ISAFG 2015 Proceedings Scien6fic Commi:ee Paolo Ajmone Marsan, Università Ca:olica del Sacro Cuore, Italy Lorenzo Bomba, Università Ca:olica del Sacro Cuore, Italy Stefano Capomaccio, Università Ca:olica del Sacro Cuore, Italy Licia Colli, Università Ca:olica del Sacro Cuore, Italy Jose Fernando Garcia, Universidade Estadual Paulista Júlio de Mesquita Filho, Brazil Marco Milanesi, Università Ca:olica del Sacro Cuore, Italy Riccardo Negrini, Università Ca:olica del Sacro Cuore, Italy Ezequiel Luis Nicolazzi, Parco Tecnologico Padano, Italy Andrea Rosa6, EAAP Tad Sonstegard, USDA Animal Genomics & Improvement Laboratory, USA Bruno Stefanon, University of Udine, Italy Alessandra Stella, Parco Tecnologico Padano, Italy Yuri Utsunomiya, Universidade Estadual Paulista Júlio de Mesquita Filho, Brazil John Williams, Parco Tecnologico Padano, Italy Organizing Commi:ee Paolo Ajmone Marsan, Università Ca:olica del Sacro Cuore, Italy Stefano Capomaccio, Università Ca:olica del Sacro Cuore, Italy Licia Colli, Università Ca:olica del Sacro Cuore, Italy Elisa Eufemi, Università Ca:olica del Sacro Cuore, Italy Jose Fernando Garcia, Universidade Estadual Paulista Júlio de Mesquita Filho, Brazil Claudia Vacchelli, Università Ca:olica del Sacro Cuore, Italy Luigi Lucini, Università Ca:olica del Sacro Cuore, Italy Elena Murelli, Università Ca:olica del Sacro Cuore, Italy Tad Sonstegard, USDA Animal Genomics & Improvement Laboratory, USA Elia Vajana, Università Ca:olica del Sacro Cuore, Italy Poster List GENOMICS AND EPIGENOMICS 1 A GENOME-­‐WIDE ASSOCIATION STUDY FOR DAILY MILK PRODUCTION IN EGYPTIAN BUFFALO Nermin k. El-­‐Halawany, Hamdy Abdel-­‐Shafy, Abd El-­‐Monsif A. Shawky and Ahmed F.M. Al-­‐Tohamy 2 A GENOME-­‐WIDE ASSOCIATION STUDY FOR FEED CONVERSION EFFICIENCY IN PIGS Justyna Horodyska, Ruth M. Hamill, Henry Reyer, Patrick Varley and Klaus Wimmers 3 ACCURACY OF IMPUTED GENOTYPES OF NELORE CATTLE POPULATIONS IN COMMERCIAL GENOTYPING PANELS AND CUSTOMIZED Andre Vieira do Nascimento, José Fernando Garcia, Andrea Renata da Silva Romero, Yuri Tani Utsunomiya, Adam Tai6 Harth Utsunomiya and Alexeia Barufab Grisolia 4 ALENTEJANO PIG: ONE IMPORTANT PIECE OF THE PUZZLE TO UNCOVER THE GENETIC BASIS OF LIPOGENESIS Andreia J Amaral, Maria C. Bressan, Carlos Be:encourt, João Almeida, João Sá, Margarida Gama-­‐Carvalho, José Santos-­‐
Silva, Ana T Belo, Olga Moreira, Rui Bessa and Luis Gama 5 ANALYSIS OF METHYLATION OF LEPR GENE PROMOTER IN IBERIAN PIGS Yolanda Núñez, Rita Benítez, Almudena Fernández, Clemente López-­‐Bote, Antonio González-­‐Bulnes and Cris6na Óvilo 7 AUTOMATIC FUNCTIONAL ANNOTATION OF REGULATORY ELEMENTS Daniel R. Zerbino, Nathan Johnson, Thomas Jue:emann, Steven P. Wilder, David Richardson, Avik Da:a, Laura Clarke and Paul R. Flicek 8 BOVINE GENETIC DISEASE FREQUENCIES: A NATIONAL PERSPECTIVE ON COMMERCIAL AND PEDIGREE CATTLE IN IRELAND Ma:hew McClure, Sinead Waters, Francis Kearney, Andrew Cromie, Jennifer McClure, Paul Flynn, Rebecca Weld, Donagh Berry and Mike Mullen 9 COMBINING HIGH DENSITY GENOTYPING AND EXOME SEQUENCING TO IDENTIFY DELETERIOUS MUTATION IN ITALIAN HOLSTEIN BULLS Marco Milanesi, Stefano Capomaccio, Yuri T. Utsunomiya, Lorenzo Bomba, Licia Colli, Elisa Eufemi, Jan-­‐Thijs van Kaam, Ka6a Cappelli, Ezequiel L. Nicolazzi, Stefano Biffani, Riccardo Negrini, José Fernando Garcia, Carl J. Rubin, Alessandro Nardone, Nicolò P. P. Maccio:a, Alessio Valen6ni, John L. Williams and Paolo Ajmone-­‐Marsan 1
0 COPY NUMBER VARIATIONS IN THE GENOME OF SOUTH AFRICAN CATTLE: CORRELATIONS, PATHWAYS AND GENETIC DIVERSITY Magretha Diane Wang, Charles Heiffer, Kennedy Dzama and Farai Catherine Muchadeyi 1
1 COST-­‐EFFECTIVE GENOTYPIC CHARACTERIZATION IN CHICKENS USING NEXT-­‐GENERATION SEQUENCING Fábio Pér6lle, Clarissa Boschiero, José Ribamar Nunes, Vinícius Henrique da Silva, Carlos Guerrero-­‐Bosagna, Mônica Corrêa Ledur and Luiz Lehmann Cou6nho 1
2 DETECTION OF LOCI AFFECTING HORN DEVELOPMENT AND COAT COLOR IN BOS INDICUS CATTLE Adam Tai6 Harth Utsunomiya, Romulo Claudio Morozini Padula, Thayla De Sousa Sussai, Ludmilla Balbo Zavarez, Yuri Tani Utsunomiya, Marco Milanesi, Rafael Silva Cipriano, Maria Margareth Teodoro Caminhas and José Fernando Garcia 1
3 DNA METHYLATION PATTERN OF HYPOTHALAMUS AND OVARY IN CAPRA HIRCUS Stefano Frabni, Emanuele Capra, Barbara Lazzari, Beatrice Coizet, Debora Groppeb, Pietro Riccaboni, Alessandro Pecile, Silvana Arrighi, Stefania Chessa, Bianca Cas6glioni, Alessia Giordano, Davide Prave:oni, Andrea Talen6, Le6zia Nicoloso, John L. Williams, Paola Crapaldi, Alessandra Stella and Giulio Pagnacco 1
4 EFFECTS OF METHYL-­‐DONOR RICH MATERNAL DIET ON HEPATIC DNA METHYLATION PROFILE AND GENE EXPRESSION OF THE PIG OFFSPRING REVEALED BY REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) AND RNA-­‐SEQ Nares Trakooljul, Michael Oster, Yang Du, Eduard Murani, Siriluck Ponsuksili and Klaus Wimmers 1
5 EPIGENETIC CHANGES AS STRESS BIOMARKERS IN AVICULTURE Simone Ceccobelli, Gianpiero Marconi, Piera Di Lorenzo, Marika Bocchini, Emidio Alber6ni, Emiliano Lasagna and Francesca Maria Sar6 1
7 GENE NETWORKS FOR FEED EFFICIENCY IN NELORE CATTLE: INTEGRATION OF GENOME WIDE ASSOCIATION AND LIVER AND MUSCLE TRANSCRIPTOME INFORMATION. Priscila S N Oliveira, Andressa O. Lima, Polyana C. Tizioto, Wellison J. da S. Diniz, Marcela M. de Souza,, Luis L. Cou6nho, James M. Reecy, Jeremy F. Taylor, Maurício A. Mudadu and Luciana C. A. Regitano 1
8 GENETIC CONTRIBUTIONS TO TRAINING PROGRESSION IN THOROUGHBRED RACEHORSES Gabriella Farries, Paul A McGebgan, Ka6e Gough, Beatrice A McGivney, Lisa M Katz and Emmeline W Hill 1
9 GENETIC INTROGRESSION THROUGH SELECTION IN DOMESTIC CHICKENS: INSIGHT FROM WHOLE GENOME SEQUENCE ANALYSIS Raman Akinyanju Lawal and Olivier Hano:e 2
0 GENOME-­‐WIDE ANALYSIS OF MILK QUALITY TRAITS OF COMISANA SHEEP BY CANONICAL DISCRIMINANT ANALYSIS. Gius6no Gaspa, Mariasilvia D'Andrea, Corrado Dimauro, Silvia Sorbolini, Nicolò Maccio:a and Fabio Pilla 2
1 GENOME-­‐WIDE ASSOCIATION STUDY FOR IGG ANTI-­‐LEISHMANIA (LEISHMANIA) INFANTUM RESPONSE IN DOGS EXPOSED TO LUTZOMYIA LONGIPALPIS Luís Fábio Da Silva Ba6sta, Yuri Tani Utsunomiya, Rafaela Beatriz Pintor Torrecilha, Thaís Bruna Ferreira da Silva, Raíssa Dias de Andrade, Thaíse Yumie Tomokane, Acácio Duarte Pacheco, Mary Marcondes, José Fernando Garcia, Cáris Maroni Nunes and Márcia Dalastra Lauren6 2
2 GENOMIC RETROSPECTIVE EVALUATION OF 20 YEARS OF SELECTION IN ITALIAN HOLSTEIN BULLS FOR FEET AND LEGS TRAIT. Andrea Talen6, Marco Milanesi, Ezequiel L. Nicolazzi, Stefano Frabni, Beatrice Coizet, Giulio Pagnacco, John L. Williams, Alessio Valen6ni, Alessandro Nardone, Jan-­‐Thijs Van Kaam, Paolo Ajmone-­‐Marsan and Paola Crepaldi 2
3 GENOMIC TOOLS ALLOW ROBUSTNESS DETECTION IN RED-­‐LEGGED PARTRIDGES (ALECTORIS RUFA) Natalia Sevane, Javier Cañon, Ignacio Gil and Susana Dunner 2
4 GHAP: AN R PACKAGE FOR GENOME-­‐WIDE HAPLOTYPING Yuri Tani Utsunomiya, Marco Milanesi, José Fernando Garcia and Paolo Ajmone-­‐Marsan 2
5 IDENTIFICATION AND CHARACTERIZATION OF COPY NUMBER VARIANTS IN CATTLE Rabia Letaief, Dominique Rocha and Mekki Boussaha 2
6 IDENTIFICATION OF GENOMIC REGIONS RELATED WITH BACKFAT THICKNESS IN NELLORE CATTLE Minos Esperandio Carvalho, Fernando Reys Baldi, Miguel Henrique de Almeida Santana, Ricardo Vieira Ventura, Gerson Antonio Oliveira Jr, Rachel Santos Bueno, Marina Nadai Bonin, Fernanda Marcondes Rezende and Jose Bento Sterman Ferraz 2
7 IDENTIFICATION OF KNOWN AND NOVEL QTLS FOR BODY SIZE IN BOS INDICUS COWS Tamíris Sayuri Aguiar, Yuri Tani Utsunomiya, Márcio Da Silva Costa, Anirene Galvão Tavarez Pereira, Haroldo Henrique de Rezende Neves, Roberto Carvalheiro, Adriana Santana do Carmo, Johann Sölkner, José Lindenberg Sarmento and José Fernando Garcia 2
8 IDENTIFICATION OF NOVEL SNPS OF OVINE PRL GENE AND THEIR ASSOCIATION WITH MILK PRODUCTION TRAITS Ozge Ozmen and Selim Kul 2
9 IDENTIFICATION OF SIGNATURES OF SELECTION AND ASSESSING THE DIVERSITY OF EAST AFRICAN SHORTHORN ZEBU MITOCHONDRIAL DNA Hussain Bahbahani, Joram Mwacharo and Olivier Hano:e 3
0 IDENTIFYING GENOMIC REGIONS RELATED TO RIB-­‐EYE AREA USING GENOTYPES FROM COMBINED SNP PANELS Miguel Henrique de Almeida Santana, Ricardo Vieira Ventura, Minos Esperandio Carvalho, Gerson Antonio Oliveira Junior, Mateus C Freua, Haja N Kadarmideen and José Bento Sterman Ferraz 3
1 INVESTIGATION OF BOS INDICUS AND BOS TAURUS ADMIXTURE IN SANGA CATTLE FROM UGANDA BY WHOLE-­‐
GENOME SEQUENCE ANALYSIS. Lorenzo Bomba, Hans D Daetwyler, Iona M MacLeod, Sunduimijid Bolormaa, Amanda J Chamberlain, Licia Colli, Marco Milanesi, Elia Vajana, Ben J Hayes, Paolo Ajmone-­‐Marsan and The NEXTGEN Consor6um 3
2 INVESTIGATION OF GENOMIC REGIONS ASSOCIATED WITH HEAT STRESS RESPONSES IN PIGS Kwan-­‐Suk Kim, Zewdu Edea, Jacob T. Seibert, Jason W. Ross, Lance H. Baumgard and Max F. Rothschild 3
3 INVESTIGATION OF SOX-­‐6 AS A CANDIDATE GENE FOR PORCINE GROWTH, CARCASS AND MEAT QUALITY TRAITS Rui Zhang, Chris6ane Neuhoff, Chris6ne Große-­‐Brinkhaus, Muhammad Jasim Uddin, Mehmet Ulas Cinar, Dawit Tesfaye, Ernst Tholen, Chris6an Loor and Karl Schellander 3
4 MITF GENE LOCUS IS ASSOCIATED WITH COAT COLOR VARIATION OF ETHIOPIAN CATTLE POPULATIONS ADAPTED TO DIFFERENT ALTITUDE ENVIRONMENTS Zewdu Bedada and Kwan-­‐Suk Kim 3
5 MOLECULAR CHARACTERIZATION AND GENETIC DISTANCE EVALUATION BETWEEN TWO SHEEP BREEDES: THE TUNISIAN BARBARINE AND TUNIS SHEEP IN USA. Gammoudi Anis and Bedhiaf Sonia 3
6 MOLECULAR KARYOTYPING OF THE PORCINE GENOME IN A SINGLE FISH EXPERIMENT Gothami Fonseka, Rebecca O’Connor, Richard Frodsham, Mar6n Lawrie and Darren Griffin 3
7 NOVEL VARIANTS OF THE EQUINE ALPHA-­‐S2 CASEIN (CSN1S2) AND THEIR ASSOCIATION WITH GENE EXPRESSION LEVEL Jakub Cieslak, Piotr Pawlak, Lukasz Wodas, Alicja Borowska, Anna Stachowiak, Kamila Puppel, Beata Kuczynska, Magdalena Luczak, Lukasz Marczak and Mariusz Mackowski 3
8 ON THE GENETIC STRATIFICATION OF IMMUNOLOGICAL RESPONSE TO VISCERAL LEISHMANIASIS IN DOGS Rafaela Beatriz Pintor Torrecilha, Luis Fabio Ba6sta, Yuri Tani Utsunomiya, Raíssa Dias De Andrade, Thaís Bruna Ferreira Da Silva, Thaíse Yumie Tomokane, Acácio Duarte Pacheco, Mary Marcondes, Cáris Maroni Nunes, Márcia Dalastra Lauren6 and José Fernando Garcia 3
9 PRNP POLYMORPHISMS IN FOUR ITALIAN SHEEP BREEDS Emiliano Lasagna, Ludovica Curcio, Carla Sebas6ani, Marcella Ciullo, Piera Di Lorenzo, Simone Ceccobelli, Francesca Maria Sar6, Giovanni Pezzob and Massimo Biageb 4
0 SELECTIVE SWEEP MAPPING IN TWO ORIGINAL OVINE BREEDS FROM THE BASQUE COUNTRY Otsanda Ruiz, Jorge Langa, Fernando Rendo, Carmen Manzano, Mikel Iriondo and Andone Estonba 4
1 SINGLE NUCLEOTIDE POLYMORPHISM ASSOCIATION STUDY IN SELECTIVE SWEEP REGIONS OF HANWOO (KOREAN CATTLE) Eunbi Ko and Duhak Yoon 4
3 THE FAANG PROJECT'S COMMITMENT TO DATA STANDARDS, ANNOTATION AND SHARING Ian Streeter, David Richardson, Laura Clarke, Paul Flicek and The FAANG Consor6um 4
4 THE PHYLOGENETIC STRUCTURE OF LEISHMANIA SPECIES REVEALED BY GENOME-­‐WIDE SINGLE-­‐COPY ORTHOLOGOUS PROTEINS Fernanda Müller de Oliveira, Flávia Florêncio de Athayde, Pier Kenji Rauschkolb Katsuda Ito, Yuri Tani Utsunomiya, Ashton Trey Belew, José Fernando Garcia, Najib M. El Sayed and Cáris Maroni Nunes 4
5 UNVEILING GENOMIC REGIONS THAT DISTINGUISH THE ASSAF SHEEP FROM ITS PARENTAL AWASSI BREED Elisha Gootwime, Alexander Rosov, Andrey Shirak and Eyal Seroussi 4
6 USE OF PACBIO PLATFORM FOR RESEQUENCING OF TOLL-­‐LIKE RECEPTOR GENES IN THE INDIGENOUS CZECH CATTLE BREEDS Karel Novák and Věra Mátlová 4
7 VARIABILITY OF BOVINE SERUM AMYLOID A3 AND SOMATIC CELL SCORE Dominga Soglia, Stefano Sartore, Sandra Maione, Ezequiel Luis Nicolazzi, Roberto Rasero and Paola Sacchi TRANSCRIPTOMICS 4
8 WHOLE-­‐EXOME SEQUENCING OF IRISH AI BULLS WITH DIVERGENT FERTILITY PHENOTYPES Ronan Whiston, Emma Finlay, Cliona O'Farrelly and Kieran Meade 4
9 A REPERTOIRE OF BOVINE TRANSCRIPTION FACTORS Marcela De Souza, Juan Vaquerizas, Adhemar Zerlo6ne and Luciana C. A. Regitano 5
0 ACUTE AND DELAYED TRANSCRIPTIONAL RESPONSE OF MUSCLE TISSUE TO TRANSIENT VARIATION OF INCUBATION TEMPERATURE IN BROILERS Watcharapong Naraballobh, Nares Trakooljul, Eduard Murani, Carsten Krischek, Sabine Janisch, Michael Wicke, Siriluck Ponsuksili and Klaus Wimmers 5
1 ALTERED MICRORNA EXPRESSION AND PRE-­‐MRNA SPLICING EVENTS ARE ASSOCIATED WITH MYCOBACTERIUM AVIUM SUBSPECIES PARATUBERCULOSIS INFECTION IN NEWBORN CALVES REVEALING THE COMPLEXITY OF THE HOST RESPONSE Guanxiang Liang, Yongjuan Guan, Nilusha Malmuthuge, Philip Griebel and Le Luo Guan 5
2 AN EGWAS ANALYSIS OF THE PORCINE WHOLE BLOOD TRANSCRIPTOME Ta6ana Maroilley, Maria Ballester, Gaétan Lemonnier, Marie-­‐José Mercat, Yvon Billon, Marco Moroldo, Claire Rogel-­‐Gaillard and Jordi Estellé 5
3 BREED-­‐RELATED CHANGES IN MIRNA EXPRESSION IN BOVINE SATELLITE CELLS ENTERING DIFFERENTIATION Anna Ciecierska, Edyta Przydatek and Tomasz Sadkowski 5
4 BULL SPERM MIRNAS PROFILING IN MOTILE AND LOW MOTILE CELL POPULATIONS Federica Turri, Emanuele Capra, Teresa Maria Gliozzi, Paola Cremonesi, Barbara Lazzari, Alessandra Stella and Flavia Pizzi 5
5 CALCIUM SIGNALING PATHWAY CAN CONTRIBUTE TO BROILER MUSCLE DISORDERS IN WOODEN BREAST – WHITE STRIPING ABNORMALITIES Paolo Zambonelli, Mar6na Zappaterra, Maurizio Mazzoni, Massimiliano Petracci, Francesca Soglia, Federico Sirri, Claudio Cavani and Roberta Davoli 5
6 CHANGES IN HEPATIC GENE EXPRESSION BETWEEN EFFICIENT AND INEFFICIENT NELORE CATTLE PRIMARILY APPEAR TO BE RELATED TO METABOLIC PROCESSES UNDERLYING OXIDATIVE STRESS. Luciana C.A. Regitano, Jeremy F. Taylor, Mauricio A. Mudadu, Robert D. Schnabel, Jared E. Decker, Gerson B. Mourão, Marcela M. Souza, Luiz L. Cou6nho, Andressa O. Lima, Priscila S.N. Oliveira and Polyana C. Tizioto 5
7 CHANGES IN MATERNAL NUTRITION IN EARLY PREGNANCY IMPACT FETAL OVARIAN TRANSCRIPTOME. Heni Falcao da Costa, Maria Carolina Villani Miguel, Alexandre Pedroso, Sarita Priscila Gobbo, Flavia Lombardi Lopes, Juliana Ragina Peiro and Guilherme De Paula Nogueira 5
8 CIRCULATING SERUM MICRORNAS AS NOVEL BIOMARKERS FOR BOVINE TUBERCULOSIS Carolina N. Correia, Nicolas N. Nalpas, Kirsten E. McLoughlin, David A. Magee, Ronan G. Shaughnessy, John A. Browne, Adam O. Whelan, H. Mar6n Vordermeier, Eamonn Gormley, Bernardo Villarreal-­‐Ramos, Stephen V. Gordon and David E. MacHugh 5
9 COLOSTRUM AND MATURE GOAT MILK: A TRANSCRIPTOME PROFILING BY RNASEQ Alessandra Crisà, Fabrizio Ferrè, Giovanni Chillemi and Bianca Moioli 6
0 COMPARATIVE ANALYSIS OF SIGNATURE GENES IN PRRSV-­‐INFECTED PORCINE MONOCYTE-­‐DERIVED DENDRITIC CELLS AT DIFFERENTIAL ACTIVATION STATUSES. Laura Miller, Yongming Sang and Frank Blecha 6
1 COMPARISON AMONG CO-­‐EXPRESSION NETWORKS OF PLURIPOTENT CELL POPULATIONS FROM PORCINE, BOVINE AND MURINE EMBRYOS Gianluca Mazzoni, Kris6ne Freude, Vanessa Jane Hall, Kaveh Mashayekhi, Poul Hy:el, Andras Dinnyes and Haja Kadarmideen 6
2 COMPARISON OF MIRNA PROFILES BETWEEN PROLIFERATING, DIFFERENTIATING AND DIFFERENTIATED SATELLITE CELLS OF BULLS OF DIFFERENT BREEDS Tomasz Sadkowski, Anna Ciecierska and Alicja Majewska 6
3 DIET INDUCED MILK FAT DEPRESSION ALTERS THE MAMMARY TRANSCRIPTOME IN LACTATING DAIRY COWS Sirja Viitala, Daniel Fischer, Laura Ven:o, Heidi Leskinen, Alireza R. Bayat, Kevin J. Shingfield and Johanna Vilkki 6
4 EFFECT OF DIETARY SUPPLEMENTATION OF BROILER CHICKENS WITH THE NATURAL ANTIOXIDANTS HESPERIDIN AND NARINGIN ON THE EXPRESSION OF LIPOGENESIS RELATED GENES AND FATTY ACID PROFILE Ariadne L. Hager-­‐Theodorides, Nina A. Dragona, Katerina Moschou, Chris6na Kappou, Ilias Arkoumanis, Michael Goliomy6s, Maria Charismiadou, Panagio6s Simitzis, Theofilos Massouras and Stelios G Deligeorgis 6
5 EFFECT OF SWINE GENOTYPE (PURE IBERIAN VS DUROC CROSSBRED) ON BíCEPS FEMORIS MUSCLE TRANSCRIPTOME AT BIRTH Miriam Ayuso, Almudena Fernández, Yolanda Núñez, Rita Benítez, Beatriz Isabel, Ana Isabel Fernández, Ana Isabel Rey, Antonio González-­‐Bulnes, Juan Medrano, Ángela Canovas, Clemente López-­‐Bote and Cris6na Óvilo 6
6 EFFECT OF SWINE GENOTYPE AND AGE ON LONGISSIMUS DORSI MUSCLE TRANSCRIPTOME Miriam Ayuso, Almudena Fernandez, Yolanda Nuñez, Rita Benítez, Beatriz Isabel, Ana I Fernández, Ana I Rey, Antonio González-­‐Bulnes, Juan F Medrano, Angela Canovas, Clemente J López-­‐Bote and Cris6na Óvilo 6
7 EVALUATION OF BCL2 AND PTX3 GENES EXPRESSION IN SWINE CUMULUS CELL CULTURED IN DIFFERENT MEDIA Calin Mircu, Oana Boldura, Camelia Tulcan and Ioan Huțu 6
8 EXPRESSION ANALYSIS OF SELECTED CANDIDATE GENES IN BUFFALO OOCYTES (BUBALUS BUBALIS) BEFORE AND AFTER MATURATION WITH DIFFERENT QUALITY BASED ON MORPHOLOGICAL ASSESSMENT Ashraf El-­‐Sayed, Dalia A. Ahmed, Salem M. Salem and Ashraf H. Barkawi 6
9 FIRST IDENTIFICATION OF POTENTIAL GENOMIC POLYMORPHISMS WITH FUNCTIONAL EFFECTS ON FEED EFFICIENCY BY LIVER RNA-­‐SEQ IN NELLORE CATTLE Pamela A. Alexandre, Gabriel C. M. Moreira, Jose Bento S. Ferraz, Miguel H. A. Santana and Heidge Fukumasu 7
0 GENOMICS AND SYSTEMS BIOLOGY OF BOAR TAINT AND MEAT QUALITY IN PIGS Markus Drag, Lise:e J. A. Kogelman, Lene Meinert, Hanne Maribo and Haja N. Kadarmideen 7
1 GOEXPRESS: AN R/BIOCONDUCTOR PACKAGE FOR THE IDENTIFICATION AND VISUALISATION OF ROBUST GENE ONTOLOGY SIGNATURES THROUGH SUPERVISED LEARNING OF GENE EXPRESSION DATA Kévin Rue-­‐Albrecht, Paul A. McGebgan, Belinda Hernández, David A. Magee, Nicolas C. Nalpas, Andrew C. Parnell, Stephen V. Gordon and David E. MacHugh 7
2 HARDERIAN GLAND TRANSCRIPTOME RESPONSE OF TWO DISTINCT INBRED LINES TO COMBINED STRESSORS OF NEWCASTLE DISEASE VIRUS AND HEAT PEROT SAELAO, Ying Wang, Ali Nazmi, Rodrigo Gallardo, David Bunn, Susan Lamont and Huaijun Zhou 7
3 IDENTIFICATION OF REGULATORY CANDIDATE GENES FOR PORCINE PRODUCTIVE TRAITS USING AN EGWAS APPROACH Angel Mario Mar6nez Montes, Anixa Muiños Bühl, Almudena Fernández Muñoz, Mª Carmen Rodríguez Valdovinos, Carmen Barragán Alcaide, Yolanda Nuñez Moreno, Rita María Benítez Yáñez, Josep Maria Folch, Noelia Ibañez Escriche and Ana Isabel Fernández Ávila 7
4 IL-­‐22 AS A MAJOR CYTOKINE ORCHESTRATING THE BOVINE RESISTANCE AGAINST TICK INFESTATION Daniela D Moré, Mauricio A Mudadu, Wilson Malago Junior, Claudia G C Gomes, Fernando F Cardoso and Luciana C A Regitano 7
5 LONG-­‐SOUGHT LEPTIN EMERGES FROM CHICKEN GENOME’S DARK-­‐SIDE: EXPRESSION PATTERN OF GC-­‐RICH AVIAN LEP FITS AUTO/PARACRINE RATHER THAN ENDOCRINE FUNCTION Eyal Seroussi, Yuval Cinnamon, Sara Yosefi, Olga Genin, Julia Gage-­‐Smith, Nima Rafa6, Susanne Bornelöv, Leif Andersson and Miriam Friedman-­‐Einat 7
6 MICRORNAS EXPRESSION IN HYPOTHALAMIC-­‐PITUITARY-­‐GONADAL AXIS IN GOAT Emanuele Capra, Stefano Frabni, Barbara Lazzari, Beatrice Coizet, Debora Groppeb, Pietro Riccaboni, Alesssandro Pecile, Silvana Arrighi, Stefania Chessa, Bianca Cas6glioni, Andrea Talen6, Le6zia Nicoloso, Alessia Giordano, Davide Prave:oni, Paola Crepaldi, John L. Williams, Giulio Pagnacco and Alessandra Stella 7
7 MIRNAS AS REGULATORS OF GENE EXPRESSION MODULATE ENERGY METABOLISM OF SKELETAL MUSCLE Siriluck Ponsuksili, Pun6ta Siengdee, Nares Trakooljul, Eduard Murani, Manfred Schwerin and Klaus Wimmers 7
8 POST-­‐WEANING BLOOD TRANSCRIPTOMIC DIFFERENCES BETWEEN YORKSHIRE PIGS DIVERGENTLY SELECTED FOR RESIDUAL FEED INTAKE Jack Dekkers, Dan Ne:leton, Nguyen Yet, Haibo Liu and Christopher Tuggle 7
9 RNA-­‐SEQ ANALISYS OF BROILER LIVER TISSUE REVEALS THE BENEFICIAL EFFECTS OF ORIGANUM VULGARE DIETARY SUPPLEMENTATION. Marcella Sabino, Andrea Verini-­‐Supplizi, Stefano Capomaccio, Lorenzo Bomba, Gabriella Cobellis, Mar6na Torricelli, Paolo Ajmone-­‐Marsan, Ka6a Cappelli and Massimo Trabalza-­‐Marinucci 8
0 SERPINA1 GENE EXPRESSION IN OVINE MILK DURING LACTATION Cinzia Marchitelli, Alessandra Crisà, Francesco Napolitano and Bianca Moioli 8
1 SNP CALLING ON TRANSCRIPTOME APPLIED IN GENOME ENABLED PREDICTIONS Mohammad Hossein Banabazi, Ardeshir Neja6 Javaremi, Ikhide G. Imumorin, Mostafa Ghaderi Zefrei and Seyed Reza Miraei Ash6ani 8
2 THE LONG NON-­‐CODING RNA TRANSCRIPTOME OF THE BOVINE MAMMARY GLAND AND POTENTIAL REGULATORY ROLES IN FATTY ACID SYNTHESIS Eveline M. Ibeagha-­‐Awemu, Ran Li and Pier-­‐Luc Dudemaine 8
3 TRANSCRIPTIONAL PROFILING OF MAMMARY GLAND AND MILK FATTY ACID COMPOSITION IN RESPONSE TO DIETS SUPPLEMENTED WITH FLAX AND HEMP SEED IN DAIRY GOATS Stefania Chessa, Paola Cremonesi, Emanuele Capra, Barbara Lazzari, Giovanna Ba:elli, Federica Turri, Stefania Colombini, Luca Rapeb and Bianca Cas6glioni 8
4 TRANSCRIPTOME RESPONSE OF SMALL INTESTINE OF ASCARIDIA GALLI INFESTED AND NON-­‐INFESTED VILLAGE CHICKENS FROM TWO AGRO-­‐ECOLOGICAL ZONES OF SOUTH AFRICA Dikeledi Petunia Malatji, Este VanMarle-­‐Koster and Cathrine Farai Muchadeyi 8
5 WHOLE TRANSCRIPTOME ANALYSES OF IMMUNE SYSTEM CELLS AFTER COMPETITION IN ANGLO-­‐ARABIAN RACES HORSES: INSIGHTS ON TRANSCRIBED EXONS, INTRONS AND REPEATS Stefano Capomaccio, Andrea Giontella, Andrea Verini-­‐Supplizi, Silvia Sorbolini, Ma:eo Picciolini, Francesca Crucianelli, Giovanni Paolo Biggio, Raffaele Cherchi, Maurizio Silvestrelli and Ka6a Cappelli OTHER 8
