq and RNA-seq analysis identified 655 SlMYC2 target genes that contain at least one
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genomic region bound by SlMYC2 and exhibit SlMYC2-dependent expression, including 50 TF genes.
Further evidence from biochemical and genetic experiments supported that the NAC transcription
factor JA2L is an intermediate TF for MYC2-directed wound-responsive geneexpression and the ERF
transcription factor ERF1D is an intermediate TF for MYC2-directed pathogen-responsive
geneexpression. Thus, the signaling cascades by which SlMYC2 executes its critical effect on
resistance to B. cinerea have been elucidated.
*1316-TH. MOLECULAR IDENTIFICATION OF A GENE AFFECTING TRICHOME IV AND V DENSITY IN
TOMATO
Kashaninia A.1,2, van Heusden S.1, Firdaus S.1,2, van Kaauwen M.1, Visser R.G.F.1, Vosman B.1
1
Wageningen UR Plant Breeding, PO Box 386, 6700 PB Wageningen, The Netherlands; 2Graduate
School Experimental Plant Sciences, Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen,
the Netherlands
Contact: Atiyeh Kashaninia, [email protected], [email protected]
Trichomes are present on the above-ground surfaces of plants. They reflect radiation, reduce water
loss and act as physical barriers for small insects. Trichomes and especially their glands are the place
where specific secondary metabolites are produced that play a key role in pathogen and pest
resistance. Glandular trichomes type IV are largely covering the aerial parts of some wild tomato
species, including Solanum galapagense. This trichome type is absent on cultivated tomato, which is
abundantly populated by non-glandular trichomes type V. The non-glandular trichome V is similar to IV
except for the glandular head. The pathway regulating trichome (glandular and non-glandular)
formation in Solanaceae is not well understood. In this study, a gene affecting trichome density,
present in the Wf1 QTL (Firdaus et al. 2013), was identified and map based cloned. The gene is
involved in the formation of trichome types IV and V. Suppression of the gene expression by RNAi in S.
galapagense and S. lycopersicum decreased the number of type IV and V trichomes. In S.
galapagense the proportion of glandular and non-glandular trichomes also changed. Overexpression
in S. lycopersicum and S. galapagense significantly increased the density of trichomes V and IV. The
data suggest that this gene is involved in regulation of trichome type IV/V formation.
Firdaus, et al. (2013) Theor. Appl. Genet. 126: 1487-1501
METABOLITES, FLAVOR AND QUALITY
*1406-TH. IDENTIFICATION AND FINE MAPPING OF SEED SPECIFIC FLAVONOIDS
USING LYCOPERSICUM PENNELLII INTROGRESSION LINES
Alseekh S.1, Tohge T.1, Ofner I.2, Osorio S.3, Zamir D.2. Fernie A.R.1
1
Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; 2Institute of plant
Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel;
3
Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y
Mediterranea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
Contact: Saleh Alseekh, [email protected]
Exotic germplasm represents an important source for expansion of the allelic and hence the
phenotypic diversity in inbred crop species which have lost much of this diversity following artificial
selection. The set of 76 introgression lines (ILs) resulting from crosses between the
domesticated Solanum lycopersicum (cv. M82) and its distant relative Solanum pennellii, have been
much used in order to characterize the genetic architecture of a number of morphological, and
metabolic traits. Previously, we have conducted a large-scale metabolic quantitative trait loci (mQTL)
analysis on the ILs, we have identified 679 mQTL that affect the accumulation of flavonoid,
phenylpropanoids and a range of glycoalkaloids in tomato fruit. Here, we extended our work and
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describe an LC-MS based mQTL analysis of secondary metabolites in tomato seed, we identified loci
responsible for the accumulation of seed specific flavonoids and glycoalkaloids. In addition, we took
the advantage of recently available backcross S.pennellii backcross inbred lines (BILs) for fine mapping
and identified a novel and seed specific glycosyl transferase gene underlying the accumulation of
kaempferol-3-O-sophoroside-7-O-rhamnoside in tomato seeds.