6 ARCTIC ARK. HUMAN-­‐ANIMAL ADAPTATIONS TO THE ARCTIC ENVIRONMENT: NATURAL AND FOLK SELECTION PRACTICES (ARC-­‐ARK) Juha Kantanen, Florian Stammler, Nasser Ghanem, Anna Gossman-­‐Stammler, Nuccio Mazzullo, Jaana Peippo, Tiina Reilas, Päivi Soppela, Ilma Tapio and Mervi Honkatukia 8
7 DATA INTEGRATION AND NETWORK RECONSTRUCTION WITH MUSCLE METABOLOME AND MEAT QUALITY DATA IN PIG TO HIGHLIGHT NEW BIOMARKERS FOR PORK QUALITY ASSESSMENT Julia Welzenbach, Chris6ne Große-­‐Brinkhaus, Chris6ane Neuhoff, Chris6an Loor, Karl Schellander and Ernst Tholen 8
8 DECONSTRUCTING THE PIG SEXOME: METABOLOMICS IN HEAVY PIGS DISCOVERS SEX RELATED DIMORPHISMS IN METABOLIC BIOMARKERS AND PATHWAYS Samuele Bovo, Gianluca Mazzoni, Daniela Giovanna Calò, Giuliano Galimber6, Flaminia Fanelli, Marco Mezzullo, Giuseppina Schiavo, Emilio Scob, Annamaria Manisi, Antonia Bianca Samorè, Francesca Bertolini, Paolo Trevisi, Paolo Bosi, Stefania Dall'Olio, Uberto Pago:o and Luca Fontanesi 8
9 MILK'S MICROBIOTA DURING THE PERIPARTURIENT PERIOD IN HOLSTEIN COWS: POSSIBLE IMPLICATION ON ANIMAL HEALTH AND MILK QUALITY Paola Cremonesi, Federica Riva, Emanuele Capra, Vi:orio Tedde, Maria Filippa Addis, Laure:a Turin, Claudia Pollera, Marco Severgnini, Joel Filipe, Giulio Curone, Noemi Viscon6, Daniele Vigo and Bianca Cas6glioni 9
0 PHYLOGENETIC NETWORK AND ENTEROTYPES OF THE GUT MICROBIOTA OF 60-­‐DAYS OLD PIG Yuliaxis Ramayo-­‐Caldas, Nuria Mach, Patricia Lepage, Florance Levenez, Cathrine Denis, Gaetan Lemonnier, Jean-­‐Jacques Leplat, Yvon Billon, Mustapha Berri, Joel Dore, Claire Rogel-­‐Gaillard and Jordi Estelle GENOMICS & EPIGENOMICS -­‐ Abstract N° 1 A GENOME-­‐WIDE ASSOCIATION STUDY FOR DAILY MILK PRODUCTION IN EGYPTIAN BUFFALO Nermin k. El-­‐Halawany1, Hamdy Abdel-­‐Shafy2, Abd El-­‐Monsif A. Shawky1 and Ahmed F.M. Al-­‐
Tohamy1 1 Department of Cell Biology, Na6onal Research Centre, El Buhouth St., 12311, Giza, EG 2 Department of Animal Produc6on, Faculty of Agriculture, Cairo University, El-­‐Gamaa St., 12613, Giza, EG Due to the lack of efficient pedigree informa6on in Egyp6an buffaloes, tradi6onal ways of gene6c improvement is limited. Alterna6vely, selec6ng animals based on genomic informa6on may open a window of opportunity to improve milk produc6on in a sustainable way. A first step in this respect is to accurately map associated genomic loci and es6mate the gene6c effect size for each locus. Therefore, the objec6ve of the current study was to iden6fy genomic regions associated with daily milk yield in Egyp6an buffaloes using Axiom Buffalo Genotyping Array 90K. Average milk yield devia6ons (YD) were calculated for the first three lacta6ons of 150 buffaloes using 66,392 daily milk records by a mixed model procedure implemented in the SAS sorware. Subsequently, YDs were used as response variable in a genome-­‐wide associa6on study (GWAS). For genotypes, we used AffyPipe for Affymetrix Axiom genotyping workflow and PLINK sorware to check the quality of genotypes. Arer quality control, 70,182 SNPs were remaining with total genotyping rate of 99.8%. A GWAS was performed using a mixed linear model implemented in the sorware GCTA. In this model, the polygenic effect was included to account for the genomic rela6onship. In addi6on, we evaluated the amount of the phenotypic variance explained by the available gene6c informa6on using REML method in the GCTA. Our results iden6fied 47 single nucleo6de polymorphisms (SNP) associated with YDs in Egyp6an buffaloes. The convincing associa6ons were located on chromosomes 6, 7, 8, 11, 13, 20, and 24. The most significant locus was located on chromosome 7 spanning 3.5 Mb and coincided with previously reported QTL in US Holstein and Norwegian Red ca:le. As well as iden6fying associa6ons within known QTL, a number of novel loci were detected. The most notable of these loca6ons were the regions of chromosomes 20 and 24 where several significant SNPs were located within narrow chromosomal regions (0.41 and 1.47 Mb, respec6vely). The heritability es6mate for YDs based on genomic rela6onships matrix was 0.18, which is similar to the es6mated heritability for milk yield traits in previously studies in Italian and Egyp6an buffaloes using classical animal model and pedigree. In conclusion, the GWAS iden6fied several chromosomal regions associated with daily milk yield. Further inves6ga6on of these loca6ons with addi6onal data is necessary to validate the associa6ons and iden6fy the causa6ve muta6ons. GENOMICS & EPIGENOMICS -­‐ Abstract N° 2 A GENOME-­‐WIDE ASSOCIATION STUDY FOR FEED CONVERSION EFFICIENCY IN PIGS Justyna Horodyska1, Ruth M. Hamill1, Henry Reyer2, Patrick Varley3 and Klaus Wimmers2 1 Food Chemistry and Technology, Teagasc Food Research Centre, Ashtown, 15, Dublin, IE Research Unit Molocular Biology, Research Ins6tute for the Biology of Farm Animals (FBN), Wilhelm-­‐Stahl-­‐
Allee 2, 18196, Dummerstorf, DE 3 The Hermitage, Hermitage Gene6cs, Sion Road, -­‐, Kilkenny, IE 2 Feed conversion efficiency (FCE) is a measure of how well an animal converts feed into live weight. The objec6ve of this study was to iden6fy genomic regions associated with FCE in pigs. A total of 952 commercial line Maxgro boars, that show an individual varia6on in feed conversion ra6o (FCR), were genotyped using Illumina Porcine SNP60 BeadChips. Arer quality control, the remaining 51,661 SNPs were tested for an associa6on with es6mated breeding values (EBVs) for FCR. SNP-­‐trait associa6on analysis was implemented with a mixed linear model, including an iden6ty-­‐by-­‐state (IBS) matrix. A list of genes, closest to most prominent SNPs, was created allowing a maximum distance of 1 Mb between the marker and genes. In total 240 SNPs reached the threshold of sugges6ve significance for an associa6on with EBV for FCR (-­‐log10[p-­‐value] ≥ 4.3). The largest number of associated SNPs were located on SSC1 (46 SNPs) and SSC4 (42 SNPs) followed by SSC6 (16 SNPs) and SSC15 (12 SNPs). A total of 25 SNPs mapping to 10 porcine autosomes crossed the Bonferroni-­‐adjusted genome-­‐wide significance threshold (-­‐log10[p-­‐value] ≥ 6). Of the 25 SNPs, 5 were located within a 2.37 Mb segment on SSC4. The most significantly associated SNP (H3GA0013204) was located 129.8 Kb from the nearest annotated gene, METTL11B. In addi6on, the marker ALGA0026230 mapped in an intronic region of F5 gene. On SSC15 the most significant SNP (MARC0015113) was located in an intron of DIS3L2 gene. In a neighbouring chromosomal region, SNP ALGA0119312 mapped 228 Kb from ARL4C, which is the closest iden6fied gene. Two significant SNPs (ASGA0028724 and ALGA0035847) on SSC6 were located 29.26 Kb and 471.21 Kb from the nearest annotated genes, FGR and PTPRU, respec6vely. The SNP, H3GA0002102, mapped to SSC1 was located in an uncharacterised gene ENSSSCG00000004415 and its nearest annotated gene, CD164, was located within 33.37 Kb. In summary, the present study demonstrated a number of chromosomal regions significantly associated with breeding value for feed conversion efficiency in pigs. These regions were described for the first 6me, although some of them were located not far from previously reported QTLs. Puta6ve candidate genes mapping near the significant SNPs will be examined. GENOMICS & EPIGENOMICS -­‐ Abstract N° 3 ACCURACY OF IMPUTED GENOTYPES OF NELORE CATTLE POPULATIONS IN COMMERCIAL GENOTYPING PANELS AND CUSTOMIZED Andre Vieira do Nascimento1, José Fernando Garcia2, Andrea Renata da Silva Romero1, Yuri Tani Utsunomiya2, Adam Tai6 Harth Utsunomiya3 and Alexeia Barufab Grisolia1 Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Rodovia Dourados/Itahum km 12, 79804, Dourados, BR 2 Faculdade Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de Acesso Prof Paulo Donato Castellan, 14884, Jabo6cabal, BR 3 Faculdade de Medicina Veterinária, Universidade Estadual Paulista, Rua Clovis Pestana 793, 16050, Araçatuba, BR 1 The cost of high density single nucleo6de polymorphism (SNP) genotyping plaŒorms is s6ll prohibi6ve for the rou6ne evalua6on of large numbers of animals. A cost-­‐effec6ve alterna6ve is the predic6on (i.e., imputa6on) of genome-­‐wide genotypes using lower density panels and genotypes of reference animals. This procedure can rely on commercial or custom SNP panels. The la:er is deemed to be more accurate, as the selec6on of markers is designed specifically for the targeted popula6on. Here, we aimed at evalua6ng the imputa6on performance of commercially available and custom panels of SNP markers in two samples of Nellore animals (Bos indicus). The two samples differed in terms of breeding program of origin. The first sample (P1) comprised 522 individuals genotyped for the Illumina BovineSNP50 BeadChip v2 assay (50k, ~50,000 SNPs). The second sample (P2) included 96 individuals genotyped for the Illumina BovineHD BeadChip assay (HD, ~777,000 SNPs). In order to facilitate comparisons between groups, we extracted 50k genotypes from the HD markers in group P2. Commercial and custom panels were tested with densi6es between 3,000 (3k) and 7,000 (7k) markers. Customiza6on was performed considering intermarker distances and minor allele frequency (MAF). Three reference popula6ons were used: P1, P2, and P1 + P2. Fireen animals from each group were randomly sampled and used as test popula6on for genotype imputa6on. Both reference and test popula6ons were submi:ed to quality control using the GenABEL v.1.8-­‐0 package in R v3.0.2. We used the imputa6on procedure implemented in FImpute v2.2. Twenty four imputa6on procedures were performed. The accuracy of imputa6on was assessed via the percentage of correctly imputed alleles (PCIA) and the percentage of correctly imputed genotypes (PCIG). The results were submi:ed to the Kruskal-­‐Wallis test to check if there were differences in accuracy between the commercial and customized panels. The accuracy of imputa6on showed be:er results for higher density panels. The custom panel was more sa6sfactory when compared to the commercial 7k density (p <0.01), obtaining average gain of accuracy of 1.1% and 2.6% for PCIA and PCIG, respec6vely. Similar results were found for the 3k panel. For both panels and densi6es, the accuracy values were higher when the reference and imputa6on animals belonged to the same group. The highest accuracy was observed when the animals of the reference popula6ons and imputa6on were the group containing the greatest number of individuals and higher kinship (P1). The customized panels for Nellore showed gains in predic6ng genotypes compared to commercial density 7k. The accuracy of imputa6on varied according to kinship and size of the reference popula6on GENOMICS & EPIGENOMICS -­‐ Abstract N° 4 ALENTEJANO PIG: ONE IMPORTANT PIECE OF THE PUZZLE TO UNCOVER THE GENETIC BASIS OF LIPOGENESIS Andreia J Amaral1, Maria C. Bressan2, Carlos Be:encourt3, João Almeida2, João Sá1, Margarida Gama-­‐Carvalho1, José Santos-­‐Silva2, Ana T Belo2, Olga Moreira2, Rui Bessa4 and Luis Gama4 1 BioISI-­‐ Biosystems and Integra6ve Sciences Ins6tute, University of Lisbon, Campo Grande, 1749, Lisbon, PT Estação Zootécnica Nacional, Ins6tuto Nacional de Inves6gação Agrária e Veterinária, Fonte Boa, 2005, Santarém , PT 3 Centro de Reprodução Animal da Herdade da Abóboda, Direcção Regional de Agricultura e Pescas do Alentejo, Herdade da Abóboda, 7830, Vila Nova e São Bento, PT 4 Faculdade de Medicina Veterinária, University of Lisbon, Av. da Universidade Técnica, 1300, Lisbon, PT 2 In contrast to commercial pig breeds, Iberian pigs (of which Alentejano is a branch raised in southern Portugal) are characterized by producing high-­‐quality meat, and consequently pork products, which are highly valued by consumers. This is largely due to the inherent ability of Iberian pigs to deposit intra-­‐muscular and subcutaneous fat, especially when they are finished on pasture and acorn, producing carcasses with higher propor6on of oleic fa:y acid (>53%), which is of higher nutri6onal value for the human diet. This inherent ability must have a gene6c background, which is not well understood, and is highly dependent on an environmental factor, the availability of acorns in the finishing diet. To our knowledge, no specific muta6ons have been associated with fa:y acid profiles, even though previous research using a QTL approach indicates that gene6c variability, especially in some regions of chromosome 4, may be related with lipid metabolism. We have conducted a GWAS study that aimed to compare Alentejano (N=30) and commercial (N=30) pigs, which were finished on pasture and acorn. All animals were genotyped using the 60K SNP chip and ~40 parameters related with performance and meat quality, including protein and fa:y acid profiles have been measured. This work will contribute to unravel the gene6cs underlying the Alentejano ability to produce pork of higher nutri6onal value. GENOMICS & EPIGENOMICS -­‐ Abstract N° 5 ANALYSIS OF METHYLATION OF LEPR GENE PROMOTER IN IBERIAN PIGS Yolanda Núñez1, Rita Benítez1, Almudena Fernández1, Clemente López-­‐Bote2, Antonio González-­‐Bulnes3 and Cris6na Óvilo1 1 Mejora Gene6ca Animal, INIA, Ctra. A6, km 7.5, 28040, Madrid, ES 2 Produccion Animal, UCM, Facultad Veterinaria, 28040, Madrid, ES Reproduccion Animal, INIA, Ctra. A6, km 5.9, 28040, Madrid, ES 3 The lep6n receptor (LEPR) is a candidate gene for growth and fatness due to its main role in the hypothalamic control of energy homeostasis. LEPR gene expression has been shown to be influenced by prenatal programming processes. Maternal nutri6onal restric6on in Iberian sows has been associated to a down-­‐regula6on of the LEPR gene in female offspring at birth, in rela6on with an increased predisposi6on for a higher appe6te, growth and fat deposi6on. Prenatal programming of gene expression can be related to epigene6c modifica6ons, as changes in DNA methyla6on pa:erns of regulatory regions. The objec6ve of this work was to analyse methyla6on levels in CpG islands located in LEPR promoter in adult Iberian pigs subjected to prenatal caloric restric6on (R) vs regular prenatal feeding (C). The LEPR promoter region was predicted with different sorwares (Promoter scan, Genoma6x) in a 1000 bp region on 5’UTR of the porcine LEPR gene (FN677933) and CpG island was iden6fied with CpG Island Explorer sorware inside this promoter. Genomic DNA was obtained from hypothalamic samples of 31 females (15R and 16C) and 20 males (9R and 11C), cleaned and bisulphite-­‐
converted. Pyrosequencing was employed to analyse methyla6on levels of 20 CpG sites located inside LEPR promoter, in four different assays. Assays were designed with Pyromark Assay Design 2.0 sorware, CpG op6on. Calibra6on curves were generated to assess the validity and sensi6vity of the pyrosequencing assays. Sanger sequencing was employed to study the methyla6on status of the complete surrounding promoter regions. Pyrosequencing analyses revealed very low levels of methyla6on in all CpG sites analysed, with mean values ranging from 0 to 15%. Most CpG sites showed methyla6on levels from 0% to 5%, preven6ng the study of nutri6onal or sex effects on methyla6on. Sanger sequencing confirmed the lack of methyla6on of the whole promoter region. Results suggest discarding LEPR promoter methyla6on as mechanism driving func6onal differences in gene expression arer maternal caloric restric6on in Iberian pigs. GENOMICS & EPIGENOMICS -­‐ Abstract N° 7 AUTOMATIC FUNCTIONAL ANNOTATION OF REGULATORY ELEMENTS Daniel R. Zerbino1, Nathan Johnson1, Thomas Jue:emann1, Steven P. Wilder1, David Richardson1, Avik Da:a1, Laura Clarke1 and Paul R. Flicek1 Ensembl, European Molecular Biology Laboratory, European Bioinforma6cs Ins6tute , Wellcome Trust Genome Campus, CB10, Hinxton, GB 1 Ensembl is one of the world’s leading sources of informa6on on the structure and func6on of vertebrate genomes. It provides up-­‐to-­‐date, comprehensive and consistent databases that bring together genome sequences, genes, non-­‐coding RNAs, known variants, etc. We rou6nely support animal genome research communi6es by annota6ng new or updated assemblies. Ensembl now provides automated annota6ons of regulatory elements from experimental evidence. We process the available public datasets produced by projects such as ENCODE or BLUEPRINT using a unified pipeline and make them available in a single loca6on. The data is synthesised into the Regulatory Build, which defines func6onally ac6ve regions and assigns them a func6on wherever possible. Given a set of ac6ve regions along the genome, their ac6vity levels can then be reliably determined in a new sample with a reduced set of assays. We are currently focused on human and mouse annota6ons, but are planning on integra6ng datasets from other species as they become available. Having largely automated the build process, we can employ it on a new species with great speed, provided sufficient experimental data is gathered together. Our goal is to progressively refine this annota6on of the genome into regulatory elements, to reach the quality level of the gene annota6ons that Ensembl already produces. To enrich this annota6on, we are looking at an array of technologies and assays to determine the links between enhancers and their target genes, such as eQTLs or Hi-­‐C data. In parallel, we are developing tools for basic research in epigenomics. For example, the WiggleTools browser allows users to remotely compute sta6s6cs on large collec6ons of data, as produced for example by the BLUEPRINT project, without downloading data or sorware. Our simplified representa6on of epigenomes can also be used to quickly compute differences between cell types, and establish clear differen6a6on pathways. This opens the way for rapid iden6fica6on of cell type based on epigenomic markers. GENOMICS & EPIGENOMICS -­‐ Abstract N° 8 BOVINE GENETIC DISEASE FREQUENCIES: A NATIONAL PERSPECTIVE ON COMMERCIAL AND PEDIGREE CATTLE IN IRELAND Ma:hew McClure1, Sinead Waters4, Francis Kearney1, Andrew Cromie1, Jennifer McClure1, Paul Flynn3, Rebecca Weld3, Donagh Berry4 and Mike Mullen2 1 Irish Ca:le Breeding Federa6on, Highfield house, Shinagh, 00000, Bandon, IE 2 Animal & Grassland Research and Innova6on Centre, Teagsac , ., 00000, Grange, IE 3 Weatherbys Ireland, Johnstown, IE Animal and Grassland Research and Innova6on Centre, Teagsac, Moorepark, 00000, Fermoy, IE 4 Historically one only discovered if an animal was a carrier for a gene6c disease arer it had produced an affected offspring. Once iden6fied the livestock producer typically had two choices 1) cull any ancestor or rela6ve of the affected progeny, or 2) risk producing another calf affected calf. As molecular tests for causa6ve muta6ons became available carrier animals could be iden6fied, but oren only AI bulls or elite pedigree animals were tested. Commercial producers tried to minimize their gene6c disease risk by purchasing bulls assumed to be free of gene6c diseases. To aid ca:le genomics in Ireland a low cost, custom bovine Illumina single nucleo6de polymorphism (SNP) genotype panel (Interna6onal Dairy & Beef panel; IDB) was developed which contains 40 validated probes for Mendelian diseases. Currently, >140,000 Irish commercial and pedigree beef and dairy animals have been genotyped with the IDBv2 and carrier animals have been iden6fied for all but 6 of the validated disease probes. Knowing an animal’s gene6c disease status will allow producers more informed breeding decisions and the ability to minimize gene6c disease risk. As new gene6c diseases are iden6fied, the IDB can also be used to rule out any previously known muta6ons and iden6fy the genomic loca6on of the causa6ve muta6on. GENOMICS & EPIGENOMICS -­‐ Abstract N° 9 COMBINING HIGH DENSITY GENOTYPING AND EXOME SEQUENCING TO IDENTIFY DELETERIOUS MUTATION IN ITALIAN HOLSTEIN BULLS Marco Milanesi1, Stefano Capomaccio1, Yuri T. Utsunomiya2, Lorenzo Bomba1, Licia Colli1, Elisa Eufemi1, Jan-­‐Thijs van Kaam3, Ka6a Cappelli4, Ezequiel L. Nicolazzi5, Stefano Biffani6, Riccardo Negrini1, José Fernando Garcia7, Carl J. Rubin8, Alessandro Nardone9, Nicolò P. P. Maccio:a10, Alessio Valen6ni9, John L. Williams5 and Paolo Ajmone-­‐Marsan1 1 Is6tuto di Zootecnica, Univeristà Ca:olica del Sacro Cuore, via Emilia Parmense, 84, 29122, Piacenza, IT Departamento de Medicina Veterinária Preven6va e Reprodução Animal, UNESP -­‐ Univ Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884, Jabo6cabal -­‐ SP, BR 3 Ufficio Ricerca & Sviluppo, Associazione Nazionale Allevatori bovini razza Frisona Italiana -­‐ ANAFI, Via Bergamo, 292, 26100, Cremona, IT 4 Dipar6mento di Medicina Veterinaria, Università di Perugia, Via S. Costanzo, 4, 06126, Perugia, IT 5 Bioinforma6cs core, Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, IT 6 Is6tuto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche -­‐ CNR, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, IT 7 Departamento de Apoio, Produção e Saúde Animal, UNESP -­‐ Univ Estadual Paulista, Rua Clóvis Pestana, 79, 16050, Araçatuba -­‐ SP, BR 8 Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, C11:3. Husargatan, 3, 75237, Uppsala, SE 9 Dipar6mento per l’Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via San Camillo de Lellis, 