*1407-TH. METABOLOMIC ANALYSIS TO EVALUATE THE EFFECT OF DROUGHT STRESS ON
SELECTED AFRICAN EGGPLANT LEAVES
Mibei E.K.1, Ambuko J.2, Giovannoni J.3, Onyango A.N.1, Owino W.O.1
1
Department of Food Science and Technology, Jomo Kenyatta University of Agriculture and
Technology, Kenya; 2Department of Plant Science and Crop Protection, University of Nairobi,
Kenya; 3Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, New York,
14853
Contact: Willis Owino, [email protected]
Drought stress is one of the main abiotic stresses that affect the growth and survival of crops
worldwide. This leads to sequential morphological, physiological, molecular and biochemical changes
that can have adverse effects on plant growth, development and productivity. African eggplants
(Solanum aethiopicum and S. macrocarpon) are among the most economically important and valuable
vegetable and fruit crops. They have been reported to adapt and thrive well under drought stress. This
might be due to the accumulation and or presence of metabolites which are essential for plant growth,
development, stress adaptation and defense. Despite this, these diversified metabolites which arise
due to these stresses have not been well defined. This study was therefore, carried out with the
objective of monitoring the metabolite profiles of some African eggplant accessions under drought
stress at different stages of growth. Nineteen accessions of African eggplants were studied. The
tissues were extracted using standard method with ribitol as internal standard and derivatized with Nmethyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA). Metabolite analyses were carried on a Varian CP3800 GC coupled to a CombiPal autosampler and a Varian 1200L triple quadrupole MS. The
metabolite identification was carried out with the Golm, Germany metabolomics library software and
the mass spectra of individual gas chromatographic peaks were compared to a spectral library.
Changes in metabolite contents were identi?ed in the accessions and metabolites that were potentially
important with respect to stress responses were characterized. Characteristic metabolites for the
stress were identified. Proline, glutamate, sucrose, fructose and TCA cycle metabolites were shown to
be strongly correlated to stress. The principal component analysis (PCA) showed a clear discrimination
between the different accessions, growth stages, stressed and control accessions. The results of this
study illustrates that water stress has significant impact on the concentrations of some amino acids,
sugars and organic acids. This defines the common aspects associated with water stress effects on
vegetable quality and therefore will definitely add value to the study of stress tolerance in crops.
Keywords: Drought stress, African eggplants, metabolite profiling
*1408-TH. REDUCTION IN STEROIDAL GLYCOALKALOID LEVELS IN SOLANUM
TUBEROSUM AFFECTS DEVELOPMENT OF COLORADO POTATO BEETLE
Paudel J.R.1, Davidson C.1, Shukla M.1, Song J.2, Campbell L.2, Itkin M.3, Aharoni A.4, Tai H.1
1
Agriculture and AgriFood Canada, Fredericton Research and Development Centre, Fredericton, NB,
Canada; 2 Agriculture and AgriFood Canada, Kentville Research and Development Centre, Kentville,
NS, Canada; 3Department of Vegetable Research, ARO-Volcani Center, Bet Dagan,
Isreal; 4 Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Isreal
Contact: Jamuna Risal Paudel, [email protected]
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Steroidal glycoalkaloids (SGAs) are major secondary metabolites in potato. SGAs are toxic to humans
and, therefore, level of SGAs in potato tubers for human consumption are under regulatory control and
reducing SGAs is a target for breeding. The role of SGAs in potato interaction with Colorado potato
beetle (CPB), Leptinotarsa decemlineata (Say), a major defoliating pest, was investigated. CPB is
difficult to control due to its diverse and flexible life cycle and the development of resistance to many
insecticides. Levels of SGAs in S. tuberosum cv. Bintje were reduced by RNAi mediated silencing
of Glycoalkaloid Metabolism 4 (GAME4), a gene encoding a cytochrome P450 enzyme involved in an
oxidation step in the conversion of cholesterol to SGAs. GAME4 RNAi lines have reduced levels of
solanine and chaconine, two major SGAs of cultivated potato. Other differences in metabolic profile
included increased levels of phenylpropanoids and steroidal glycosides. We examined the survival,
leaf consumption, and development of CPB on detached leaves from wild type and GAME4 RNAi
potato plants. Early instar larvae (L1-L3) feeding on GAME4 RNAi leaves had lower survival rates
compared to those feeding on wild-type leaves. However, CPB feeding on GAME4 RNAi foliage
developed from larval to adult stages faster than those feeding on wild-type plants. There was no
difference in CPB leaf consumption between GAME4 RNAi and wild-type. These results suggest that
reducing SGAs have a negative effect on CPB development.