01100, Viterbo, IT 10 Dipar6mento di Agraria, Università degli Studi di Sassari, Piazza D'Armi, 17, 7100, Sassari, IT 2 Deleterious muta6ons naturally occur in wild and domes6c animal species. Their des6ny is either to rapidly disappear or to remain at low frequency in the popula6ons. Some may increase in frequency when in linkage with alleles controlling traits under natural or anthropogenic selec6on. This increase may be quick and substan6al when deleterious variants are carried by high gene6c value sires widely use in ar6ficial insemina6on. Here we searched for deleterious variants in the Italian Holstein popula6on combining in a three step approach high density SNP genotyping of 1009 AI bulls and exome sequence data from 18 bulls, selected from opposite tails of the male and female fer6lity EBV distribu6on. In the first step PLINK analysis of high density genotypic data detected 64,215 haplotype blocks of high LD. Among these 261 contained one class of homozygous haplotypes having frequency significantly lower than expected and some6mes completely missing. These were classified as deleterious haplotypes likely carrying deleterious variants in coding or regulatory sequences. In the second step a custom pipeline was developed to trim and align exome sequences. SNPs and InDels were called, filtered and finally annotated using VEP sorware. A total of 9229 muta6ons likely inducing a change in protein func6on (premature stop codons, muta6ons causing frameshirs, alterna6ve splicing sites or changing protein structure) were iden6fied. These were classified as deleterious variants. The third step combined results obtained in the first two steps. A total of 83 deleterious variants in 61 deleterious haplotypes were iden6fied and further inves6gated. Conserva6on across vertebrate species (using phastCons and phyloP score) and concordance between SNP genotype and sequence results were used to filter the co-­‐mapping results. Variants passing these filters are in genes involved in embryonic and postnatal survival or associated to gene6c defects in human and mouse. Their likely deleterious effect is being confirmed in a large popula6on of bulls and cows. Acknowledgments This research was supported by the Italian Ministry of Agriculture, grant INNOVAGEN, and by the EU FECUND project. GENOMICS & EPIGENOMICS -­‐ Abstract N° 10 COPY NUMBER VARIATIONS IN THE GENOME OF SOUTH AFRICAN CATTLE: CORRELATIONS, PATHWAYS AND GENETIC DIVERSITY Magretha Diane Wang2, Charles Heiffer2, Kennedy Dzama1 and Farai Catherine Muchadeyi2 1 Department of Animal Sciences, University of Stellenbosch, Private BAg X1, 7602, Ma6eland, ZA Biotechnology PlaŒorm, Agriculture Research Council, Private Bag X5, 0110, Pretoria, ZA 2 Structural varia6ons found within the genome cons6tute a major source of inter-­‐individual gene6c varia6on. Recently discovered copy number varia6ons (CNVs) are modifica6ons in DNA structure comprising of dele6ons, duplica6ons and inser6ons greater than 1kb in size. Detected in those genes responsible for specific biological func6ons such as immunity, lacta6on, reproduc6on and rumina6on, CNVs are thought to be primary role-­‐players in breed forma6on and adapta6on. South Africa has a diverse ecology with harsh environmental condi6ons and a broad spectrum of parasites and diseases that pose challenges to livestock produc6on. Muta6ons, adapta6on, selec6ve breeding, isola6on and gene6c drir have created an enormous diversity of local ca:le popula6ons that demonstrate an enhanced ability to survive in the harsh condi6ons. Composite ca:le breeds have also been developed to u6lize the hardiness of indigenous breeds and the produc6on poten6al of the exo6c breeds. The prevalence of CNVs within these breeds of ca:le is not understood. Illumina Bovine50K Beadchip data and PennCNV were u6lized in this study to iden6fy CNVRs within the genome of 288 animals from 7 South African ca:le breeds, including indigenous, exo6c, composite and cross breeds. 356 unique CNV regions (CNVRs) ranging from 36kb to 4.1Mb in size were iden6fied across breeds. PANTHER overrepresenta6on analyses demonstrated significant enrichment of a number of biological processes, molecular func6ons, cellular components and protein classes by correlated CNVRs. 198 CNVRs that were present in more than 1 animal were u6lized as gene6c markers to assess within and between breed diversity. Pairwise associa6on analyses performed with GENEPOP online sorware program demonstrated 102 and 7 of the CNVRs in the exo6c and indigenous breeds to have a significant (p≤0.05) pairwise associa6on. Breed gene6c distances were ascertained and phylogene6c trees drawn. Increasing evidence has suggested that CNVs play a primary role in inter-­‐individual diversity a:ribu6ng to both normal phenotypic varia6on and major varia6ons in complex traits such as suscep6bility to disease. This study successfully iden6fied, characterized and analyzed CNVRs within South African ca:le breeds. Gene6c diversity of indigenous, exo6c, composite and crossbred animals of South African was ascertained using CNVRs. GENOMICS & EPIGENOMICS -­‐ Abstract N° 11 COST-­‐EFFECTIVE GENOTYPIC CHARACTERIZATION IN CHICKENS USING NEXT-­‐GENERATION SEQUENCING Fábio Pér6lle1, Clarissa Boschiero1, José Ribamar Nunes1, Vinícius Henrique da Silva1, Carlos Guerrero-­‐Bosagna2, Mônica Corrêa Ledur3 and Luiz Lehmann Cou6nho1 1 Animal Science and Pastures Department, University of São Paulo, Av. Pádua Dias, 11, 13418, Piracicaba, BR 2 IBM Biology, Linköping University, Mäster Mabas väg, 581 8, Linköping, SE Gene6cs and Animal Breeding, Brazilian Agricultural Research Corpora6on, Rodovia BR-­‐153, Km 110, 89700, Concórdia, BR 3 Next-­‐genera6on sequencing (NGS) data provides a large amount of informa6on that can be used to detect single nucleo6de polymorphisms (SNPs) or to develop high-­‐throughput genomic arrays, e.g. SNP chips. However, pre-­‐designed SNP chips are not suitable for detec6ng novel polymorphisms in non-­‐model organisms, inbred popula6ons and especially in specific hybrid popula6ons developed for gene6c studies. Although, NGS have enough power to detect informa6ve polymorphisms, its high cost makes it imprac6cal to be used for animal breeding and large scale selec6on. In this study, we used an efficient and cost-­‐effec6ve genotyping by sequencing (CornellGBS) approach in order to genotype 444 chickens from five families of the EMBRAPA F2 Chicken Resource Popula6on, 10 chickens from the parental lines and 8 from the F1 genera6on. Genomic DNA was cleaved with the PstI enzyme ligated to adapters with their respec6ve barcodes and sequenced by the Illumina HiSeq2500 sequencer. We ini6ally iden6fied 318,229 SNPs using Tassel 3.0 pipeline default. Arer filter parameters, e.g. minimum taxon (0.2) and minimum site (0.9) coverages, 81,362 SNPs were retained for all samples (n=462). These represent a reliable SNP dataset of which 44,319 (53.4%) has not been previously described in the dbSNP database. This genotyping approach, to the best of our knowledge, is the first in chickens. The applied method has high performance in discovery of novel SNPs and also provides a reliable database of SNPs from mul6ple samples at low cost (~
$60/sample). This approach represents an alterna6ve to current genotyping methods, which will improve whole-­‐genome selec6on (WGS) and genome wide associa6on studies (GWAS) related to animal breading. Key words: animal breeding, chicken, GBS, GWAS, Next-­‐Genera6on Sequencing, PstI, restric6on enzyme, selec6on GENOMICS & EPIGENOMICS -­‐ Abstract N° 12 DETECTION OF LOCI AFFECTING HORN DEVELOPMENT AND COAT COLOR IN BOS INDICUS CATTLE Adam Tai6 Harth Utsunomiya1, Romulo Claudio Morozini Padula2, Thayla De Sousa Sussai2, Ludmilla Balbo Zavarez3, Yuri Tani Utsunomiya3, Marco Milanesi4, Rafael Silva Cipriano2, Maria Margareth Teodoro Caminhas1 and José Fernando Garcia1 Departamento de Apoio, Produção e Saúde Animal, UNESP -­‐ Univ Estadual Paulista, Rua Clóvis Pestana, 79, 16050, Araçatuba -­‐ SP, BR 2 Departamento de Medicina Veterinária, Centro Universitário Católico Salesiano Auxilium, Rodovia Senador Teotônio Vilela s/n, 16016, Araçatuba -­‐ SP, BR 3 Departamento de Medicina Veterinária Preven6va e Reprodução Animal, UNESP -­‐ Univ Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884, Jabo6cabal -­‐ SP, BR 4 Is6tuto di Zootecnica, Università Ca:olica del Sacro Cuore, via Emilia Parmense, 84, 29122, Piacenza, IT 1 We performed genome-­‐wide scans for loci affec6ng polled/horned (PH) and white/dark coat color (CC) phenotypes in 481 Nellore bulls (Bos indicus) genotyped for over 777,000 single nucleo6de polymorphism (SNP) markers. Binary scores were obtained from majority vo6ng of image analysis performed by five observers. Arer quality checks, 401 and 131 animals and 471,957 and 468,662 SNPs were retained in the analysis of PH and CC, respec6vely. Phenotype-­‐genotype associa6ons were tested using a mixed model approach. The most significant SNP for PH (p = 1.23e-­‐18) was located on chromosome (CHR) 1:78.7 kb, nearby the well know POLL locus. Several studies using different taurine breeds and taurine x indicine crosses have mapped the polled phenotype to the cetromeric region of CHR1. However, the causal muta6on is s6ll unknown and different genes have been suggested to regulate the presence/absence of horns and its development. The most significant SNP for CC (p = 2.05e-­‐16) was found on CHR13:64.15 kb, in the immediate vicinity of ASIP. This gene encodes for the agou6 signaling protein, a pep6de antagonist of MC1R (melanocyte-­‐s6mula6ng receptor). It is also known that four variants of MC1R are responsible for producing Black/Red phenotypes in different ca:le breeds and although MC1R has been widely reported in coat color studies in ca:le, other genes are involved. As ASIP is an antagonist of MC1R, our findings suggest that a func6onally reciprocal muta6on affec6ng the tyrosinase pathway underlies the white/dark coat color phenotype in Nellore ca:le. GENOMICS & EPIGENOMICS -­‐ Abstract N° 13 DNA METHYLATION PATTERN OF HYPOTHALAMUS AND OVARY IN CAPRA HIRCUS Stefano Frabni1, Emanuele Capra2, Barbara Lazzari4, Beatrice Coizet1, Debora Groppeb1, Pietro Riccaboni1, Alessandro Pecile1, Silvana Arrighi3, Stefania Chessa2, Bianca Cas6glioni2, Alessia Giordano1, Davide Prave:oni3, Andrea Talen61, Le6zia Nicoloso3, John L. Williams5, Paola Crapaldi1, Alessandra Stella2 and Giulio Pagnacco1 Dipar6mento di Scienze Veterinarie e Sanità Pubblica, Università degli Studi di Milano, Via Celoria, 10, 20133, Milano, IT 2 Is6tuto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche UOS di Lodi, Via Einstein, 26900, Lodi, IT 3 Dipar6mento di Scienze Veterinarie per la salute, la produzione animale e la sicurezza alimentare, Università degli Studi di Milano, Via Celoria, 10, 20133, Milano, IT 4 PTP, Parco Tecnologico Padano, Via Einstein, 26900, Lodi, IT 5 School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, 5371, Adelaide, AU 1 One of the key determinants in the control of gene expression in mammals, and the most common covalent modifica6on of DNA in eukaryotes, is methyla6on at the carbon 5 of cytosine residues. DNA methyla6on pa:erns can be inherited and influenced by environment, diet and aging, and disrupted in diseases. Although methylomes from several 6ssues were inves6gated in some species, goats are s6ll unexplored. We analysed the methylome of hypothalamus and ovary from 3 adult Saanen goats, trying to take the first steps on the poten6al epigene6c involvement in goat biology. In order to evaluate differen6ally methylated regions, we used Methylated DNA binding domain sequencing (MBD-­‐seq), with enrichment of methylated DNA fragments and next genera6on sequencing (NGS -­‐ Hiseq 2000 Illumina). We produced at least 20 million reads per sample, covering an average of about 30% of the goat genome. Further analyses were performed to iden6fy peaks corresponding to hyper-­‐methylated regions. Chromosomes 12 and 20 showed the lowest density of methylated fragments on both 6ssues, while chromosomes 18 and 19 the highest. We also inves6gated methyla6on distribu6on in the different genomic regions: promoter, intron, exon, downstream of gene, distal and intergenic. Introns showed the highest methyla6on frequency on both hypothalamus (34.6% on the total of the region detected) and ovary (39.1%). Matching the methyla6on pa:ern of hypothalamus versus ovaries of the three goats under study we looked for the biological and molecular pathways involving genes with 6ssue-­‐specific methyla6on peaks. Pathways with the highest p-­‐values (P < 0.001) affect RNA binding in ovary, and regula6on of the immune system processes in hypothalamus. This is the first work dealing with a global methyla6on pa:ern in Capra hircus: our pioneering results could be helpful for a deeper comprehension of the complex epigene6c machinery in this species. Acknowledgement The research was funded by GenHome project. GENOMICS & EPIGENOMICS -­‐ Abstract N° 14 EFFECTS OF METHYL-­‐DONOR RICH MATERNAL DIET ON HEPATIC DNA METHYLATION PROFILE AND GENE EXPRESSION OF THE PIG OFFSPRING REVEALED BY REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) AND RNA-­‐SEQ Nares Trakooljul1, Michael Oster1, Yang Du1, Eduard Murani1, Siriluck Ponsuksili1 and Klaus Wimmers1 Ins6tute for Genome Biology, Leibniz-­‐Ins6tute for Farm Animal Biology, Wilhelm-­‐Stahl-­‐Allee 2, 18196, Dummerstorf, DE 1 Epigene6c mechanisms regulate gene ac6vity and hence animal phenotypes by introducing chemical modifica6ons to DNA and/or chromosomes such as DNA methyla6on and histone acetyla6on rather than changes of the underlying DNA sequence. Gesta6onal nutri6on and in utero environment can imprint life-­‐long impacts on the phenotypic outcomes of the offspring possibly via intervening epigene6c mechanisms/marks including DNA methyla6on. However, the molecular basis s6ll remains to be elucidated especially mapping of the responsive loci. In this study, we inves6gated the effects of methyl-­‐donor rich maternal diet on liver DNA methyla6on and gene expression of the pig offspring at 91d post-­‐concep6on and 150d post-­‐
natal in German Landrace (DL) and Pietrain (Pi) breeds using Reduced Representa6on Bisulfite Sequencing (RRBS) and RNA-­‐Seq. Differen6al expression analysis of the RNA-­‐Seq data showed that nucleic acid metabolism pathways were influenced by the methyl-­‐donor-­‐rich maternal diet at the fetus stage, while lipid metabolism pathways were affected at the growing stage (150d). An average of 67.41 % of the RRBS reads (135.3 million in total) were uniquely mapped to the pig reference genome (susScr3/ Sscrofa10.2) using BS-­‐Seeker2. Mean percentage of methylated cytosine was 43.73 ± 2.4, 0.35 ± 0.06 and 0.41 ± 0.09 in the CpG, CHG and CHH context, respec6vely. The RRBS reads were preferen6ally mapped to CpG islands, CpG-­‐island shores, promoters and 5´UTR. CDS, introns and 3´UTR were moderately covered. Differen6ally methylated CpGs (DMCs) were detected between maternal dietary treatments (methyl-­‐donor rich vs control), developmental stages (150d vs 91dpc), and breeds (DL vs Pi) sugges6ng dynamic pa:erns of DNA methyla6on associated with aforemen6oned factors. Several DMCs were mapped to the 5´-­‐regulatory regions. A significant inverse correla6on between gene expression (log2 RPKM) and DNA methyla6on level of the upstream CpG cluster (<100 kb) was observed including for CBFA2T3 (SSC6), CPEB4 (SSC16) and TUBB4B (SSC1). Overall, our results provide evidence reinforcing that methyl-­‐donor rich maternal diet has a lifelong impact on the pig offspring par6ally via intervening the DNA methylome and this may have an implica6on in livestock produc6on and management. THIS WORK HAS BEEN ACKNOWLEDGED WITH THE THIRD PLACE IN THE POSTER COMPETITION
GENOMICS & EPIGENOMICS -­‐ Abstract N° 15 EPIGENETIC CHANGES AS STRESS BIOMARKERS IN AVICULTURE Simone Ceccobelli1, Gianpiero Marconi1, Piera Di Lorenzo1, Marika Bocchini1, Emidio Alber6ni1, Emiliano Lasagna1 and Francesca Maria Sar61 Dipar6mento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX giugno, 74, 06121, Perugia, IT 1 The study of epigene6c changes is important for the assessment of environmental stressors effects in aviculture. In fact, animals can employ regulatory strategies, such as DNA methyla6on, to enable rela6vely rapid adapta6on to new condi6ons. At this regard, cytosine methyla6on might play an integral role in the regula6on of gene expression at both the transcrip6onal and post-­‐transcrip6onal levels. Stress due to high density is the first cause of disease, oren related to gene6c modifica6ons such as methyla6on (addi6on or replacement of methyl group in nucleic acids and/or proteins). In this study, the Methyla6on Sensi6ve Amplified Polymorphism (MSAP) approach was used to assess the extent of cytosine methyla6on under density stress in three different gene6c types characterized by different trend of growth (ROSS 308-­‐fast growing, Kabir-­‐medium growing, Ancona-­‐slow growing). The study was carried out with 10 chickens/mq (control group) and 25 chickens/mq (experimental group); at the end of experiment, 50% of animals bred in high density were taken back to low density condi6ons (recovery group). From all sacrificed animals a sample of liver 6ssue was taken and used to isolate genomic DNA for the M-­‐SAP techniques inves6ga6on employing two isoschizomers with a different sensi6vity to methyla6on (HpaII and MspI). Our preliminary results highlight a different level of methyla6on between selected genotypes (39.88% in ROSS 308 and 38.73% in Kabir) and the autochthonous genotype (42.38% in Ancona). Moreover, the two types showed different methyla6on strategies in response to growth stress. In fact, while ROSS 308 and Kabir decreased number of methyla6on sites (39.46% vs 39.88% for ROSS 308, and 37.90% vs 38.73% for Kabir), Ancona increased it (43.11% vs 42.38%). Interes6ng polymorphisms will be sequenced in order to infer the role of methylated/
demethylated genes in metabolic pathways related to growth stresses. These methyla6on-­‐
polymorphisms could be therefore used as biomarkers to select chicken genotypes more resistant to environmental stresses, allowing an important improvement in poultry management. Acknowledgements This work has been funded under the Fondazione Cassa di Risparmio di Perugia project number 2010.011.0436 GENOMICS & EPIGENOMICS -­‐ Abstract N° 17 GENE NETWORKS FOR FEED EFFICIENCY IN NELORE CATTLE: INTEGRATION OF GENOME WIDE ASSOCIATION AND LIVER AND MUSCLE TRANSCRIPTOME INFORMATION Priscila S N Oliveira1, Andressa O. Lima2, Polyana C. Tizioto1, Wellison J. da S. Diniz2, Marcela M. de Souza,2, Luis L. Cou6nho3, James M. Reecy4, Jeremy F. Taylor5, Maurício A. Mudadu1 and Luciana C. A. Regitano1 Animal Science, Embrapa Ca:le Southeast , Rodovia Washington Luiz, Km 234 s/nº, Fazenda Canchim, 13560, São Carlos, BR 2 Gene6cs, Federal University of São Carlos, Rodovia Washington Luís, Km 235, s/n -­‐ Jardim Guanabara, , 13565, São Carlos, BR 3 Animal Science, University of São Paulo, Pádua Dias -­‐ Vila Independencia,, 13418, Piracicaba, BR 4 Animal Science, Iowa State University, 2255 Kildee Hall, 50010, Ames, US 5 Animal Science, University of Missouri, 135B Animal Science Research Center, 65211, Columbia, US 6 Animal Science, Embrapa Ca:le Southeast , Rodovia Washington Luiz, Km 234 s/nº, Fazenda Canchim, 13560, São Carlos, BR 1 Feed efficiency is a very important livestock produc6on trait. Elucida6ng the gene networks and pathways that underlie phenotypic varia6on using genome-­‐wide associa6on studies (GWAS) and RNAseq results has been u6lized to be:er understand the iden66es and func6on of genes that are poten6ally responsible for QTL. Previously, we reported a GWAS for 10 feed efficiency related traits that u6lized the BovineHD BeadChip (770K) genotypes from 593 Nelore steers using a Bayesian approach. An associa6on weight matrix (AWM) was constructed to elucidate the gene networks that are related to feed efficiency, in which the top 1% associated SNPs for each of the 10 target traits were u6lized. A SNP had to be significantly associated with residual feed intake (RFI) and/or a minimum of two other traits to be included in the matrix. Column-­‐wise Pearson correla6on coefficients between RFI and the other 9 target traits were calculated using the es6mated addi6ve effect of each SNP. These analyses yielded 4,493 SNPs for RFI (33,272 SNPs across all traits), which were used to infer linked genes based on the 1,954,404 correla6ons within a network. Arer applying Par6al Correla6on and Informa6on Theory (PCIT) and considering only significant correla6ons >0.99, we iden6fied 752 SNPs as nodes and 4,489 SNPs as edges. The network was next filtered using genes iden6fied as being differen6ally expressed in RNA-­‐seq analyses of the liver and muscle 6ssues of Nelore beef ca:le with divergent RFI phenotypes. The genes ATF3 (Ac6va6ng transcrip6on factor 3), CASQ2 (Calsequestrin 2), NIN ninein (GSK3B interac6ng protein), PCDH7 (Protocadherin 7), PRUNE2 (Prune Homolog 2,) and TIPARP (TCDD-­‐inducible poly (ADP-­‐ribose) were implicated by AWM and the RNA-­‐seq analyses as poten6al func6onal candidates related to biological processes that underlie feed efficiency in Nelore ca:le. GENOMICS & EPIGENOMICS -­‐ Abstract N° 18 GENETIC CONTRIBUTIONS TO TRAINING PROGRESSION IN THOROUGHBRED RACEHORSES Gabriella Farries1, Paul A McGebgan1, Ka6e Gough1, Beatrice A McGivney1, Lisa M Katz1 and Emmeline W Hill1 College of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, 4, Dublin, IE 1 Introduc6on Ap6tude for early training and racing is highly variable in racing Thoroughbred horses; this has implica6ons for prepara6on for early racing. It is hypothesised that this varia6on is heritable. Using training data, phenotypes relevant to training progression may be tested for heritable components. Methods A cohort of n=414 Thoroughbreds trained in the same racing yard were genotyped using the Illumina SNP70 Equine BeadChip. Dates of work days (intense sprint exercise bouts) were recorded between 1997-­‐2014. Phenotypes inves6gated were age in days at first work day (n=388) and interval in weeks between first and second work day (n=395). MSTN g.
6649373C>T genotype, previously associated with age at first win (unpublished) was recorded for each horse. Marker heritability (h^2) was es6mated using GCTA, and tests for genome wide associa6on were performed using GenAbel. Genome wide significance was determined using the Bonferroni correc6on, and sex and MSTN were used as covariates. Results Age at first work day had a heritability of h^2=0.27 using addi6ve gene6c variance with sex as a covariate, and h^2=0.21 using sex and MSTN. However, high standard error for these es6mates means they are not significant. Age at first work day between MSTN g.6649373C>T genotypes showed significant differences between CC horses and TT horses (p=7x10-­‐5), as well as between heterozygotes and TT horses (p=0.001). On average TT horses performed their first work day 5 weeks later than heterozygotes, and 6.5 weeks arer CC horses, irrespec6ve of the trainer’s knowledge of the MSTN genotype. Tests for genome wide associa6on did not iden6fy significant markers for this trait. However, interval in weeks between first and second work day showed significant associa6ons on chromosomes 1, 4 and 23. Heritability from addi6ve and dominant gene6c variance was h^2=0.30 using sex as a covariate and 0.33 using sex and MSTN. High standard error meant these es6mates were not significant. Conclusions This early inves6ga6on supports a role for MSTN g.6649373C>T genotype in determining age at first work day. No significant associa6ons between other gene6c loci and age at first work day, or accurate measurement of heritability could be determined in the current sample. Significant associa6ons with interval in weeks between first and second work day were iden6fied, however further refinement of the phenotype is needed to be:er determine func6onal implica6on GENOMICS & EPIGENOMICS -­‐ Abstract N° 19 GENETIC INTROGRESSION THROUGH SELECTION IN DOMESTIC CHICKENS: INSIGHT FROM WHOLE GENOME SEQUENCE ANALYSIS Raman Akinyanju Lawal 1 and Olivier Hano:e1 School of Life Sciences, The University of Nobngham, University Park, NG72R, Nobngham, GB 1 Domes6ca6on of chicken occurred for at least 5400 years ago from its main maternal ancestor, Gallus gallus spp. From its centre(s) of domes6ca6on in South and/or Southeast Asia, domes6c chicken has migrated to different parts of the world and adapt to varying agro-­‐ecological condi6ons. Indigenous chickens represent a major asset to farmers. They have been subjected to both natural and human-­‐driven selec6on leading to a mosaic of gene6c structure and extensive phenotypic diversity. In this study, we assess the presence of introgressed haplotypes from non-­‐Gallus gallus jungle fowl species (G. sonnera6i, G. lafaye6i and G. varius) into domes6c chicken’s popula6on using full genome sequence analysis. We present the results from two indigenous chicken popula6ons from Ethiopia. Following, a new admixed pooled popula6on heterozygosity (Hp) analysis approach, and pairwise popula6on specific Fst analysis, several candidates’ popula6on or domes6c specific introgressed selected genomic regions were iden6fied. Outputs from this study are expected to contribute to advance knowledge on the evolu6onary history and adapta6on of wild and domes6c fowls. GENOMICS & EPIGENOMICS -­‐ Abstract N° 20 GENOME-­‐WIDE ANALYSIS OF MILK QUALITY TRAITS OF COMISANA SHEEP BY CANONICAL DISCRIMINANT ANALYSIS Gius6no Gaspa1, Mariasilvia D'Andrea2, Corrado Dimauro1, Silvia Sorbolini1, Nicolò Maccio:a1 and Fabio Pilla2 1 Dipar6mento di Agraria, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, IT Dipar6mento Agricoltura, Ambiente e Alimen6, Università degli Studi del Molise, Via Francesco de Sanc6s, 86100, Campobasso, IT 2 Milk fa:y acid (FA) profile may affects market values of sheep dairy products. Milk fat composi6on has also a relevant impact both on human health and environmental issue (FA as proxy methane emission). However, the FA profile is complex phenotypes regulated by a network of genes ac6ng in a very complex manner. The recent availability of high-­‐throughput plaŒorm is a powerful tool to iden6fy genomic region associated with milk FA. The analysis of high-­‐dimensional genomic and phenotypic data, requires ad hoc sta6s6cal approaches. In this framework, the Canonical Discriminant Analysis (CDA) can be used to inves6gate the genomic determinism of FA profile. CDA is a classifica6on technique whose main objec6ves are: a) the assessment of the adequacy of a classifica6on, given a group variable (FA profiles in our case); b) objects assignment to one of the involved known groups (e.g. genotypes at thousand loci). Objec6ve of the present study is to test CDA with the aim of iden6fy genomic region associated to milk FA. A total of 198 sheep of the breeding nucleus located at Asciano (Italy) were genotyped with the Illumina BeadChip (54,241 SNPs). Arer data edi6ng 46,465 SNP and 178 animals were used. The FA profiles of 178 sheep was determined (67 FA variables), and a selected panel of 17 FA was later used. The raw phenotypes were corrected for the fixed effect of parity, days in milk and for the random animal effect, predicted through the inclusion of the genomic rela6onship matrix. The residuals of the previous model were used as an mul6-­‐dimensional phenotypes and analyzed with CDA. One CDA at 6me was run for each SNP. The genotype, coded as 0,1 or 2, were used as classificatory variables and the FA profile was used to es6mate the canonical func6on (CF) able to discriminate the individual with different genotype.The ability of FA profile to discriminate among animals that carried different allele was evaluated by mul6variate Wilks’ lambda sta6s6cs computed at each locus. Twenty-­‐four SNP (in 10 chromosomes) whose genotypes were highly discriminated using the CF of FA profile were found. Some of them were nearby genes previously reported to affect the milk fat composi6on. Some example are SNP OAR3_184274860 (171,674,185 bp) close to IGF1 located in OAR3 (171,252,000 bp); s29492 (64,853,293 bp) near to GHRHR (65,348,751 bp) on OAR4 and OAR14_37391612 (35,940,842 bp) close to LCAT (34,760,867bp) on OAR14. Acknowledgement: MIPAF (grant INNOVAGEN). GENOMICS & EPIGENOMICS -­‐ Abstract N° 21 GENOME-­‐WIDE ASSOCIATION STUDY FOR IGG ANTI-­‐
LEISHMANIA (LEISHMANIA) INFANTUM RESPONSE IN DOGS EXPOSED TO LUTZOMYIA LONGIPALPIS Luís Fábio Da Silva Ba6sta1, Yuri Tani Utsunomiya2, Rafaela Beatriz Pintor Torrecilha2, Thaís Bruna Ferreira da Silva1, Raíssa Dias de Andrade1, Thaíse Yumie Tomokane1, Acácio Duarte Pacheco2, Mary Marcondes2, José Fernando Garcia2, Cáris Maroni Nunes2 and Márcia Dalastra Lauren61 Laboratory of Pathology of Infec6ous Disease, School of Medicine, University of São Paulo, Av. Dr. Arnaldo, 455, Cerqueira César, CEP 01246903, 01246, São Paulo, SP, BR 2 Department of Support, Produc6on and Animal Health; Department of Clinic, Surgery and Animal Reproduc6on, Universidade Estadual Paulista, Clóvis Pestana, 793, Ipanema, CEP 16050680 , 1605, Araçatuba, SP, BR 1 Leishmania (Leishmania) infantum is the protozoan responsible for visceral leishmaniasis (VL), a neglected zoonosis that affects about 500,000 people a year and may be lethal if not treated. The domes6c dog (Canis lupus familiaris) is the major reservoir of VL and exhibits highly variable clinical responses. From the immunological point of view, highly ac6ve parasite infec6on is marked by increased immunoglobulin G (IgG) level. Here, we sought evidence for loci affec6ng differences in IgG produc6on in 189 dogs from endemic area genotyped for 173,662 single nucleo6de polymorphism (SNP) markers by Illumina® CanineHD BeadChip assay. Exposure to the vector was assumed upon detec6on of an6bodies an6-­‐saliva of the Lutzomia longipalpis sand fly. Serum IgG an6-­‐L. (L.) infantum were quan6fied by enzyme-­‐linked immunosorbent assay (ELISA). Phenotypes were normalized using a Box-­‐Cox transforma6on, and the following linear model was applied to both traits: y ~ mean + age + sex + vaccina6on + deltamethrin collar + origin. The residuals from the fi:ed model were used as pseudo-­‐phenotypes for the genome-­‐wide associa6on (GWA) analyses, which were performed using the EMMAX method. Only markers and samples presen6ng a call rate of at least 90% were considered. Addi6onally, SNPs with minor allele frequency lower than 2% were removed prior to the GWA scan. Markers were priori6zed for inves6ga6on based on a significance level of 1 x 10e-­‐4. We observed a gradual rise of IgG levels associated with increasing severity of the disease (p < 0.001). A total of 185 dogs and 143,971 SNPs passed all filtering criteria. Eighteen SNPs were declared significant, which were in the vicinity of posi6onal candidates likely involved in IgG produc6on or resistence/suscep6bility to Leishmania infec6on, such as: CD180 on chr2 (p=8.81x10e-­‐5) that cooperates with toll-­‐like receptor 4 to induce produc6on of IgG and subsets of memory B lymphocytes, independent of T cells response; FLT on chr25 (p=7.9x10e-­‐5) that codes for a tyrosine kinase receptor involved in apoptosis, prolifera6on and differen6a6on of hematopoie6c cells; NOX on chr30 (p=2.14x10e-­‐5) that encodes NADPH oxidase responsible for the cataly6c one-­‐electron transfer of oxygen to generate superoxide or hydrogen peroxide, related as leishmanicidal molecules. These findings suggest that gene6c control may underly IgG produc6on in canine visceral leishmaniasis in a polygenic manner. GENOMICS & EPIGENOMICS -­‐ Abstract N° 22 GENOMIC RETROSPECTIVE EVALUATION OF 20 YEARS OF SELECTION IN ITALIAN HOLSTEIN BULLS FOR FEET AND LEGS TRAIT Andrea Talen61, Marco Milanesi2, Ezequiel L. Nicolazzi3, Stefano Frabni1, Beatrice Coizet1, Giulio Pagnacco1, John L. Williams4, Alessio Valen6ni5, Alessandro Nardone5, Jan-­‐Thijs Van Kaam6, Paolo Ajmone-­‐Marsan2 and Paola Crepaldi1 1 Department of veterinary science and public health, University of Milan, Via Celoria 10, 20133, Milan, IT 2 Is6tuto di Zootecnica, Università Ca:olica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, IT Bioinforma6cs core facility, Fondazione Parco Tecnologico Padano, Via Einstein, Cascina Codazza, 26900, Lodi, IT 4 School of Animal and Veterinary Science, University of Adelaide, Mudla Wirra Road, 5371, Roseworthy SA, AU 5 Dipar6mento per l’Innovazione dei sistemi Biologici, Agroalimentari e Forestali, Università degli studi della Tuscia, Via San Camillo de Lellis, 01100, Viterbo, IT 6 Research and Development, Associazione Nazionale Allevatori Frisona Italiana, via Bergamo, 292, 26100, Cremona, IT 3 Under strong direc6onal selec6on, allele frequencies rapidly change, allowing the iden6fica6on of genomic regions carrying genes and variants that control selected traits, as produc6on, func6onal and morphological traits. Here we searched selec6on sweeps by birth date regression on EBVs and the analysis of changes in allele frequencies. Genomic retrospec6ve evalua6on of recent selec6on was performed in 2918 Italian Holstein bulls born between 1979 and 2011. Genotype data from SELMOL, PROZOO and INNOVAGEN projects were used. Es6mated Breeding Value (EBVs) for 32 traits were provided by the Italian Holstein associa6on (ANAFI). Bulls were genotyped with BovineSNP50 v.1 and BovineHD SNPchips. SNPs posi6ons were updated to UMD3.1 using SNPchiMp v.3. Genotypes were imputed using BEAGLE (v.3.3.4) to obtain HD genotypes for all individuals. Arer quality control, a total of 2918 animals and 613,956 SNPs were included in the working dataset. Birth date regressed on Feet and Legs EBV shows a strong posi6ve trend in the birth date interval analyzed. To detect genomic regions involved, we first iden6fied PLUS-­‐ and MINUS-­‐
variant animals for the target EBV over the total year range (134 bulls, group OVERALL) and within each birth year (130 bulls, group BY_YEAR). Then, SNP allelic frequencies, within each group, were obtained for PLUS and MINUS variants pools and the absolute allele frequency difference (delta) was calculated. Mean delta values were es6mated in overlapping sliding windows of 50 SNPs. Only windows with the mean delta above the 75th percen6le + 1.5*Interquar6le range were retained. Only overlapping regions between OVERALL and BY_YEAR group were retained. These regions cover the 0.84% of the total windows analyzed. Among these, two regions seem par6cularly interes6ng. The ~686 Kb region on BTA10 (from posi6on 62,578 to 63,264 Kb) had the highest mean delta on BY_YEAR. The ~417 Kb region on BTA20 (from posi6on 40,738 to 41,155 Kb) had the highest mean delta on OVERALL. Bioinforma6c analysis is underway to iden6fy candidate genes, QTLs and metabolic pathways under selec6on for this trait. Acknowledgement The research was supported by the project SELMOL, PROZOO and INNOVAGEN (Italian MIPAAF Ministry). We are grateful to ANAFI for providing EBVs. GENOMICS & EPIGENOMICS -­‐ Abstract N° 23 GENOMIC TOOLS ALLOW ROBUSTNESS DETECTION IN RED-­‐LEGGED PARTRIDGES (ALECTORIS RUFA) Natalia Sevane1, Javier Cañon1, Ignacio Gil1 and Susana Dunner1 Animal Produc6on, Universidad Complutense de Madrid, Av. Puerta de Hierro, s/n, 28040, Madrid, ES 1 Present and future challenges for wild partridge popula6ons include the resistance against possible disease transmission arer restocking with cap6ve-­‐reared individuals, and the need to cope with the stress prompted by new dynamic and challenging scenarios, including consequences of climate change. Selec6on of individuals with the best immune func6on may be a good strategy to improve general immunity, and hence adapta6on to stress. In this study, non-­‐infec6ous challenges with phytohemagglu6nin (PHA) and sheep red blood cells allowed the classifica6on of red-­‐legged partridges (Alectoris rufa) according to their overall immune responses (IR). Skin from the area of injec6on of PHA and spleen, both from animals showing extreme high and low IR, were selected to inves6gate the transcrip6onal profiles underlying the different ability to cope with pathogens and external aggressions. RNA-­‐seq yielded 97 million raw reads from eight sequencing libraries and about 84% of the processed reads were mapped to the reference chicken genome. Differen6al expression analysis iden6fied 1488 up-­‐ and 107 down-­‐regulated loci in individuals with high IR versus low IR. Partridges displaying higher innate IR show an enhanced ac6va6on of host defence gene pathways complemented with a 6ghtly controlled desensi6za6on that facilitates the return to cellular homeostasis. These findings indicate that the immune system’s ability to respond to environmental aggressions extensively involved transcrip6onal and post-­‐transcrip6onal regula6ons, and expand our understanding on the molecular mechanisms of the avian immunity system, opening the possibility of improving disease resistance or robustness using genome assisted selec6on approaches for increased innate IR in partridges. GENOMICS & EPIGENOMICS -­‐ Abstract N° 24 GHAP: AN R PACKAGE FOR GENOME-­‐WIDE HAPLOTYPING Yuri Tani Utsunomiya1, Marco Milanesi2, José Fernando Garcia3 and Paolo Ajmone-­‐Marsan2 Departamento de Medicina Veterinária Preven6va e Reprodução Animal, UNESP -­‐ Univ Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884, Jabo6cabal -­‐ SP, BR 2 Is6tuto di Zootecnica, Università Ca:olica del Sacro Cuore, Via Emilia Parmense 84, 29122, Picenza, IT 3 Departamento de Apoio, Produção e Saúde Animal, UNESP -­‐ Univ Estadual Paulista, Rua Clóvis Pestana, 79, 16050, Araçatuba -­‐ SP, BR 1 The use of genome-­‐wide single nucleo6de polymorphism (SNP) markers in genomics relies on the concept of linkage disequilibrium and tagging, such that the informa6on from unobserved sequence variants can be indirectly captured by correla6on with nearby surrogate polymorphic sites. The majority of the methods available for the analysis of SNP data considers single markers, ignoring that signals coming from unobserved variants may be be:er modeled by the use of phase and haplotype informa6on. In spite of the increasing interest of the community in migra6ng from single-­‐marker to haplotype analyses, the absence of standards and tools to perform haplotype calls from phased data hampers the progress in the field. Therefore, we present the Ghap v1.0 R package, which implements func6ons for manipula6ng haplotypes from phased SNP data. The package can import popular input formats (e.g., Beagle3 and SHAPEIT2), construct haplotype libraries from user-­‐defined blocks, and generate a matrix of haplotype counts per individual (0, 1 or 2). As a general framework, this matrix can be used in third party sorwares as they were bi-­‐allelic SNP markers, facilita6ng the incorpora6on of haplotype informa6on in exis6ng pipelines. Addi6onally, the package also computes kinship matrices and popula6on gene6cs sta6s6cs, such as Hardy-­‐Weinberg Equilibrium, FST, heterozygosity, frequency and expected and observed number of homozygotes. The package is available for tes6ng at the github repository: h:ps://bitbucket.org/marcomilanesi/ghap GENOMICS & EPIGENOMICS -­‐ Abstract N° 25 IDENTIFICATION AND CHARACTERIZATION OF COPY NUMBER VARIANTS IN CATTLE Rabia Letaief1, Dominique Rocha1 and Mekki Boussaha1 UMR1313, Géné6que Animale et Biologie Intégra6ve, INRA, Domaine de Vilvert, 78352, Jouy en Josas, FR 1 Structural variants including Copy Number Variants (CNVs) are an important class of gene6c changes in mammals. They were discovered for the first 6me in Human. CNVs are defined as gain or loss of DNA segments ranging from 50 pb to several megabases. Several studies revealed CNVs’ involvement in phenotypic changes in many species including ca:le. These studies showed more significant effect of CNVs than SNPs (Single Nucleo6de Polymorphisms). The majority of CNV studies in ca:le used SNP genotyping data. More recently, CNVs iden6fica6on became more exhaus6ve and precise using very high-­‐throughput-­‐based sequencing approaches. Up to now, there are very few studies which combine both genotyping-­‐ and sequencing-­‐based methods in ca:le. In addi6on, only one study surveyed CNVs in French bovine breeds, using genotyping data. In the present study, we analyzed whole-­‐genome sequences of 250 bulls, and genotyping data for 4,500 animals using the Illumina BovineSNP HD BeadChip. These animals were from 20 different beef and dairy breeds. Search for CNVs was performed using Pindel, CNVnator, Delly and BreakDancer tools for sequencing data and PennCNV and GADA sorwares for genotyping data. Predicted CNVs were subsequently merged in order to define poten6al CNV regions. A panel of predicted CNVs will be validated using different methods such as CGH array, SNP genotyping or quan6ta6ve PCR. The impact of CNVs on rou6nely measured traits in ca:le will also be assessed later on. GENOMICS & EPIGENOMICS -­‐ Abstract N° 26 IDENTIFICATION OF GENOMIC REGIONS RELATED WITH BACKFAT THICKNESS IN NELLORE CATTLE Minos Esperandio Carvalho1, Fernando Reys Baldi2, Miguel Henrique de Almeida Santana1, Ricardo Vieira Ventura1, Gerson Antonio Oliveira Jr1, Rachel Santos Bueno1, Marina Nadai Bonin3, Fernanda Marcondes Rezende4 and Jose Bento Sterman Ferraz1 1 Med. Veterinary, University of Sao Paulo, Duque de Caxias, 225, 13625, Pirassununga, BR 2 Animal Science, Sao Paulo State University, Via Prof. Paulo Donato Castellani, 14884, Jabo6cabal, BR 3 Beef Ca:le, Embrapa Beef Ca:le, Av. Radio Maia, 830, 79106, Campo Grande, BR Med. Veterinary, Federal University of Uberlandia, Av. Para, 1720, 38400, Uberlandia, BR 4 The aim of this study was to iden6fy, by ssGWAS, genomic regions that poten6ally have associa6on with backfat thickness in Nellore ca:le. Phenotypes were obtained of 782 Nellore bulls slaughtered at around 24 months of age. The steak from the 12th rib was used to measure backfat thickness, where the values varying between 0 and 15 mm, with mean equal to 4.07mm. Animals were genotyped with Illumina Bovine