*1409-TH. NITRIC OXIDE OVERPRODUCTION IN TOMATO SHR MUTANT ALTERS CELLULAR
HOMEOSTASIS AND SUPPRESSES FRUIT GROWTH AND RIPENING
Bodanapu R., Gupta S.K., Basha P.O., Sakthivel K., Sadhna, Sreelakshmi Y., Sharma R.
Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences,
University of Hyderabad, Hyderabad-500046, India
Contact: Rameshwar Sharma, [email protected]
Nitric oxide (NO) plays pivotal role in growth and disease resistance in plants. It also acts as secondary
messenger in signaling pathway for several plant hormones. Despite its clear role in regulating plant
development, its role in fruit development is not known. In an earlier study, we described a short
root (shr) mutant of tomato, whose phenotype results from hyperaccumulation of nitric oxide (NO). The
molecular mapping localized shr loci in 2.5 Mb region of chromosome 9. The shr mutant showed
sluggish growth, with smaller leaves, flowers and was less fertile than wild type. The shr mutant
showed reduced fruit size and slower ripening of the fruits post-mature green stage to the red ripe
stage. Comparison of metabolite profiles of shr fruits with wild type fruits during ripening revealed
significant shift in the patterns. In shr fruits intermediates of tricarboxylic acid (TCA) cycle were
differentially regulated than WT indicating NO affected the regulation of TCA cycle. The accumulation
of several amino acids, particularly tyrosine was higher, whereas most fatty acids downregulated
in shr fruits. Among plant hormones at one or more stages of ripening, C2H4, IAA and IBA increased
in shr, whereas ABA declined. Our analyses indicate that retardation of fruit growth and ripening
in shr mutant likely results from influence of NO on central carbon metabolism and endogenous
phytohormones levels.
*1410-TH. LIP1 REGULATES THE PRODUCTION OF FATTY ACIDS DERIVED VOLATILE ORGANIC
COMPOUNDS IN TOMATO FRUIT
Liu Z.1, Tieman D.M.1, Taylor M.G.1, Klee H.J.1
1
Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
Contact: Zhongyuan Liu, [email protected]
A diverse set of volatile organic compounds arising from fatty acids (FA-VOCs) accumulated in tomato
ripe fruit are quite important to the fruit flavor. However, the completed biosynthetic pathway to a large
part of such volatile compounds is still ambiguous. The contents of most FA-VOCs are relatively low in
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cultivated tomato fruits (Solanum lycopersicum var. M82) and far more abundant in the closely related
species Solanum pennellii. Here, we identified a member of LIPASE genes family from S. pennellii (LIP1)
affecting the biosynthesis of multiple FA-VOCs by QTL mapping a near isogenic lines population
constructed from the cross of introgression line and M82. We show that the difference in some of the
FA-VOCs contents between M82 and S. pennellii are associated with the remarkably different
expression level of LIP1 during fruit ripening. With RNAi approaches, we further validate that the
content of a broad range of FA-VOCs such as cis-4-Decenal (C10), trans, trans-2,4-Decadienal (C10),
Octanal (C8), trans-2-heptenal (C7) and partial C5 volatiles are regulated by the transcription level
of LIP1 while other C5 or C6 volatiles remain unaffected. These results illustrate at a molecular level
how closely related species exhibit major differences in volatile production by altering the expression
of a volatile-associated gene and shed light to the genetic manipulation of fruit flavor.
*1411-TH. METABOLIC CHARACTERIZATION OF PENJAR ACCESSIONS DURING RIPENING AND
POSTHARVEST STORAGE
Kumar R., Sharma R., Sreelakshmi Y.
Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad,
Hyderabad-500046, India
Contact: Sreelakshmi Y, [email protected]
Many of the Penjar accessions of tomato that are widely grown in the Mediterranean region are known
to exhibit a prolonged shelf life. The molecular basis for the long shelf life of many of these accessions
was shown to be the alcobaca mutation, which leads to a substitution of valine to aspartic acid at
106th position of NAC-NOR protein. In the present study, we examined 4 different Penjar accessions in
greater detail to uncover the metabolic basis underlying the prolonged shelf life. Out of four Penjar
accessions, three had alc mutation as expected, whereas, one turned out to be a novel allele for nor,
with only 6 amino acids in the encoded protein. Consistent with the nature of the mutations, all these
accessions exhibited delayed ripening, and prolonged shelf life, both on-vine and off-vine compared to
AC (Ailsa Craig, reference cultivar). Interestingly, these accessions displayed differences in the fruit
phenotype, and the fruit colour varied from orange to red. Apparently, mutations innor also attenuated
carotenoid levels in Penjar accessions by suppressing the gene expression of phytoene synthase 1, a
key rate limiting enzyme for carotenoid biosynthesis. Though the pattern of ethylene burst is similar in
AC and Penjar fruits, consistent with delayed ripening and lower carotenoid content, the ethylene
emission from Penjar fruits was significantly lower than AC. In addition, a concerted down regulation of
a number of cell wall modifying genes was observed in Penjar fruits compared to AC, contributing to
their prolonged shelf life. Metabolite profiling using GC-MS during ripening and postharvest storage
revealed the differential accumulation of Krebs cycle intermediates and other primary metabolites in
Penjar fruits which may contribute towards long shelf life and the data would be presented.
1412-TH. COMBINED METABOLIC QUANTITATIVE TRAITS LOCI (mQTL)
AND EXPRESSION QTL
(eQTL) ANALYSIS IN A RECOMBINANT INBRED LINE POPULATION
Gonda I.1, Ashrafi H.2, Strickler S.R.1, Ma Q.1, Sun H.1, Mueller L.A.1, Sacks G.L.3, Klee H.J.4, Howe K.5,
Thannhauser T.W.5, Alseekh S.6, Fernie A.R.6, Fei Z.1,5, Foolad M.R.7, Giovannoni J.J 1,5
1
Boyce Thompson Institute, Cornell University Campus, Ithaca, NY, USA; 2Department of Horticultural
Science, North Carolina State University, Raleigh, NC, USA; 3Department of Food Science, Stocking
Hall, Cornell University, Ithaca, NY, USA; 4Horticultural Sciences Department, University of Florida,
Gainesville, FL, USA; 5USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA;
6
Max-Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany; 7Department of Plant
Science, The Pennsylvania State University, University Park, PA, USA
Contact: Itay Gonda, [email protected]
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The quality of tomato fruit is affected by the presence and composition of various metabolites
including sugars, acids, pigments and volatile compounds. While information about structural
biosynthetic genes of various important metabolites is increasing, additional genes and loci governing
their production and accumulation often remain uncharacterized. Quantitative trait loci (QTL) for these
metabolic traits can be detected by various methods, but pinpointing them down to the causative gene
requires substantial effort. Here we used a tomato recombinant inbred line (RIL) population consisting
of 148 families from an interspecific cross between Solanum lycopersicum (NC EBR-1) and Solanum
pimpinellifolium (LA2093) to map metabolic trait loci using an ultra-high resolution genetic map of this
population. The genetic map was constructed using genotyping-by-sequencing technology followed
by SNP calling and determination of the genetic bins. Focusing on the ripe fruit pericarp, we have
quantified various chemical traits including central metabolites, untargeted specialized metabolites as
well as volatile compounds. By using model selection QTL analysis, we were able to narrow some
known metabolic quantitative trait loci (mQTL) in addition to detecting novel mQTLs. Several QTLs for
different traits were co-localized, suggesting the possibility of common regulation for these traits.
Moreover, we have measured gene expression in the entire population by RNA-seq, enabling the
simultaneous detection of expression QTL (eQTL). We have focused on known structural genes of
various volatile compounds and carotenoids, and generated eQTLs that were grouped as cis-acting or
trans-acting. Co-localization of mQTL and eQTL allowed us to detect loci controlling expression of
genes affecting the relevant traits. This work demonstrates an efficient process for increasing mapping
resolution with expression candidate discovery toward accelerated gene discovery and simultaneous
development of information applicable to molecular breeding efforts.
OTHER TOPICS
*1504-TH. THE SOLANUM LYCOPERSICOIDES INTROGRESSION LINES: DEFINITIONS OF
INTROGRESSED REGIONS AND IDENTIFICATION OF FRUIT QUALITY LOCI
Feder A.1, Strickler S.R.1, Sun H.1, Ma Q.1, Xu Y.1, Shi Y.1, Peralta J.M.1, Freschi J.R.1, Fei Z.1, Klee H.J.2,
Giovannoni J.1.
1
Boyce Thompson Institute for Plant Research and USDA- ARS, Cornell University, Ithaca,
NY; 2Horticultural Sciences Department, University of Florida, Gainesville, FL
Contact: Ari Feder, [email protected]
Wild relatives of the cultivated tomato are a valuable source of important traits. Still, most of this
potential natural variation remains poorly characterized. Supplying food and nutritional demands in the
21th century will be enhanced by our ability to understand natural variation, pinpoint the underlying
genes and introduce them successfully into breeding programs. Toward this end, we have focused on
aS. lycopersicoides introgression line (IL) population where molecular marker targeted segments of this
species’ chromosomes have been integrated into the cultivated S. lycopersicum genome. S.
lycopersicoides is the most distant member of the tomato clade, making this genetic cross of highly
polymorphic genomes a valuable resource for genetic discovery in addition to development of novel
breeding targets. Both field and greenhouse-based screens of the population focused primarily on fruit
maturation and quality traits have elucidated at least 10 loci affecting carotenoid profiles in fruits, a
subset of them also showing variation in broader fruit ripening parameters. RNA-seq analysis of these
fruit tissues is near completion and will enable precise localization of the introgressions and will help
elucidate the molecular basis of the genetic loci underlying these traits. These efforts will lead to a
better understanding of fruit maturation and quality processes and supply plant breeders with
additional tools.
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*1505-TH. EVOLUTION AND DIVERSIFICATION OF SOLANACEAE FRUITFULL GENES
Maheepala D.C.1, Strahl M.2, Emerling C.A.3, Macon J.1, Litt A.1
1
Botany and Plant Sciences, University of California, Riverside, CA, USA; 2Department of Genetics and
Genomic Sciences, Icahn School of Medicine at Mount Sinai, Manhattan, NY, USA; 3Museum of
Vertebrate Zoology, University of California, Berkeley, CA, USA.
Contact: Dinusha Maheepala, [email protected]
The eudicot FRUITFULL (euFUL) genes are transcription factors that have been shown to function in
fruit development. In the dry dehiscent fruits of Arabidopsis, a euFUL gene is involved in lignifying the
dehiscence zone, and in Solanaceae, evidence points to a similar role in Nicotiana capsules. euFUL
genes are also expressed in tomato, which, however, lacks lignification. This indicates a potential
change in function for euFUL genes in fleshy fruits. As part of a larger project designed to elucidate the
genetic changes that accompanied the shift from dry to fleshy fruit, we are characterizing euFUL gene
evolution to characterize selection patterns and to determine if changes in sequence or copy number
are correlated with changes in morphology. A whole genome duplication early in core eudicot
diversification resulted in two euFUL lineages: euFULI, and euFULII. There is evidence of a Solanaceae
genome triplication, but we have only been able to find evidence of four, rather than the expected six,
euFUL genes: FUL1 and FUL2 in euFULI, and MBP10 and MBP20 in euFULII. However, we have not
been successful in recovering MBP10 sequences from species that diverged prior to Nicotiana. This
may be due to their low expression level; however MBP10 and MBP20 genes are located on the same
chromosome, suggesting these two genes may be a consequence of a tandem duplication rather than
a whole genome multiplication. This tandem duplication may have occurred just prior to the
divergence of Nicotiana, and may not have affected earlier diverging species. To characterize the
evolutionary dynamics of the euFUL lineage in Solanaceae, we generated transcriptomes, which we
previously successfully used to identify a Nicotiana MBP10 gene, from Schizanthus grahamii, Cestrum
nocturnum, and Brunfelsia spp. and are analyzing these along with existing sequence data. Our
preliminary analyses show purifying selection, inconsistent with a change in function in the shift to
fleshy fruit. This suggests that functional changes are not the result of sequence changes, but may be
due to changes in expression or downstream targets. We have identified sequence motifs that
characterize euFULI proteins, but none that distinguish sequences from dry and fleshy-fruited species.
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