beadchip HD®GGPi (74K). Based on another Nellore popula6on genotyped for Illumina beadchip BovineHD® (777K), genotypes were imputed by FImput sorware. Analyses were performed using a pedigree composed by 6,276 animals and, assuming contemporary group (farm and slaughter batch) as fixed effect and age at slaughter as a covariate. Single step analyses were realized by Blupf90 program considering windows of 10 markers (SNP) to es6mate their effects, this procedure enables the iden6fica6on of regions associated with backfat thickness along the chromosomes. Arer quality control (MAF <0.05%, call rate <90%), 463.995 SNPs in autosomal chromosomes were used in the associa6on analyses. Based on that, 16 regions in 11 different chromosomes (2, 6, 7, 8, 9, 14, 15, 17, 22, 23 and 29), that explained more than 1% of the addi6ve variance, were explored and some genes were iden6fied in these regions, as PDE6D, PCSK5, PRDM1, TPD52, EXT1, ITGA9 and U6. With ssGWAS method using high density panel was possible to iden6fy regions related with backfat thickness in Nellore beef ca:le. Posteriorly, these genes and their pathways will be inves6gated to evaluate their importance for meat quality traits. GENOMICS & EPIGENOMICS -­‐ Abstract N° 27 IDENTIFICATION OF KNOWN AND NOVEL QTLS FOR BODY SIZE IN BOS INDICUS COWS Tamíris Sayuri Aguiar1, Yuri Tani Utsunomiya1, Márcio Da Silva Costa2, Anirene Galvão Tavarez Pereira3, Haroldo Henrique de Rezende Neves1, Roberto Carvalheiro1, Adriana Santana do Carmo1, Johann Sölkner4, José Lindenberg Sarmento2 and José Fernando Garcia1 Faculdade de Ciências Agrárias e Veterinárias. Jabo6cabal, UNESP -­‐ Universidade Estadual Paulista. , Via de Acesso Prof. Paulo Donato Castellan, Vila Industrial, 14884, Jabo6cabal , BR 2 Pós-­‐Graduação em Ciência Animal, UFPI – Universidade Federal do Piauí., Campus Universitário Ministro Petrônio Portella, Bairro Ininga, 64049, Piaui, BR 3 ESALQ -­‐ Departamento de Agroindústria, alimentos e nutrição, USP-­‐ Escola Superior de Agricultura “Luiz de Queiroz”, Av. Pádua Dias, 11 , 1341, Piracicaba, BR 4 Department of Sustainable Agricultural Systems, Division of Livestock Sciences, BOKU -­‐ University of Natural Resources and Life Sciences,, Gregor-­‐Mendel-­‐Straße 33, 1180, Viena, AT 1 We performed a genome-­‐wide scan for loci affec6ng birth weight (BW) in 761 Nellore cows (Bos indicus) genotyped for over 777,000 single nucleo6de polymorphism (SNP) markers. Records were pre-­‐adjusted for the fixed effects of age of dam at calving and contemporary group. Es6mates of marker effects were obtained using the BayesC method, assuming that a small frac6on of the SNPs (0.1%) had normally-­‐distributed effects on the trait. Addi6onally, as the effect of a quan6ta6ve trait locus (QTL) is deemed to be distributed across nearby SNPs in linkage disequilibrium in the BayesC analysis, the addi6ve variance explained by markers was smoothed across the genome by summing over sliding windows of 1 Mb, sliding 50 kb at a 6me. Windows explaining 1% or more of the addi6ve variance were declared QTLs. The SNPs selected by the BayesC analysis could account for as much as 33.0% of the phenotypic variance of BW. A total of 10 candidate regions were iden6fied. Interes6ngly, two well known QTLs for BW on chromosomes 6 and 14 were detected in this analysis. The QTL at 14:24.05-­‐26.05Mb maps to the PLAG1 (pleiotropic adenoma gene 1) region, which is deemed to affect fetal growth and reproduc6on by the trans-­‐ac6ng regula6on of the expression of insulin-­‐like growth factors. The QTL at 6:36.8-­‐38.75 Mb is in the immediate vicinity of NCAPG (non-­‐SMC condensin I complex, subunit G; also known as HCAP-­‐G) and LCORL (ligand dependent nuclear receptor corepressor-­‐like). The la:er gene was shown to be associated with development and body size in horses. Also, recent studies indicated that polymorphisms in the NCAPG gene may affect carcass size in ca:le. Addi6onally, a novel QTL was also iden6fied on the segment spanning chromosome 2:104.1-­‐105.8 Mb, mapping to the short stature homeobox gene (SHOX). Dele6ons of this gene have been shown to cause growth failure in children with short stature. These findings should contribute to the further gene6c dissec6on of body size and growth in Bos indicus ca:le. GENOMICS & EPIGENOMICS -­‐ Abstract N° 28 IDENTIFICATION OF NOVEL SNPS OF OVINE PRL GENE AND THEIR ASSOCIATION WITH MILK PRODUCTION TRAITS Ozge Ozmen1 and Selim Kul2 Gene6cs, Ankara University , Faculty of Veterinary Medicine, Diskapi, , 06110, Ankara, TR Animal Breeding, Firat University , Faculty of Veterinary Medicine, 23110, Elazig, TR 1 2 Prolac6n is a polypep6de produced not only by the pituitary gland but also by mammary gland. This hormone has over 300 func6ons and it plays a crucial role in mammary gland development and lactogenesis. Therefore, PRL also could be used as a posi6onal marker gene associated with milk produc6on and composi6on traits. The purpose of the study was to iden6fy genotype frequencies of single nucleo6de polymorphisms the intron 2 in ovine PRL gene and its possible associa6on genotypes with milk traits in dairy sheep breeds by means of PCR-­‐RFLP and DNA sequencing assays. A hundred firy blood samples each from Sakiz, Akkaraman and Awassi ewes, with total of 450 samples were used in the experiment. Animals were chosen at random and were 4 years old, mul6parous and lacta6ng ewes and in their third lacta6on. PRL genotype AA showed a strong associa6on with milk yield content , whereas the animals carrying BB genotype had a higher fat percentage value in the Sakiz, Akkaraman and Awassi sheep breeds. Haplotype analysis of the obtained sequences showed the presence of 48 single nucleo6de polymorphisms in the PRL intron 2 region. A total of 12 haplotypes were detected, but no significant associa6ons with milk produc6on traits have been found. In the present study, we have reported here for the first 6me 48 SNPs of the PRL gene for intron 2 and its associa6on with milk traits in Sakiz, Akkaraman and Awassi sheep breeds. GENOMICS & EPIGENOMICS -­‐ Abstract N° 29 IDENTIFICATION OF SIGNATURES OF SELECTION AND ASSESSING THE DIVERSITY OF EAST AFRICAN SHORTHORN ZEBU MITOCHONDRIAL DNA Hussain Bahbahani1, Joram Mwacharo1 and Olivier Hano:e1 School of Life Sciences, University of Nobngham, University Park, NG7 2, Nobngham, GB 1 The full mtDNA sequences of several modern ca:le breeds have confirmed two separate domes6ca6on centres for the taurine Bos taurus taurus and zebu Bos taurus indicus subspecies in the Near East and the Indian subcon6nent respec6vely. These sequences have further divided modern ca:le to different sub-­‐haplogroups, encompassing the main T (taurine-­‐
specific) and I (zebu-­‐specific) macro-­‐haplogroups, with some breeds carrying rare Q and R haplogroups. Given the importance of the mitochondria in cell energy produc6on, mtDNA is expected to be a target of natural selec6on. We report here the comparison of the full mtDNA sequences of indigenous East African Shorthorn Zebu ca:le (EASZ) with ca:le breeds from Europe, Africa and Asia addressing three ques6ons i) the extent of EASZ mtDNA gene6c diversity; ii) the presence of signatures of selec6on in taurine mtDNA compared to zebu mtDNA; and iii) within African ca:le. Our results indicated that the EASZ mtDNA sequences are all of the taurine type and members of T1a, T1b and T1b1 sub-­‐haplogroups. Nineteen taurine-­‐zebu non-­‐synonymous variants were detected, but none seem to be associated with a selec6ve advantage for taurine mtDNA. Based on ω ra6o analyses, purifying selec6on is the main selec6on pressure targe6ng EASZ mtDNA with less selec6ve constrains at the ATP6 and ATP8 genes. Interes6ngly, within African ca:le, we iden6fied a posi6ve selec6on signal in the Cox-­‐2 gene in the T1b/T1b1 sub-­‐haplogroups, together the most common sub-­‐haplogroups on the con6nent. GENOMICS & EPIGENOMICS -­‐ Abstract N° 30 IDENTIFYING GENOMIC REGIONS RELATED TO RIB-­‐
EYE AREA USING GENOTYPES FROM COMBINED SNP PANELS Miguel Henrique de Almeida Santana1, Ricardo Vieira Ventura3, Minos Esperandio Carvalho2, Gerson Antonio Oliveira Junior2, Mateus C Freua2, Haja N Kadarmideen1 and José Bento Sterman Ferraz2 Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Fredericksberg, DK 2 Veterinary Medicine, Faculty of Animals Sciences and Food Engineering, University of São Paulo, Duque de Caxias Norte 225, 13635, Pirassununga, BR 3 Beef Improvement Opportuni6es, ., X, Ontario, CA 1 Carcass yield is very important for beef ca:le industry’s profit, and can be es6mated by ultrasound measurement of rib-­‐eye area (REA). The genomic and biological knowledge about this phenotype could be used for its improvement and this can be achieved by iden6fying genomic regions of large effect on this trait via genome-­‐wide associa6on studies (GWAS). The aim of this study was to iden6fy genomic regions related to REA by GWAS using a combina6on of two high-­‐density SNP panels. Genotype data from Illumina BovineHD® (777,962 SNPs) of 2604 bulls and from Affymetrix BOS1® (648,855 SNPs) of 279 bulls were combined to make a super-­‐dense panel (SDP) resul6ng in 1,260,707 SNPs. Phenotypes of REA (74.3±9.6 cm2) from 893 young Nellore bulls (484±71 kg, 21.5±1.2-­‐mo old), with their genotypes imputed to SDP (via FImpute), were used to perform GWAS with GRAMMAR-­‐Gamma associa6on test. The contemporary group and age were included as fixed effects and the significance threshold was computed as α/√nsnp where α is the nominal significance threshold of 0.05 and nsnp is total number of SNPs used in the analysis. Arer genotypic quality control, 941,033 SNPs in autosomal chromosomes (Chr) were used in associa6on analysis and seventy-­‐nine SNPs were significantly associated. Significant markers were on 17 different Chr and the most significant SNP was rs515977238 (Chr14:10387248, p=3.03x10-­‐7). However, we focus on Chr 1, 3, 5, 8, 17 and 20 with 16, 23, 5, 8, 5 and 9 significant SNPs, respec6vely. This GWAS using higher-­‐
density panel iden6fied some important genomic regions related to REA in beef ca:le. This can lead to other studies focused in these regions and herearer metabolic pathways that can be important to improving carcass yield and thereby profitability. GENOMICS & EPIGENOMICS -­‐ Abstract N° 31 INVESTIGATION OF BOS INDICUS AND BOS TAURUS ADMIXTURE IN SANGA CATTLE FROM UGANDA BY WHOLE-­‐GENOME SEQUENCE ANALYSIS Lorenzo Bomba1, Hans D Daetwyler2, Iona M MacLeod5, Sunduimijid Bolormaa2, Amanda J Chamberlain4, Licia Colli1, Marco Milanesi1, Elia Vajana1, Ben J Hayes2, Paolo Ajmone-­‐
Marsan1 and The NEXTGEN Consor6um6 Is6tuto di Zootecnica e BioDNA Centro di Ricerca sulla biodiversità e sul DNA an6co, Università Ca:olica del Sacro Cuore, via Emilia Parmense 84, 29122, Piacenza, IT 2 Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, research ring , 3086, Bundoora, AU 3 School of applied System Biology, La Trobe University, research ring , 3086, Bundoora, AU 4 Dairy Futures Coopera6ve Research Center, Dairy Futures Coopera6ve Research Center, research ring , 3086, Bundoora, AU 5 Department of Agriculture and Food System, University of Melbourne, Parkville, 3010, Melbourne, AU 6 NEXTGEN, EU funded project, FP7, 1000, Bruxelles, BE 1 African and Iranian ca:le have a complex history that s6ll needs to be fully elucidated. In par6cular, African "Sanga" ca:le likely derive from a cross between taurine and indicine breeds introduced in Africa 4000 and 2000-­‐3000 years ago, respec6vely. Iranian ca:le came from Bos taurus domes6ca6on center, and are thus generally considered of taurine origin, even if an introgression from Zebu during their migra6on to Africa 2000-­‐1500 years ago cannot be excluded. Ca:le crosses between Bos indicus (Bi) and Bos taurus (Bt) have composite chromosomes with Bt and Bi segments. Sor6ng out those segments would confirm genomic regions, poten6ally under divergent selec6on in African and Iranian ca:le, to be of indicine or taurine origin. By using whole genome sequences from 157 animals (Bt: Australian Angus (n=30), Jersey of Australian origin (n=30) and Australian Holstein (n=30); cross: Ugandan ca:le (n=26), Iranian ca:le (n=9); Bi: Australian Brahamans (n=32)), we iden6fied the Bt or a Bi ancestry of cross chromosome segments. Preliminary results suggest that 35% of the Ugandan ca:le genomes have Bi origin, 23% have taurine origin and the rest was unassigned. We iden6fied blocks of indicine origin in crossbred on chromosome 7 and 13, and a block of en6rely taurine origin on chromosome 23 in both crossbred and zebu subjects. Sliding window Fst analysis revealed a peak in the region of chromosome 7 previously iden6fied. Such region could poten6ally be under posi6ve selec6on in crosses. Genes in this region are involved in fer6lity and oxida6ve stress, as already reported by Porto-­‐Neto et al. (2013). Also the chromosome 13 region, of indicine origin, appears under posi6ve selec6on in zebu. This region overlaps the BMP2 gene involved in lipid metabolism. The taurine block in chromosome 23 overlaps the major histocompa6bility complex class II which is know to harbors 30 described CNV. This region was found to be in balancing selec6on. The high number of CNV in this region may indeed bias the variant calling by picking up mostly the taurine one. In conclusion, the present findings highlighted the presence in Iranian and Ugandan ca:le of genomic regions of indicine origin poten6ally linked to adapta6on to the tropical environment. GENOMICS & EPIGENOMICS -­‐ Abstract N° 32 INVESTIGATION OF GENOMIC REGIONS ASSOCIATED WITH HEAT STRESS RESPONSES IN PIGS Kwan-­‐Suk Kim1, Zewdu Edea1, Jacob T. Seibert2, Jason W. Ross2, Lance H. Baumgard2 and Max F. Rothschild2 1 Animal Science, Chungbuk Na6onal University, 1 Chungdae-­‐ro, Seowon-­‐gu, 36276, Cheongju, KR 2 Animal Science, Iowa State University, Kildee Hall, 50011, Ames, US Despite the well recogni6on of the effect of heat stress on pig produc6on and health, yet genomic regions responsible for varia6on in heat stress tolerance largely remain unexploited. The objec6ve of this study was to iden6fy chromosomal regions responsible for differences in biological responses during heat stress in maternal pigs. Physiological parameters recorded during the experimental periods include rectal and skin temperatures, respira6on rate, feed intake, body weight gain and loss and feed efficiency. A total of 236 crossbred female pigs were genotyped using GGP-­‐Porcine HD BeadChip which nearly contains 70,000 SNPs. Genome-­‐wide associa6on test was examined using single –locus mixed linear model method which includes a kinship matrix as a random effect. The mean rectal temperature under heat stress (39.82 ± 0.42 °C) was significantly higher than the mean under thermo-­‐neutral zone (39.03 ± 0.24 °C; P<0.0001). Heat stress increased respira6on rate (61%, P <0.0001), rectal temperature (2%, P<0.0001) and skin temperature (18%, P < 0.0001). Feed intake was significantly reduced to 1.80 ± 0.52 kg/day from was 2.47 ± 0.49 kg/day when animals were subjected to heat stress condi6ons. The region between 28 Mb and 29 Mb on chromosome 16 (5 SNPs) explained about 6% of the observed varia6on for delta respira6on and contained growth hormone (GHR) which is known to be associated with heat stress. The other important candidate gene with the close proximity to GHR is PAIP1 (29,584,628-­‐29,658,098 bp) which is known to be responsive to heat shock. Another SNP marker (ALGA0032572) which accounted for 7% and 5% of the varia6on for delta rectal temperature (1st) and delta respira6on, respec6vely was detected on SSC5 (69Mb)and located within TEAD4 (RTEF-­‐1) gene. The SNPs explaining the largest propor6on of variance and related to apoptosis or cellular stress (GHR, PAIP1, E2F3, NNMT, and TEAD4) are poten6al candidates for physiological adapta6on to heat stress. Further analyses of these detected regions will likely reveal poten6al candidate genes and suggest molecular mechanisms contribu6ng to the variability in the biological response of pigs to environmentally induced hyperthermia. GENOMICS & EPIGENOMICS -­‐ Abstract N° 33 INVESTIGATION OF SOX-­‐6 AS A CANDIDATE GENE FOR PORCINE GROWTH, CARCASS AND MEAT QUALITY TRAITS Rui Zhang1, Chris6ane Neuhoff1, Chris6ne Große-­‐Brinkhaus1, Muhammad Jasim Uddin2, Mehmet Ulas Cinar3, Dawit Tesfaye1, Ernst Tholen1, Chris6an Loor1 and Karl Schellander1 Ins6tute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115, Bonn, DE 2 School of Veterinary Science, University of Queensland, Via Warrego Highway, 4343, Ga:on, AU 3 Department of Animal Science, Erciyes University, Talas Bulvari 99, 38039, Kayseri, TR 1 The muscle pH value during post-­‐mortem period is one of the best predictors for meat quality (Monin, 1998) and associated with tenderness, water holding capacity and meat colour (Fernandez et al., 1994; Fernandez and Tornberg, 1994; van Laack et al., 2001). SOX-­‐6 is a versa6le transcrip6on factor and highly expressed in skeletal muscle. SOX-­‐6 can repress the specifica6on of slow fiber type during skeletal muscle differen6a6on. Muscle fiber is an important determinant for meat quality. This study was done to inves6gate the polymorphisms and expression of SOX-­‐6 to support its candidacy for growth, carcass, and meat quality traits in pigs. Two single nucleo6de polymorphisms (SNPs), rs81358375 and rs321666676, in SOX-­‐6 intron and exon were genotyped in Pietrain (Pi) and Duroc × Pietrain (DuPi) F2 popula6on. It was shown that rs81358375 was associated with pH 45 min post mortem (p.m.) in loin (pH1L), carcass length, dressing percentage, the thickness of backfat and side fat in Pi popula6on and with front backfat thickness and daily gain from birth to 30 kg (body weight) in DuPi popula6on. As for rs321666676, it was associated with conduc6vity 45 min (Con1L) and pH 24 h (pH24L) p.m. in loin, meat colour and the thickness of front backfat in Pi popula6on. In DuPi popula6on, protein level of SOX-­‐6 in high pH1L pigs was decreased compared with low pH1L pigs, while there was no significant difference for the mRNA expression. Furthermore, microRNAs targe6ng SOX-­‐6 were differently regulated between low and high pH1L pigs. This study shows that SOX-­‐6 is significantly associated with porcine growth, carcass, and meat quality traits based on chromosome posi6on, gene6c associa6on and gene expression. GENOMICS & EPIGENOMICS -­‐ Abstract N° 34 MITF GENE LOCUS IS ASSOCIATED WITH COAT COLOR VARIATION OF ETHIOPIAN CATTLE POPULATIONS ADAPTED TO DIFFERENT ALTITUDE ENVIRONMENTS Zewdu Bedada1 and Kwan-­‐Suk Kim1 Animal Science, Chungbuk Na6onal University, 410 Seongbong-­‐ro-­‐Heungduk-­‐gu, Department of Animal Science, 361-­‐7, Cheongju, KR 1 Along with environmental adapta6on, breed hybridiza6on contributed for the arrays of coat color phenotypes observed today among Ethiopian ca:le popula6ons. Breeds adapted to low-­‐
land agro-­‐ecology (Borana, Ogaden and Begait) display white, gray and combina6on of white and black with different levels of spobng. To the contrast, breeds adapted to high –al6tude environments such have Arsi, Arado and Guraghe are mainly display solid black, red, brown or mixture of various colors. Here we compared Ethiopian ca:le popula6ons characterized by heterogeneous coat color phenotypes for MITF locus iden6fied from 80K indicus SNP chip. When comparing the two groups of popula6ons (spo:ed and non-­‐spo:ed) we detect significant (P < 0.01) and high gene6c differen6a6on (Fst = 0.17), which indicate that the MITF locus might be influencing the observed coat color varia6ons among Ethiopian ca:le popula6ons adapted to different ecological condi6ons. GENOMICS & EPIGENOMICS -­‐ Abstract N° 35 MOLECULAR CHARACTERIZATION AND GENETIC DISTANCE EVALUATION BETWEEN TWO SHEEP BREEDES: THE TUNISIAN BARBARINE AND TUNIS SHEEP IN USA Gammoudi Anis1 and Bedhiaf Sonia2 Department of animal produc6on , I.N.A.Tunis (na6oanl Insitute of Agriculture Tunis, 43, Avenue Charles Nicolle 1082 -­‐Tunis-­‐ Mahrajène TUNISIE Tél: (+216) 71 287 110 / 71 289 431 / 71 892 785, 1082, Mahrajène, TN 2 Produc6on animal, INRATunis (Na6onal Ins6tute of Agronomic Research in Tunis), Rue Hédi Karray 2049 Ariana TUNISIE, 2049, Hédi karray, TN 1 A total of 116 blood samples of Barbarine breed raised in the central of Tunisia (Sidi Bouzid and Kairouan) and a total of 28 samples of Tunis sheep breed were used in this study. The main objec6ve was to evaluate the gene6c distance between the Barbarine and Tunis sheep of United States of America which was originated from the Barbarine. A panel of 28 microsatellites recommended by FAO was used in this study. Main results showed polymorphisms of 100% and 95% respec6vely for Tunis sheep and the Barbarine. The parameter values of the gene6c diversity of Tunis and Barbarine were 5,6 and 6,1 for the average number of alleles; -­‐0,014 and 0,295 for Fis; 0,687 and 0,485 for the observed heterozygosity. Fixa6on Index was 0.141 showing an overall deficit of heterozygo6es of 14%. The Fst coefficient was 0.119 showing that a large propor6on (88%) of the total gene6c varia6on was explained by the varia6on within popula6ons and the rest of this variability (12%) was allocated to the differences between popula6ons. The gene6c distance between the two breeds showed that the popula6on "Tunis" was far from the 10 other Barbarine popula6ons. Gene6c diversity within popula6ons and gene6c diversity inter popula6on (fixa6on index or F sta6s6cs, analysis of PCA results) showed that the existence of gene6cally dis6nct subpopula6ons. Two major implica6ons could be derived: 1) Possibil6es of selec6on within the iden6fied on subpopula6ons and 2) The urgence of preserving the iden6fies subpopula6ons before they become ex6nct. Keywords: Sheep, Barbarine, Tunis, diversity, microsatellites, gene. GENOMICS & EPIGENOMICS -­‐ Abstract N° 36 MOLECULAR KARYOTYPING OF THE PORCINE GENOME IN A SINGLE FISH EXPERIMENT Gothami Fonseka1, Rebecca O’Connor1, Richard Frodsham2, Mar6n Lawrie2 and Darren Griffin1 1 School of Biosciences, , University of Kent, , Stacey Building, UK, Canterbury. CT2 7NJ, GB Research and Development , Cytocell Ltd, Cambridge , Technopark, Newmarket Road,, UK, Cambridge. CB5 8PB, GB 2 Gross chromosomal aberra6ons such as transloca6ons are known to affect the fer6lity in most animal species. In pigs most of these remain undiagnosed due to lack of suitable tools available for breeders and veterinarians in the pig breeding industry. Here we introduce a simple fluorescence in situ hybridisa6on (FISH) based test named “The Porcine Chromoprobe Mul6probe® System” that uses porcine subtelomeric probes for the en6re karyotype in order to iden6fy these abnormali6es with greater accuracy. We then explain a case study where we u6lised this device to iden6fy a cryp6c transloca6on present in a boar, which could not previously be detected using standard karyotype analysis. FISH was performed using the Porcine Chromoprobe Mul6probe® System. The device consists of a glass slide divided into 24 squares; 19 squares carries subtelomere specific probes for both the p and q arms for each chromosome labelled in contras6ng colours. The probes are reversibly dried on to the device. During the FISH protocol the dried probes are re-­‐suspended using hybridisa6on buffer and then exposed to a corresponding glass slide with 24 equivalently sized squares, each spo:ed with the fixed pig cell sample containing metaphase spreads. Following co-­‐denatura6on, hybridisa6on occurs overnight. Next day, arer stringency washes and counterstaining, slides are ready for analysis. Case study: A male boar that showed low prolificacy was suspected to have chromosomal aberra6ons. Even though rou6ne karyotyping test was performed with the metaphases cultured from the boar, no abnormali6es were detected. The pig sample was tested using the newly developed Porcine Chromoprobe Mul6probe® System with the inten6on of finding any cryp6c transloca6on that might have been missed by standard karyotyping. A balanced cryp6c reciprocal transloca6on involving the q arms of chromosomes 5 and 6 was iden6fied. Cytocell’s Porcine Chromosome Paints were then used in order to validate these results. Results confirm the previous observa6ons gained from the Pig subtelomere device. Our results so far demonstrate that the Porcine Chromoprobe Mul6probe® System allows for robust and comprehensive analysis of the porcine karyotype in a 6me and cost-­‐effec6ve format. The system has been proven to iden6fy cryp6c transloca6ons that were previously undetectable by standard karyotyping illustrates the validity of the tool for the iden6fica6on of chrochromo GENOMICS & EPIGENOMICS -­‐ Abstract N° 37 NOVEL VARIANTS OF THE EQUINE ALPHA-­‐S2 CASEIN (CSN1S2) AND THEIR ASSOCIATION WITH GENE EXPRESSION LEVEL Jakub Cieslak1, Piotr Pawlak2, Lukasz Wodas1, Alicja Borowska1, Anna Stachowiak1, Kamila Puppel3, Beata Kuczynska3, Magdalena Luczak4, Lukasz Marczak4 and Mariusz Mackowski1 1 Department of Horse Breeding, Poznan University of Life Sciences, Wolynska 33, 60637, Poznan, PL Department of Gene6cs and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60637, Poznan, PL 3 Department of Animal Science, Ca:le Breeding Division, Warsaw University of Life Sciences, Ciszewskiego 8, 02786, Warsaw, PL 4 Department of Natural Products Biochemistry, Ins6tute of Bioorganic Chemistry, Noskowskiego 12/14, 61704, Poznan, PL 2 Despite caseins are the minor frac6on of mare's milk proteins their inves6ga6ons are steel of interest, mainly because of their role in modula6on of milk physicochemical proper6es and its allergenic poten6al. Among equine casein genes and protein products of their expression, the most limited informa6on is available for CSN1S2 (alpha-­‐s2 casein). Based on direct sequencing of the equine CSN1S2 cDNA (obtained on the basis of RNA isolated from mares’ milk soma6c cells) we described the presence of the two polymorphic forms (variants A and B, please see: KP658381 and KP658382 GenBank sequences), which differ in the presence or lack of the two exons (encoding the 17 aa serine-­‐rich pep6de). Predicted changes in protein sequence were confirmed by mass spectrometry analysis. Further studies revealed that this varia6on is an effect of the large (1.3 kb) dele6on in the genomic DNA, which occurs the most frequently in the cold-­‐blooded horses and Haflingers. Unfortunately, due to very complicated molecular context of the described dele6on (the beginning and the end located symmetrically in the perfectly duplicated region) its exact localiza6on is impossible, but despite of it, the effect of the dele6on on CSN1S2 protein structure is always predictable. Associa6on study has indicated that discovered polymorphic variants are puta6vely associated with the CSN1S2 expression level (the highest mRNA abundance and milk protein level no6ced for individuals carrying the BB genotype). Differences in CSN1S2 milk protein content were most pronounced in the case of Polish Cold-­‐blooded Horse (p<0.01), wheras if all breeds were considered together, the calulated significancy was lower (p<0.05). Our study may be an interes6ng introduc6on for further func6onal analyses regarding e.g. the allergenicity of described CSN1S2 polymorphic variants and their impact on milk physicochemical proper6es. The study was funded by the Na6onal Science Centre (Poland), grant: 2011/03/D/NZ9/05337 GENOMICS & EPIGENOMICS -­‐ Abstract N° 38 ON THE GENETIC STRATIFICATION OF IMMUNOLOGICAL RESPONSE TO VISCERAL LEISHMANIASIS IN DOGS Rafaela Beatriz Pintor Torrecilha1, Luis Fabio Ba6sta2, Yuri Tani Utsunomiya1, Raíssa Dias De Andrade2, Thaís Bruna Ferreira Da Silva2, Thaíse Yumie Tomokane2, Acácio Duarte Pacheco4, Mary Marcondes4, Cáris Maroni Nunes3, Márcia Dalastra Lauren62 and José Fernando Garcia3 Departamento de Medicina Veterinária Preven6va e Reprodução Animal, UNESP -­‐ Univ Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884, Jabo6cabal -­‐ SP, BR 2 Departamento de Patologia, USP -­‐ Universidade de São Paulo, Av. Dr. Arnaldo, 455, 01246, São Paulo -­‐ SP, BR 3 Departamento de Apoio, Produção e Saúde Animal, UNESP -­‐ Univ Estadual Paulista, Rua Clóvis Pestana, 79, 16050, Araçatuba -­‐ SP, BR 4 Departamento de Clínica, Cirurgia e Reprodução Animal, UNESP -­‐ Univ Estadual Paulista, Rua Clóvis Pestana, 79, 16050, Araçatuba -­‐ SP, BR 1 Visceral leishmaniasis (VL) is an anthropozoonosis caused by Leishmania (Leishmania) infantum parasites. The domes6c dog (Canis lupus familiaris) is the main reservoir of the disease, and empirical clinical findings suggest that dis6nct dog breeds respond differently to infec6on, indica6ng a gene6c component in the immunological response against the disease. Here, we aimed at inves6ga6ng the existence of gene6c stra6fica6on in immunological response to VL by contras6ng infected Ro:weiler (RWL, n = 35), Labrador Retriever (LBD, n = 58) and Shepherd dogs (SPD), including German (n = 32), Belgian (n = 14), and White Swiss (n = 2) Shepherds. All samples were genotyped using the Illumina® CanineHD BeadChip assay (~170,000 markers). Benchmark indicators of response against Leishmania (L.) infantum in dogs are circula6ng an6bodies and cytokines. Therefore, we obtained phenotypic records for each animal for serum levels of immunoglobulins A (IgA), G (IgG), E (IgE) and M (IgM) by enzyme-­‐
linked immunosorbent assay (ELISA). We also measured interferon gamma (IFN-­‐ γ) and tumor necrosis factor alpha (TNF-­‐ α) in s6mulated peripheral blood mononuclear cell cultures supernadants by ELISA. Gene6c stra6fica6on was determined by a pairwise Principal Components Analysis of the genotype matrix, such that the first principal component (PC1) explained the largest gene6c differences between the two groups being compared. For each trait, phenotypes were normalized using a Box-­‐Cox transforma6on. The linear model applied to all traits was y ~ mean + age + sex + vaccina6on + deltamithrin leash + origin + PC1. The analysis revealed significantly higher levels of IgG in RWL in comparison to LBD (p = 0.037) and SPD (p = 0.008). Sugges6ve increases in IgE were also found when RWL was contrasted against the other breeds (p < 0.1). Addi6onally, RWL seemed to have higher levels of IFN-­‐ γ (p = 0.096) and TNF-­‐ α (p = 0.010) than LBD, although this trend was not observed in comparison to SPD. The only sugges6ve increase in immunoglobulins in LBD was observed for IgA in comparison to SPD (p = 0.094). Overall, these findings suggested a gene6c stra6fica6on of immune response, namely higher produc6ons of IgG, IgE, IFN-­‐ γ and TNF-­‐ α in the RWL gene6c background. GENOMICS & EPIGENOMICS -­‐ Abstract N° 39 PRNP POLYMORPHISMS IN FOUR ITALIAN SHEEP BREEDS Emiliano Lasagna1, Ludovica Curcio2, Carla Sebas6ani2, Marcella Ciullo2, Piera Di Lorenzo1, Simone Ceccobelli1, Francesca Maria Sar61, Giovanni Pezzob2 and Massimo Biageb2 Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX giugno 74, 06121, Perugia, IT 2 Area Ricerca e Sviluppo, Is6tuto Zooprofilabco Sperimentale dell’Umbria e delle Marche, Via G. Salvemini, 1, 06126, Perugia, IT 1 Prions are responsible for transmissible spongiform encephalopathies (TSEs), also called scrapie in sheep. Single nucleo6de polymorphisms (SNPs) in PRNP have been shown to play a crucial role in terms of incuba6on period and/or suscep6bility to scrapie. Considering codons 136, 154 and 171, five main alleles, associated with different degrees of suscep6bility to classical scrapie, have been detected. Allelic and genotypic PRNP frequencies were measured in four sheep breeds reared in central Italy. A total of 647 whole blood samples, taken from only females, belonging to meat breeds as Appenninica (n=169, 12 flocks) and Bergamasca (n=100, 4 flocks) and to dairy breeds as Comisana (n=100, 5 flock) and Sarda (n=278, 9 flocks) were collected. Genomic DNA was extracted by a semi-­‐automa6c extractor (BioSprint 96, Qiagen®, Hilden, Germany). Genotyping analysis of codons 136, 154, and 171 was performed following the real 6me PCR protocol. A total of 146 homozygous ARQ animals were found: 32 in Appenninica, 38 in Bergamasca, 22 in Comisana and 54 in Sarda, thus they have been sequenced to detect allelic variants with the purpose of checking their possible scrapie-­‐
protec6ve role. The allelic variant AR101RQ was found only in the Appenninica breed. The AT112RQ was detected at high level in Comisana (31.8%), followed by Bergamasca (14.5%) and Appenninica (6.3%) breeds. Sarda breed is the only one showing the AS127RQ. AF141RQ allele, responsible of suscep6bility to atypical scrapie, was not detected in Bergamasca and Comisana. Bergamasca sheep showed the AR143RQ allele in a low frequency. Data analysis confirmed the presence of ARQK176 exclusively in the Sarda sheep. In this study was not found any AT137RQ muta6on associated with good level of gene6c resistance as it was observed in Sarda breed from other Italian regions. Finally, Appenninica had a low frequency of ARQY180. The synonymous polymorphisms at codon 231 and 237 were observed in all the analysed breeds. The results obtained on the allelic variant frequencies could offer the opportunity to develop a gene6c breeding programme aimed at increasing scrapie-­‐gene6c resistance of sheep popula6ons by preserving PRNP variability. The study was supported by Italian Ministry of Health grant IZSUM 08/2011 RC (Valutazione di Nuovi Alleli Protebvi per la Scrapie AT137RQ/ARQK176 nelle Razze Ovine presen6 nel Territorio Umbro Marchigiano). GENOMICS & EPIGENOMICS -­‐ Abstract N° 40 SELECTIVE SWEEP MAPPING IN TWO ORIGINAL OVINE BREEDS FROM THE BASQUE COUNTRY Otsanda Ruiz1, Jorge Langa1, Fernando Rendo1, Carmen Manzano1, Mikel Iriondo1 and Andone Estonba1 Gene6cs, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/
EHU), Bº Sarriena s/n, 48940, Leioa, ES 1 Sheep was one of the first species to be domes6cated, approximately 11,000 years before the present in the Fer6le Crescent, resul6ng in phenotypically highly diverse breeds. The analysis of large datasets of the species offers great opportuni6es to iden6fy genomic regions undergoing this phenotypic varia6on. This is a selec6on mapping study on two original sheep breeds from the Basque Country. Sasi-­‐ardi is a semi-­‐feral breed highly adapted to mountainous areas and mainly bred as an ecological sheep because of the growing demand of meat derived from sheep raised in herds. Latxa sheep, the most widely known ovine breed from the Western Pyrenees, has been strongly selected for milk produc6on following a well established breeding program in the last 30 years. We are aimed to explore the effect of domes6ca6on and ar6ficial selec6on on the genome of Sasi-­‐ardi and Latxa sheep breeds. A whole genome resequencing of both Sasi-­‐Ardi and Latxa breeds has been performed by a Pool-­‐Seq approach. DNA pools were sequenced by Illumina HiSeq 2000 technology with an average read depth of 17×/pool. Two approaches were applied to detect selec6on signatures along the 26 ovine autosomes: 1) Pooled heterozygosity (Hp) es6mates in each breed seeking regions with reduced diversity, and 2) Fst fixa6on index es6mates to iden6fy regions with extreme gene6c differen6a6on between the two breeds. Both, Hp and Fst distribu6ons were Z-­‐transformed, and candidate regions (CR) were defined as those genomic regions with extreme values. In all, 8 CR were iden6fied on OAR2, OAR6, OAR10, OAR13, OAR18, OAR19, OAR20, and OAR22. The CR on OAR13 could be reflec6ng a common domes6ca6on event in these two ovine breeds since both of them show an extreme reduced Hp in this region previously related with growth. The most extreme Fst is detected in OAR6 due to a CR with significant reduced Hp in Latxa breed. This region has previously been strongly related with milk produc6on, and could reflect the effect of the ar6ficial selec6on applied on Latxa breed. Other CRs detected here are located near or within several QTL previously related with health,and milk produc6on (OAR20, OAR22), meat fa:y acid content (OAR2 and OAR18), or meat traits (OAR19). Overall, these results provide a general view of the genome wide map of selec6ve sweeps on Sasi-­‐ardi and Latxa sheep breeds. A deeper study of the detected regions is needed for deciphering the genes underlying specific selected traits GENOMICS & EPIGENOMICS -­‐ Abstract N° 41 SINGLE NUCLEOTIDE POLYMORPHISM ASSOCIATION STUDY IN SELECTIVE SWEEP REGIONS OF HANWOO (KOREAN CATTLE) Eunbi Ko1 and Duhak Yoon1 Department of Animal Science, Kyungpook Na6onal University, 2559 Gyeongsang daero, 74271, Sangju, KR 1 We previously detected selec6ve sweep regions (BTA2 & BTA21) through the next genera6on sequencing (NGS) of 12 Hanwoo (Korea ca:le). In these regions, we selected eight genes (PTPN4, EPB41L5, RALB, INHBB, ETFA, ISL2, RCN2, PSTPIP1) as candidate genes for causal varia6on of carcass traits. This study was performed to analyze associa6on with SNPs on candidate genes and carcass traits. Carcass traits record of backfat thickness fat (BFT), eye muscle area (EMA), carcass weight (CW), marbling score (MS), and maturity (MA) were obtained from 278 Hanwoo (141 steer and 137 cow) and total 167 SNPs were genotyped using the Fluidigm SNPtype Assay. The associa6on analyses for five gene6c modes (codominant, dominant, recessive, overdominant, addi6ve) were performed using the SNPassoc package in the R program. Sixty-­‐two SNPs (3 SNPs of BFT, 7 SNPs of EMA, 18 SNPs of CW, 3 SNPs of MS and 32 SNPs of MA) were significantly associated with at least one of gene6c mode. In single SNP analysis using the general linear model, eighteen SNPs on BFT, three SNPs on EMA, twenty SNPs on CW, three SNPs on MS and sixty SNPs on MA were significant respec6vely. These results indicate that significant SNPs detected in this study may be the gene6c markers for carcass traits in Hanwoo popula6on. GENOMICS & EPIGENOMICS -­‐ Abstract N° 43 THE FAANG PROJECT'S COMMITMENT TO DATA STANDARDS, ANNOTATION AND SHARING Ian Streeter1, David Richardson1, Laura Clarke1, Paul Flicek1 and The FAANG Consor6um1 European Molecular Biology Laboratory, European Bioinforma6cs Ins6tute, Wellcome Trust Genome Campus, CB10, Hinxton, GB 1 The Func6onal Annota6on of Animal Genomes (FAANG) consor6um aims to iden6fy all func6onal elements in animal genomes, iden6fying regions of DNA that regulate gene expression and which ul6mately control an animal's traits. Understanding this link between genotype and phenotype is of clear importance, mo6vated by the value of animals as food sources, models for human health, and as key ecological actors. The project will use func6onal assays such as RNA-­‐seq, ChIP-­‐seq and chroma6n accessibility assays, applied to many different animal species. Such assays have been used in many projects with great success in associa6ng sequence varia6on with quan6ta6ve phenotypes. To date, the majority of func6onal genomics data come from human samples, with projects such as ENCODE demonstra6ng the standards required to efficiently generate valuable data sets. FAANG is a collabora6ve effort bringing together the global communi6es of animal genomics researchers. The data will be generated by many ins6tutes around the world, and a so we need a unified and coordinated approach to data standards, data annota6on, and data sharing. Only by a coordinated approach will we ensure that the datasets produced have maximum value to the genomics communi6es using the data. FAANG has four working groups to manage the collabora6on: Animals, samples and assays (ASA); Bioinforma6cs and data analysis (B&DA); Communica6on (COM); Metadata and Data Sharing (M&DS). FAANG is defining its data standards based on those defined by ENCODE and the Interna6onal Human Epigenome Consor6um (IHEC) for bioinforma6cs, metadata, and experimental protocol. The data standards are being developed collabora6vely (h:ps://
github.com/FAANG/faang-­‐metadata). FAANG partners are commibng to a data distribu6on policy whereby all output will be shared rapidly, before publica6on, in adherence to the recommenda6ons for community resource projects defined at the Toronto Interna6onal Data Release Workshop (h:p://www.nature.com/nature/journal/v461/n7261/full/461168a.html). To facilitate data sharing FAANG will engage with major genome analysis groups such as Ensembl and encourage data sharing via the TrackHub standard used by ENCODE and IHEC to allow users to visualize the data in a genomic context. The consor6um will work to present all FAANG data in a unified manner to ensure the community has a central point to discover what data have been generated. GENOMICS & EPIGENOMICS -­‐ Abstract N° 44 THE PHYLOGENETIC STRUCTURE OF LEISHMANIA SPECIES REVEALED BY GENOME-­‐WIDE SINGLE-­‐COPY ORTHOLOGOUS PROTEINS Fernanda Müller de Oliveira1, Flávia Florêncio de Athayde1, Pier Kenji Rauschkolb Katsuda Ito1, Yuri Tani Utsunomiya3, Ashton Trey Belew2, José Fernando Garcia3, Najib M. El Sayed2 and Cáris Maroni Nunes1 Departamento de Apoio, Produção e Saúde Animal , UNESP Universidade Estadual Paulista FMVA, Rua Clóvis Pestana, 793. Jardim D. Amélia, 16050, Araçatuba, BR 2 Department of Cell biology and Molecular gene6cs, University of Maryland UMD, MD , 20742, College Park, US 3 Departamento de Reprodução Animal, UNESP Universidade Estadual Paulista FCAV, Via de Acesso Prof.Paulo Donato Castellane s/n , 14884, Jabo6cabal, BR 1 Phylogene6c analyses of highly conserved single-­‐copy orthologous proteins suggest slow evolu6on rates among trypanossoma6d species. In spite of marked differences in pathogenicity and biological cycles, parasites of the sub-­‐genera Leishmania Leishmania, Leishmania Viannia and Leishmania Sauroleishmania present a quasi-­‐monophyle6c profile. However, the simultaneous analysis of several proteins is s6ll required in order to improve the phylogene6c resolu6on of the genus. Here, we aimed at using a comprehensive genomic approach to confirm the gene6c rela6onships among Leishmania species. Single-­‐copy orthologous protein sequences were sought in six complete genomes deposited at TriTrypDB database, including Leishmania (L.) major, Leishmania (L.) infantum, Leishmania (L.) donovani, Leishmania (L.) mexicana, Leishmania (V.) brasilienses and Leishmania (S.) tarentolae. Addi6onally, the Trypanosoma cruzi and Trypanosoma brucei reference genomes were used as outgroup species. A total of forty nine single-­‐copy orthologous protein sequences were found. These proteins were either involved in the glycoly6c pathway or the trans-­‐splicing mechanism. Sequences were concatenated and aligned in a supermatrix, which was used to construct a phylogene6c tree using the Neighbor-­‐joining method. The resul6ng tree confirmed the monophyle6c behavior of the Leishmania genus. Interes6ngly, the Leishmania donovani and infantum species, which are responsible for the visceral clinical form, and the Leishmania mexicana and Leishmania major, implicated in the cutaneous form, were clustered in the same branches, respec6vely. Leishmania braziliensis (involved in muco-­‐cutaneous leishmaniasis) and Leishmania tarentolae (non-­‐pathogenic to humans) were posi6oned in dis6nct branches with larger gene6c distances in comparison with the other species. This preliminary assessment of genomic data of Leishmania spp. reinforces the current phylogene6c classifica6on. GENOMICS & EPIGENOMICS -­‐ Abstract N° 45 UNVEILING GENOMIC REGIONS THAT DISTINGUISH THE ASSAF SHEEP FROM ITS PARENTAL AWASSI BREED Elisha Gootwime1, Alexander Rosov1, Andrey Shirak1 and Eyal Seroussi1 Ruminant Science, ARO, The Volcani Center, PO Box 6, 50250, Bet Dagan, IL 1 The local Awassi breed, hardy fat-­‐tailed sheep na6ve to the Middle East, has been kept under extensive condi6ons. In Israel, intensifying sheep produc6on in the last century has been facilitated by crossing Awassi with the European East Frisian breed, crea6ng the Assaf dairy breed. Further introgression of the B (Booroola) allele of the FecB locus into the Assaf breed improved its prolificacy. Today, the Assaf morphology differs from that of its parent Awassi breed in tail and horn size, coat pigmenta6on and wool characteris6cs. It is also more prolific with less seasonality. To iden6fy genomic loci associated with crea6on of the Assaf breed, we analyzed genotypes of the Illumina Ovine SNP50 BeadChips of 141 Assaf sheep in three flocks and of 41 Awassi sheep in six flocks using EMMAX and PLINK sorware. The chromosomal regions associated with breed origin were compared to selec6on signatures obtained in 36 published genome-­‐wide associa6on studies inves6ga6ng sheep morphological and physiological traits. As most of the Assaf, but none of the Awassi, carried the Booroola muta6on, associa6on analysis for the B allele was used to validate the power of our study. Six of the 17 chromosomal regions differen6a6ng between Awassi and Assaf (CRDs) were novel to this study. An ~10-­‐Mb selec6on sweep was iden6fied on OAR6 where the Booroola muta6on is mapped. In agreement with previous studies, the most significant selec6on sweep was on OAR10, in a region containing candidate genes that affect horn type (RXFP2), climate adapta6on (ALOX5AP), coat pigmenta6on (FRY) and wool traits. Selec6on signatures on OAR2 included BNC2, which is involved in coat pigmenta6on in sheep. Five other CRDs contained KRT4, KRT75, BMPR1B, EED, FZD4 and EDARADD, which have been implicated in coat pigmenta6on in studies of their mammalian orthologues. CRDs on OAR2 included SNSD1—a candidate gene for carrying fat tail, previously iden6fied in Iranian sheep. Related to this trait, genes associated with fat distribu6on in humans, including CALCRL, TFP1, COBLL1, were located in addi6onal CRDs. Deep sequencing of Awassi and Assaf individuals revealed nonsynonymous muta6ons in some of the candidate genes. Our results highlight the major chromosomal regions that may confer an advantage to Assaf over Awassi, driving the former to be a major dairy breed in Israel and to be exported worldwide. GENOMICS & EPIGENOMICS -­‐ Abstract N° 46 USE OF PACBIO PLATFORM FOR RESEQUENCING OF TOLL-­‐LIKE RECEPTOR GENES IN THE INDIGENOUS CZECH CATTLE BREEDS Karel Novák1 and Věra Mátlová1 Molecular Gene6cs, Ins6tute of Animal Science, Přátelství 815, 10400, Prague -­‐ Uhříněves, CZ 1 The variability of disease resistance genes in the tradi6onal breeds represents a reservoir of func6onal variants for breeding programs. Rare allelic variants are supposed to reflect local infec6on pressure and may be useful in counterac6ng the gene pool erosion. Screening for the diversity of Toll-­‐like receptor genes (TLR) has been carried out in two conserved Czech breeds of ca:le, Czech Red and Czech Red Pied. The ten members of bovine TLR gene family code for key receptors that mediate early recogni6on of pathogens. The survey covered all living individuals of each breed and included the available archived samples. While Sanger sequencing of PCR amplicons has been applied to the basic three an6bacterial species (TLR1, 2 and 4), the polymorphism in other TLR genes has been discovered with NGS sequencing of pooled amplicons using the PacBio plaŒorm and subsequently validated with genotyping techniques. The polymorphism revealed was higher than reported for the European produc6on breeds. Partly, the seven SNPs found in TLR4 grouped into nine haplotypes, at least three of them being specific for these local breeds. On the other hand, some commonly spread haplotypes were greatly reduced in frequency or not detected. Although the haplotype frequencies might have been distorted by the bo:leneck in the history of both popula6ons, the presence of specific features coincides with the phenotypic dis6nctness of the local breeds. Similarly, the presumed associa6on of the Czech Red breed with the Cel6c Red and Bos taurus brachyceros are corroborated by these data. In view of the presence of produc6on herds of Czech Red Pied in parallel to the conserved nucleus herd, the effect of intensive breeding on the TLR diversity is being evaluated. In selected TLR polymorphisms, the es6ma6on of the health effects in the background of Czech Pied is in progress. GENOMICS & EPIGENOMICS -­‐ Abstract N° 47 VARIABILITY OF BOVINE SERUM AMYLOID A3 AND SOMATIC CELL SCORE Dominga Soglia1, Stefano Sartore1, Sandra Maione1, Ezequiel Luis Nicolazzi2, Roberto Rasero1 and Paola Sacchi1 1 Dipar6mento di Scienze Veterinarie, University of Turin, Largo Braccini,2, 10095, Grugliasco, IT Bioinforma6cs core, Parco Tecnologico Padano, Via Einstein Albert, 26900, Lodi, IT 2 Using a target re-­‐sequencing approach, we iden6fied all SNPs in a region of 20kb of BTA 29 containing the SAA3.2 gene, a candidate gene for mas66s resistance in Italian Holstein cows. A TruSeq Custom Amplicon Assay was designed to resequence 12 kb upstream of the promoter and 1 kb downstream of the 3’-­‐UTR (Miseq NGS technology). The DNA of 95 bulls was extracted, amplified with the custom assay and sequenced. Animals were chosen using a selec6ve genotyping approach according to their soma6c cell score breeding value–SCS(EBV). An individual average coverage threshold of 20X was considered, resul6ng in 52 high and 33 low EBV(SCS) individuals retained. A total of 446 SNPs were iden6fied but only 127 SNPs, with a minor allele frequency (MAF) lower than 0.05, were considered: 92 upstream, 8 in the promoter, 20 in gene and 7 in the downstream region. Associa6on analysis between SNPs and SCS(EBV) was carried out using two different approaches. The first approach was the MAX test proposed for case-­‐control studies by Fridlin et al. (2002), used to verify the associa6on between the binary trait ‘nega6ve-­‐posi6ve tails’ and SNPs. The second approach was the heteroscedas6c effects model (HEM) (Shen et al. 2013). This model was used with the objec6ve to capture gene6c effects that are oren quite small. All analyses were performed in R, using the package bigRR (Shen et al., 2013) and Rassoc (Zang et al., 2010), bootstraping (with 50,000 replicates) to approximate the distribu6on of the MAX test under the null hypothesis of equal genotype distribu6on in the 2 tails as described in Fontanesi et al. (2012) and using a binomial distribu6on. With the MAX test five SNP were found significant using a threshold of p-­‐value <0.1 (0.013-­‐0.075): rs137746604(A/G), rs210417381(C/T) and rs136687125 (C/T), located in the promoter region, rs42175271 (C/G) and rs378094124, located upstream of the promoter. With the HEM method three SNPs iden6fied in MAX test showed a highest heteroscedas6c effect: rs137746604 (0.030), rs136687125(0.012) and rs42175271 (0.017). In addi6on, rs42175273(A/T) and rs384439423(C/T), located upstream of the promoter, had effect > 0.0123. Analysis with different approaches (e.g. Bayesian, GRAMMAR) are underway. Although these results must be confirmed by the analysis of a large number of individuals, this inves6ga6on is our first contribu6on to the iden6fica6on of markers for gene6c resistance to mas66s in Italian Holstein. GENOMICS & EPIGENOMICS -­‐ Abstract N° 48 WHOLE-­‐EXOME SEQUENCING OF IRISH AI BULLS WITH DIVERGENT FERTILITY PHENOTYPES Ronan Whiston1, Emma Finlay1, Cliona O'Farrelly2 and Kieran Meade1 Animal & Bioscience Research Department, Teagasc, Grange, Dunsany, NA, Co. Meath, IE Compara6ve Immunology Group, Trinity Biomedical Science Ins6tute, Trinity College Dublin, NA, Dublin 2, IE 1 2 Bovine fer6lity has been iden6fied as a major problem for the Irish dairy industry. Holstein-­‐
Friesian pregnancy rates can fall as low as 25%, yet no single diagnos6c test can accurately predict fer6lity in bulls. In order to iden6fy gene6c variants affec6ng fer6lity, whole-­‐exome sequencing of Irish AI bulls was performed, using the Roche Nimblegen Developer system. Exome target design captured 202,899 exon regions (almost 57MB), including 100bp of the 5’UTR. Pregnancy rate and adjusted animal model (AAM also accounts for environmental factors including AI technician, cow health and day of the week) phenotypic records for 7,000 AI bulls were obtained; filtered and 24 bulls of high-­‐ and low-­‐fer6lity were selected for sequencing. Mean target coverage of whole-­‐exome regions was 18.5X, with 78% of the exome covered at 10X depth. GATK SNP calling iden6fied 258,870 SNPs, 12,124 inser6ons and 13,048 dele6ons. Of these, 38% were located within exons and 2.5% were located within the 5’UTR. Of the exon muta6ons, 16% were non-­‐synonymous, 17% synonymous and <1% resulted in a frameshir. SNPs with a frequency difference >25% were retained, resul6ng in 2,312 variants divergent between high and low fer6lity bulls. Furthermore, SNP associa6on analysis iden6fied 405 SNPs significantly associated with fer6lity (P<0.01). The most significant SNP was located in 3’UTR of PGRMC1 gene, the human homolog of which func6ons in steroid signalling, p450 ac6va6on and drug metabolism. From these SNPs discovered in bulls of divergent phenotypes, 669 have been added to the Interna6onal Dairy and Beef SNP chip (v3) used for na6onal genotyping and will determine their associa6on with fer6lity in large numbers of independent samples with reliable phenotypes. Finally, specific SNPs of interest will undergo func6onal valida6on to characterise their role in bull fer6lity. TRANSCRIPTOMICS -­‐ Abstract N° 49 A REPERTOIRE OF BOVINE TRANSCRIPTION FACTORS Marcela De Souza1, Juan Vaquerizas2, Adhemar Zerlo6ne3 and Luciana C. A. Regitano4 Evolu6onary Gene6cs and Molecular Biochemistry Post-­‐Gradua6on Program, Federal University of São Carlos, Rodovia Washington Luis, Km 235, 676, Sao Carlos, BR 2 Regulatory Genomics, Max Planck Ins6tute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, DE 3 Bioinforma6c Mul6-­‐user laboratory, Embrapa Agriculture Informa6cs , Av. André Tosello, nº 209 , 6041, Campinas, BR 4 Animal Biotechnology Laboratory, Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234 s/nº, Fazenda Canchim, 339, São Carlos, BR 1 Transcrip6on factors (TFs) play an important role in controlling the expression of genes in par6cular environmental condi6ons and developmental stages, which have consequences on the quan6ty and type of proteins produced by the cell. These regulators act at transcrip6on ini6a6on level by direc6ng the transcrip6on machinery to the promoter region. As far as we concern, no previous manually accurate bovine TF repertoire is available in literature. Since TFs are important regulators of gene expression, controlling many biological processes, this project aimed to compile an extensive reliable dataset of bovine TF using computa6onal methods. The bioinforma6cs analyses were performed using R sta6s6cal sorware package. The genome sequences, associated annota6on and protein domains were obtained from Ensembl, and a human repertoire assembled and manually accurate by Vaquerizas et al. (2009) was used as guide to find the bovine TFs. All genes for which the human orthologues (one-­‐to-­‐one) have been experimentally evidenced as TF were considered as bovine TF. Probable TF genes with no experimental evidence un6l 2009 were manually inspected again regarding new proofs about their TF func6on, which was found for 89 genes. Other TF databases of human and mouse were also inspected in order to find DNA binding-­‐domains (DBD) iden6fied arer 2009. The accurate DBD final list has 149 domains and it was confronted against all domains contained in all bovine genes to select the matching between these two lists. Next, bovine genes orthologues to human genes classified as non-­‐TF or that have ambiguous DBD were removed from bovine TF list. To enhance the final list, genes common to, at least, two databases were manually inspected. Regarding the DBD structure, the most common DBDs in the 981 bovine TF were the same found for humans and mice in the literature (ZNF-­‐C2H2, homeodomain and HLH), which together represent 63% of bovine repertoire. Finally, the presence or absence of the bovine TF was compared among 21 species, from Saccharomyces cerevisiae to Homo sapiens, and it made possible to iden6fy TF typically present in mammals, vertebrates or extending to all eukaryotes. A separated list was created containing 41 genes whose DBD are non-­‐promiscuous, however they do not have human orthologues neither experimental evidences. So, from now, a reliable dataset of transcrip6on factors is available for cow. TRANSCRIPTOMICS -­‐ Abstract N° 50 ACUTE AND DELAYED TRANSCRIPTIONAL RESPONSE OF MUSCLE TISSUE TO TRANSIENT VARIATION OF INCUBATION TEMPERATURE IN BROILERS Watcharapong Naraballobh1, Nares Trakooljul1, Eduard Murani1, Carsten Krischek2, Sabine Janisch3, Michael Wicke3, Siriluck Ponsuksili1 and Klaus Wimmers1 Ins6tute for Genome Biology, Leibniz Ins6tute for Farm Animal Biology (FBN), Wilhelm-­‐Stahl-­‐Allee 2, 18196, Dummerstorf, DE 2 Ins6tute of Food Quality and Food Safety, Founda6on University of Veterinary Medicine, Hannover, Bünteweg 2, 30559, Hannover, DE 3 Department of Animal Sciences, Quality of Food of Animal Origin, Georg-­‐August-­‐University Goebngen, Albrecht-­‐Thaer-­‐Weg 3, 37075, Goebngen, DE 1 Modifica6on of egg incuba6on temperature has been evidenced in several poultry species to have a wide-­‐range impact on post-­‐hatch development. In order to reveal molecular routes responsive to variable incuba6on temperature broiler eggs were incubated at increased and decreased temperature (36.8°C, 38.8°C) compared to control (37.8°C) at embryonic days (ED) 7-­‐10 and 10-­‐13, respec6vely. Subsequently, global gene expression of M. gastrocnemius was monitored at ED10, ED13 and slaughter age (D35) (6 groups; 3 6me points; 8 animals each) by microarray analysis. Increased incuba6on temperature led to slight but significant differences in body weight, meat quality traits and mitochondrial respiratory capacity, whereas decreased incuba6on temperature only had subtle effects on a few parameters. Between 113 and 738 transcripts showed shired abundance in the various treatment groups compared to the respec6ve control. As revealed by Ingenuity pathway analysis, in par6cular, increased temperature during E7-­‐10 (H10ΔC) profoundly altered pathways involved in lipid metabolism, cell signaling, energy metabolism, muscle development and func6on, and small molecule biochemistry compared to other condi6ons in embryos. Ingenuity Z-­‐scores indicated that these pathways related to nutrient metabolism and small molecule biochemistry were ac6vated. In adults, decrease incuba6on temperature during E10-­‐13 (L13ΔC) strongly changed pathways related to cellular func6on and growth, and development of organ, 6ssue and muscle as well as nutrient metabolism pathways. In summary, the study shows that shirs of incuba6on temperature at different developmental stages provoke specific acute and delayed transcrip6onal responses. The results indicate that transcrip6onal response to decreased incuba6on temperature mediates compensatory effects indica6ng considerable adaptability towards homeostasis. Increased incuba6on temperature trigger gene expression and has long term effects on the phenotype indica6ng metabolic plas6city. TRANSCRIPTOMICS -­‐ Abstract N° 51 ALTERED MICRORNA EXPRESSION AND PRE-­‐MRNA SPLICING EVENTS ARE ASSOCIATED WITH MYCOBACTERIUM AVIUM SUBSPECIES PARATUBERCULOSIS INFECTION IN NEWBORN CALVES REVEALING THE COMPLEXITY OF THE HOST RESPONSE Guanxiang Liang1, Yongjuan Guan2, Nilusha Malmuthuge1, Philip Griebel3 and Le Luo Guan1 Agricultural, Food and Nutri6onal Science, University of Alberta, 410 Agriculture/Forestry Center, T6G2P, Edmonton, CA 2 UWA Ins6tute of Agriculture and School of Animal Biology, University of Western Australia, 35 S6rling Highway, 6009, Crawley, AU 3 Vaccine and Infec6ous Disease Organiza6on, University of Saskatchewan, 120 Veterinary Road, S7N 5, Saskatoon, CA 1 Mycobacterium avium subsp. paratuberculosisis (MAP) is the causa6ve agent of Johne’s disease in ruminants. The molecular regulatory mechanism of the host response at the site of intes6nal MAP infec6on during the early subclinical stage of infec6on is s6ll not clear. In this study, surgically isolated ileal intes6nal segments were prepared in newborn calves and used to establish in vivo MAP infec6on adjacent to an uninfected control intes6nal segment. RNA-­‐seq was used to profile the whole transcriptome and the expression of microRNAs (miRNAs) one month arer MAP infec6on.. The most related func6on of differen6ally expressed mRNAs was “angiogenesis”, indica6ng that MAP may be the cause of over-­‐prolifera6on of endothelial cells. In addi6on, 46.2% of detected mRNAs displayed alterna6ve splicing events, and the pre-­‐mRNA of two genes (monocyte to macrophage differen6a6on-­‐associated and adenosine deaminase) that are related to macrophage matura6on and lysosome func6on showed significantly different splicing sites. This observa6on suggests that specific changes in the usage of pre-­‐
mRNA splicing sites may be a mechanism by which MAP escapes host immune responses. Moreover, 9 miRNAs (bta-­‐miR-­‐105a, bta-­‐miR-­‐133b, bta-­‐miR-­‐137, bta-­‐miR-­‐146b, bta-­‐miR-­‐184, bta-­‐miR-­‐196b, bta-­‐miR-­‐202, bta-­‐miR-­‐433, and bta-­‐miR-­‐1247-­‐5p) were differen6ally expressed during MAP infec6on. An integrated analysis of miRNAs and mRNAs revealed several poten6al miRNA-­‐mRNA regulatory pairs and a func6onal analysis revealed poten6al func6ons in different biological processes, such as 6ssue structure changes, bacteria recogni6on, and regula6on of the inflammatory response. In conclusion, the present study provides insight into a new molecular regulatory mechanism by which MAP may evade host immune responses during the early subclinical stage of infec6on. TRANSCRIPTOMICS -­‐ Abstract N° 52 AN EGWAS ANALYSIS OF THE PORCINE WHOLE BLOOD TRANSCRIPTOME Ta6ana Maroilley1, Maria Ballester1, Gaétan Lemonnier1, Marie-­‐José Mercat2, Yvon Billon3, Marco Moroldo1, Claire Rogel-­‐Gaillard1 and Jordi Estellé1 UMR1313 Géné6que Animale et Biologie Intégra6ve, INRA-­‐AgroParisTech, Domaine de Vilvert, 78350, Jouy-­‐
en-­‐Josas, FR 2 BIOPORC, IFIP, La Mo:e au Vicomte, 35350, Le Rheu, FR 3 UE967 GENESI, INRA, Le Magneraud, 17700, Surgères, FR 1 The blood is emerging as a source of biological informa6on linked to varia6ons in immunity capacity for several species, including swine. Our objec6ve was to iden6fy gene6c markers associated with gene expression varia6ons in blood, based on an expression genome-­‐wide associa6on study (eGWAS) using 243 Large White pigs at 60 days of age. Each pig was genotyped with the Illumina iSelect 60K Chip and transcriptome profiling was performed by using a custom gene expression 8X60K microarray (61,627 probes, Agilent Technologies). Arer remapping the probes, 44,326 expressed probes with a unique loca6on into the porcine reference genome assembly (v10.2) were analysed. Models were analysed in GenABEL’s FASTA procedure, including batch and sex as co-­‐factors and the genomic rela6onship matrix as random effect, and were corrected for mul6ple tes6ng (global FDR < 0.05). Furthermore, at the loca6on of each eGWAS peak, addi6onal associa6ons were iden6fied by tes6ng each SNP in a model including the most associated SNP as co-­‐factor. Globally, we found 4,591 significant associa6ons between one SNP and one probe (62% are cis-­‐associa6ons). Among the 3,419 probes with at least one eQTL, 70% had a cis-­‐eQTL and 89% could be assigned to a porcine gene. By using enrichment analysis, we found that associated genes were mostly related to molecular binding and RNA processing. On the other hand, 3,195 SNPs were found associated with the expression of at least one probe, with a maximum of 51 probes for one SNP located in porcine chromosome 10 and having a trans effect on 47 genes. Chromosomes 7 and 12 were enriched in eQTLs (~2,5 eQTLs by Mb). Numerous SNP-­‐gene networks were revealed with our analyses, and their biological relevance has been further explored by Ingenuity Pathway Analysis. In summary, this work is an original contribu6on to the analysis of the gene6c control of blood transcriptome in pig and will contribute to pave the way for transla6onal research toward pig precision farming. TRANSCRIPTOMICS -­‐ Abstract N° 53 BREED-­‐RELATED CHANGES IN MIRNA EXPRESSION IN BOVINE SATELLITE CELLS ENTERING DIFFERENTIATION Anna Ciecierska1, Edyta Przydatek1 and Tomasz Sadkowski1 Department of Physiological Sciences, Warsaw University of Life Sciences – SGGW, Faculty of Veterinary Medicine, Nowoursynowska 159, 02776, Warsaw, PL 1 The purpose of this study was to analyze the changes in miRNA expression profiles during early differen6a6on of satellite cells isolated from muscle 6ssue of bulls differing in produc6on traits. Experiments were performed on satellite cells isolated from semitendinosus muscle of bulls represen6ng typical beef (Limousin: LIM and Hereford: HER) and dairy (Holstein-­‐Friesian: HF) ca:le breeds. Analysis was performed using miRNA microarray method. The expression of iden6fied miRNAs was validated using real-­‐6me PCR. The analysis revealed 30 miRNAs differen6ally expressed in the satellite cells of beef breeds (LIM/HER) and dairy breed (HF) on the 2nd day of in vitro myogenesis. At the same 6me the expression of these miRNAs was similar between both beef breeds. Most of the iden6fied miRNAs (24) were up-­‐regulated and only 6 miRNAs were down-­‐regulated in the skeletal muscle cells of beef breeds. Based on the literature and Pathway Studio analysis 9 miRNAs, which were involved in skeletal muscle development, cell prolifera6on and differen6a6on (miR-­‐1 (↑), miR-­‐133a (↑), miR-­‐143 (↓), miR-­‐145 (↓), miR-­‐204 (↓), miR-­‐206 (↑), miR-­‐362-­‐3p (↑), miR-­‐486 (↑) and miR-­‐652 (↑)) were chosen for real-­‐6me PCR valida6on. Four miRNAs iden6fied as differen6ally expressed in beef vs. dairy breeds (miR-­‐1, miR-­‐133a, miR-­‐206 and miR-­‐486) are directly involved in the process of myoblast prolifera6on and differen6a6on and were classified as myomiRs. These miRNAs expressed in similar manner in semitendinosus muscle of beef bulls could be responsible for higher muscle mass gains observed in these breeds. The results obtained in this study allowed the iden6fica6on of miRNAs that could influence ca:le phenotypes giving be:er quality of beef and improving the growth of muscle mass in beef ca:le. Li:le is known about the role of majority of iden6fied miRNAs in skeletal muscle development, therefore further studies are necessary to confirm their engagement in the process of bovine myogenesis, especially in beef bulls. This research was funded by Na6onal Science Centre (Poland), Grant No. 2011/03/B/
NZ9/03987. TRANSCRIPTOMICS -­‐ Abstract N° 54 BULL SPERM MIRNAS PROFILING IN MOTILE AND LOW MOTILE CELL POPULATIONS Federica Turri1, Emanuele Capra1, Teresa Maria Gliozzi1, Paola Cremonesi1, Barbara Lazzari1, Alessandra Stella1 and Flavia Pizzi1 Is6tuto di Biologia e Biotecnologia Agraria, U.O.S di Lodi, Consiglio Nazionale delle Ricerche, via Einstein Albert, 26900, Lodi, IT 2 Parco Tecnologico Padano, Parco Tecnologico Padano, via Einstein Albert, 26900, Lodi, IT 1 Mature spermatozoa contain coding and noncoding RNAs, some of them involved in the regula6on of many physiological pathways including the control of sperm mo6lity. The presence of miRNA transcripts in sperm is now well acknowledged, but li:le is known of the func6on of novel miRNAs in sperm cells or their poten6al involvement in spermatogenesis. The aim of this study was to characterize miRNAs expression in mo6le (M) and low mo6le (LM) sperm popula6ons. Twelve frozen semen doses from 4 bulls were simultaneously thawed at 37°C and pooled. Each pool was overlaid on a dual-­‐layer (90-­‐45%) discon6nuous Percoll gradient and centrifuged at 700 g for 30 minutes at 20°C. The two popula6ons obtained (M and LM) from each tube were washed in TALP at 700 g for 10 minutes at 20°C and evaluated for sperm kine6c parameters by CASA and sperm viability and acrosomal status by flow citometry. Aliquots were kept at -­‐80°C un6l RNA extrac6on. miRNAs were extracted and small RNA libraries were generated using the Illumina Truseq Small RNA Prepara6on kit according to manufacturer’s instruc6ons and sequenced on a single lane of Illumina Hiseq 2000, obtaining about 4.6 millions of reads from each sample. Using the mirDeep algorithm, a total of 811 miRNAs were classified as known in Bos taurus (481) or novel (330). Sperm quality parameters and miRNAs distribu6on in the two popula6ons were analysed by General Linear Model Procedure (SAS). According to the sta6s6cal analysis sperm cells were successfully frac6onated in M and LM popula6ons (Total mo6lity: M = 48.4% vs LM = 4.8%; P≤0.0001). We found 37 known and 19 novel miRNAs that were differen6ally expressed in M and LM popula6ons (P≤0.0001). Furthermore 92.8 % of miRNAs were upregulated in the M popula6on. These results firstly report an integrated approach to evaluate miRNA expression between high and low mo6lity sperm popula6ons using deep sequencing. TRANSCRIPTOMICS -­‐ Abstract N° 55 CALCIUM SIGNALING PATHWAY CAN CONTRIBUTE TO BROILER MUSCLE DISORDERS IN WOODEN BREAST – WHITE STRIPING ABNORMALITIES Paolo Zambonelli1, Mar6na Zappaterra1, Maurizio Mazzoni2, Massimiliano Petracci1, Francesca Soglia1, Federico Sirri1, Claudio Cavani1 and Roberta Davoli1 Department of Agricultural and Food Sciences, DISTAL, Bologna University, Viale Fanin, 46, 40127, Bologna, IT 2 Department of Veterinary Medical Sciences, DIMEVET, Bologna University, Via Tolara di Sopra, 50, 40064, Ozzano Emilia (BO), IT 1 In the last few years, modern chicken hybrids selected for an increased breast muscle weight exhibited new breast muscle myopathies, termed “wooden breast” and “white-­‐striping”, which impair product appearance and quality proper6es. This study is aimed to preliminarily analyse the genomic basis of wooden breast and white striping (WB/WS) abnormali6es using Affymetrix expression array. For this purpose, 6 normal (NORM) and 6 WB/WS Pectoralis major muscles were obtained from the same flock of heavy broilers (males, 8 weeks of age, slaughter weight 3.8kg) slaughtered on a single day. As reported previously by our research group the histological analysis revealed the presence on WB/WS samples of an intense prolifera6on of the perimysial collagen (fibrosis) in respect to the muscular fibers that appear decreased both in number and in diameter and degenerate (necrosis). Comparing the gene expression profiles obtained for WB/WS and NORM samples, 226 differen6ally expressed genes (DEG) were found, 114 up-­‐ and 112 down-­‐regulated. A func6onal classifica6on was carried out using DAVID tools. The significant (P<.05) func6onal categories represented by the up-­‐regulated genes are: regula6on of organismal growth and cellular developmental processes related to skeletal muscle, ac6va6on of polysaccharide metabolism (extra cellular matrix and collagen), calcium and sodium metabolism. On the whole, these func6ons seem to indicate the altera6on of several cellular processes and/or ac6va6on/
regula6on of ac6ons aimed to a:empt to repair the enormous damage of the muscles. Furthermore, the analysis of the DEG reveals an altera6on of the ion homeostasis, in par6cular calcium and sodium balance. By analyzing the regulated calcium signaling pathways we observed that a set of genes was involved in the calcium homeostasis within the cells. This pathway is composed by four up-­‐regulated genes: PTGFR, GNAQ, PLCB2, and PLCD1. This pathway was reported to influence the myotubes differen6a6on and fusion. Overexpression of these four genes can be hypothesized to be involved in the high muscle growth leading to a severe myopathy in broiler Pectoralis major muscle. TRANSCRIPTOMICS -­‐ Abstract N° 56 CHANGES IN HEPATIC GENE EXPRESSION BETWEEN EFFICIENT AND INEFFICIENT NELORE CATTLE PRIMARILY APPEAR TO BE RELATED TO METABOLIC PROCESSES UNDERLYING OXIDATIVE STRESS Polyana C. Tizioto1, Jeremy F. Taylor4, Mauricio A. Mudadu1, Robert D. Schnabel4, Jared E. Decker4, Gerson B. Mourão2, Marcela M. Souza3, Luiz L. Cou6nho2, Andressa O. Lima3, Priscila S.N. Oliveira1 and Luciana C.A. Regitano1 Animal Biotechnology Laboratory, Embrapa Southeast Livestock, São Carlos, SP, Brazil, Rodovia Washington Luiz, km 234,13560-­‐970 , -­‐, São Carlos, SP, BR 2 Department of Animal Science, University of São Paulo/ESALQ, Avenida Pádua Dias -­‐ Vila Independencia, 13418-­‐260, -­‐, Piracicaba, SP, BR 3 Department of Gene6cs and Evolu6on, Federal University of Sao Carlos, Rodovia Washington Luis, Km 235, s/
n, -­‐ Jardim Guanabara, 13565-­‐905, -­‐, São Carlos, SP, BR 4 Division of Animal Sciences, University of Missouri Columbia, 920 East Campus Drive, 65211, Columbia, MO, US 1 Gene expression is a key source of varia6on between individuals and may be used to iden6fy func6onal candidate genes and pathways that control target traits. We iden6fied 112 differen6ally expressed (DE) genes in the liver 6ssues of 20 Nelore steers gene6cally divergent for Residual Feed Intake (RFI), using RNA sequencing methodology. The func6onal annota6on analysis using both DAVID v6.7 and IPA (www.qiagen.com/ingenuity) sorware revealed that the majority of the DE genes play key roles in hepa6c metabolic adapta6on to oxida6ve stress. The over-­‐represented pathways observed for the DE genes included xenobio6c metabolism, glutathione redox reac6ons I, glutathione-­‐mediated detoxifica6on, NRF2-­‐mediated oxida6ve stress and melatonin degrada6on. Genes from the cytochrome P450 and UDP-­‐
glucuronosyltransferase families, found to be down-­‐regulated in the Low-­‐RFI (efficient) group, were detected in these pathways. These genes encode several enzymes with crucial func6ons in the oxida6ve metabolism of endogenous substrates, including steroids, fa:y acids and exogenous molecules. Taking advantage of the fact that the animals that were RNA sequenced in this study also have genotypes for the Illumina BovineHD BeadChip, single nucleo6de polymorphisms (SNPs) present on the chip that mapped within DE genes and their poten6al regulatory elements (5' and 3' untranslated regions) were extracted and the Ensembl Variant Effect Predictor sorware was used to predict their func6onal effects. The majority of the SNPs lie within non-­‐coding regions; however several poten6ally func6onal muta6ons were located within exons, poten6al miRNA target sites and regulatory elements. For example, rs29010201 (missense muta6on) and rs134481079 (3’ UTR variant), located within the DE CYP2B6 and UGT2A3 genes, respec6vely, are poten6ally valuable targets for incorpora6on into molecular breeding programs. Studies targe6ng the iden6fica6on of func6onal muta6ons regula6ng DE genes may be important for understanding the biology of feed efficiency and may have u6lity for the implementa6on of genomic selec6on for feed efficiency in livestock. TRANSCRIPTOMICS -­‐ Abstract N° 57 CHANGES IN MATERNAL NUTRITION IN EARLY PREGNANCY IMPACT FETAL OVARIAN TRANSCRIPTOME Heni Falcao da Costa1, Maria Carolina Villani Miguel1, Alexandre Pedroso2, Sarita Priscila Gobbo1, Flavia Lombardi Lopes1, Juliana Ragina Peiro1 and Guilherme De Paula Nogueira1 1 DAPSA, UNESP, rua Clovis Pestana, 16050, Aracatuba, BR Consul6ng and Planning, CowTech, Rua Centro, n.1, 18680, Lencois Paulista, BR 2 Changes in maternal nutri6on during gesta6on may lead to permanent epigene6c changes in fetal development and its metabolism in adulthood. The ovary development occurs during the ini6al stage of pregnancy and need special a:en6on since the amount of non-­‐renewable germ cells are establishes. We hypothesized that either restric6on or excess of nutrients during the first sixty days of gesta6on will change fetal ovarian transcriptome. This procedure was approved by the local Trial Commi:ee for Animal Use (CEUA). Twenty-­‐one beef cows (488±24 kg, and body condi6on score-­‐ BCC= 3.1±0.1) underwent to TAI with sexed semen (female) from a single bull and were individually allocated into different diets. Control group (C) diet met the maintenance requirements for this animal category (100%; NRC, 2006), and diet of groups A-­‐high(180%) and B-­‐low(60%) of maintenance. Cows body weight and BCC were evaluated weekly to adjust the diet, arer 60 d of gesta6on fetuses were removed by colpotomy (vaginal access), weighed, dissected and ovaries weighed. The ovaries (one from each pair) were subjected to RNA Seq; the RNA was extracted by TruSeq Sample Prep Protocol Guide and mRNA sequencing was performed by the apparatus 500 HiScan (Illumina, Inc., San Diego, CA, USA), using pair-­‐end reads protocol. The mapping was made from Bos taurus genome (UMD3.1, masked version). As expected changes in maternal diet interfere in the transcriptome of fetal ovaries. The hypothesis that the interval of ovarian fetal forma6on is par6cularly sensi6ve to changes maternal nutri6on, although the nutrient demand of the fetus during this period is minimal considering the internal environment as a whole. As many as 79 of all analyzed genes were differen6ally expressed between treatments (FDR <0.05). Interes6ngly, the differences were more evident when comparing the control group clusters with the treated groups, that is, independent of diet modifica6on suffered by the cow during the first 60 days of gesta6on, the standard change, up regulated or down regulated in fetal ovaries were similar. It was concluded that there was influence on the fetal ovarian gene expression due to maternal nutri6onal change during the first 60 days of gesta6on. Differen6ally expressed genes that do not have a known role in gonadal development will be studied to iden6fy mechanisms causing change in ovarian follicular reserve. Acknowledgements: FAPESP 2011 / 50839-­‐1; CNPq 487036 / 2013-­‐3, CAPES. TRANSCRIPTOMICS -­‐ Abstract N° 58 CIRCULATING SERUM MICRORNAS AS NOVEL BIOMARKERS FOR BOVINE TUBERCULOSIS Carolina N. Correia1, Nicolas N. Nalpas1, Kirsten E. McLoughlin1, David A. Magee1, Ronan G. Shaughnessy2, John A. Browne1, Adam O. Whelan3, H. Mar6n Vordermeier3, Eamonn Gormley4, Bernardo Villarreal-­‐Ramos3, Stephen V. Gordon2 and David E. MacHugh1 Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, D4, Dublin, IE 2 UCD School of Veterinary Medicine, University College Dublin, Belfield, D4, Dublin, IE 3 TB Research Group, Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, 3NB, KT15, Addlestone, GB 4 Tuberculosis Diagnos6cs and Immunology Research Centre, UCD School of Veterinary Medicine, University College Dublin, Belfield, D4, Dublin, IE 1 Bovine tuberculosis (BTB) caused by Mycobacterium bovis is a major endemic disease affec6ng the ca:le industry in Ireland and many other countries, including Brazil. Current diagnos6c procedures fail to detect all infected animals, leading to infec6on persis6ng and transmibng in herds. In the context of BTB control and eradica6on programmes, circula6ng serum microRNA (miRNA) biomarkers represent a promising new approach to M. bovis diagnos6cs, poten6ally providing high-­‐throughput, robust and reproducible blood-­‐based assays with high sensi6vity and specificity, and with the poten6al to detect animals during the early stages of M. bovis infec6on. For the present study, ten age-­‐matched male Holstein-­‐Friesian calves were infected endobronchially (in vivo) with M. bovis (~2,000 CFU). Blood serum samples were collected at seven 6me points (-­‐2 weeks [wk] and -­‐1 wk pre-­‐infec6on; +1 wk, +2 wk, +6 wk, +10 wk, and +12 wk post-­‐infec6on) and circula6ng serum miRNA extrac6ons were performed. High-­‐
throughput miRNA-­‐sequencing (miRNA-­‐seq) was carried out using the Illumina® HiSeq® 2500 plaŒorm. Sequence reads were quality checked, adapters removed, aligned to the Bos taurus reference genome UMD3.1 and assigned to miRBase B. taurus miRNA genes to generate gene counts. Lowly expressed miRNAs were removed prior to subsequent differen6al expression analyses. These analyses revealed 73 differen6ally expressed (DE) miRNAs at +1 wk post-­‐
infec6on (compared to the pre-­‐infec6on 6me points with a mul6ple tes6ng FDR correc6on threshold ≤ 0.05), 82 DE miRNAs at +2 wk, 64 DE miRNAs at +6 wk, 66 DE miRNAs at +10 wk and 35 DE miRNAs at +12 wk. In addi6on, 29 miRNAs were iden6fied as candidate biomarkers of early M. bovis infec6on because they display differen6al expression across all post-­‐infec6on 6me points. THIS WORK HAS BEEN ACKNOWLEDGED WITH THE SECOND PLACE IN THE POSTER COMPETITION
TRANSCRIPTOMICS -­‐ Abstract N° 59 COLOSTRUM AND MATURE GOAT MILK: A TRANSCRIPTOME PROFILING BY RNASEQ Alessandra Crisà1, Fabrizio Ferrè2, Giovanni Chillemi3 and Bianca Moioli1 Animal Produc6on Research Centre (CRA-­‐PCM) , Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA) , Via Salaria 31 , 00015, Monterotondo, IT 2 Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 6, 40126, Bologna, IT 3 SCAI SuperCompu6ng Applica6ons and Innova6on Department, CINECA, Via dei Tizii 6, 00185, Rome, IT 1 Capra hircus is an economically important livestock and its milk contains a variety of bioac6ve molecules with nutraceu6cal func6ons. In this work we aimed to sequence and assemble the goat milk transcriptome corresponding at colostrum (D1) and at 120 days of lacta6on (D120). A total of 224,914,420 paired-­‐end mRNA-­‐Seq cleaned read (79bp long) were obtained and used to reconstruct transcripts with as more accuracy as possible by mean of two strategies: using the genome as reference and using a de novo assembly approach, to detect transcripts encoded in missing or mis-­‐assembled loci of the current genome assembly. Results of both approaches were compared and integrated. By using the Cufflink and Cuffmerge procedures a total of 44,635 different transcripts, organized in 33,757 tenta6ve genes, were obtained. A significant match was found for 40,353 transcripts (90%) against the NT and for 35,701 (80%) against the NR databases. The de novo assembled transcripts in the two lacta6on stages showed a relevant correspondence with the merged Cufflinks/Cuffmerge transcriptome, as detected by BLASTing the former against the la:er. We used different FPKM threshold values to conduct a global gene expression analysis and we found that at >1 FPKM, 17,188 genes were expressed in D1 and 17,751 in D120; 15,768 genes showed ubiquitous expression. CSN2, CSN3, CSN1S1, CSN1S2, LGB, LALBA, FASN, CTSD, SPP1, KRT19, M-­‐SAA3.2, FTH1, TPT1, SPPI, GLYCAM1 genes were found as highly expressed in both samples. Moreover, by using NOIseq sorware we iden6fied 329 genes differen6ally expressed between stages, among which 207 up-­‐regulated and 122 down-­‐regulated in D1 sample. We used BLASt2GO, DAVID, WebGestalt and String tools for func6onal annota6on and pathway enrichment analysis on the different gene lists. The up-­‐regulated genes in colostrum showed enrichment in terms associated to glycolysis, carbohydrate metabolism and catabolism, defense response, cytokine ac6vity, regula6on of growth, an6-­‐apoptosis, extracellular space. The downregulated genes showed enrichment in the cell morphogenesis and cytoskeleton organiza6on terms, in the cytokine-­‐cytokine receptor interac6on and in the Jak-­‐STAT signaling pathways. At the best of our knowledge, this is the first study describing the complete goat milk transcriptomic in two biologically different lacta6on stages analyzed using integra6on of two different bioinforma6c methodology. TRANSCRIPTOMICS -­‐ Abstract N° 60 COMPARATIVE ANALYSIS OF SIGNATURE GENES IN PRRSV-­‐INFECTED PORCINE MONOCYTE-­‐DERIVED DENDRITIC CELLS AT DIFFERENTIAL ACTIVATION STATUSES Laura Miller1, Yongming Sang2 and Frank Blecha2 Virus and Prion Research Unit, Na6onal Animal Disease Center, USDA-­‐ARS, 1920 Dayton Ave, 50161, Ames, IA, US 2 Departments of Anatomy and Physiology, College of Veterinary Medicine,, Kansas State University, 1600 Denison Avenue , 66506, Manha:an, KS, US 1 Ac6va6on statuses of monocy6c cells including monocytes, macrophages (MΦs) and dendri6c cells (DCs) are cri6cally important for an6viral immunity. In par6cular, some devasta6ng viruses, including porcine reproduc6ve and respiratory syndrome virus (PRRSV), are capable of directly infec6ng these cells to subvert host immunity. We have recently profiled signature genes and gene responsive pathways in MΦs at different ac6va6on statuses, and reported that MΦ polariza6on is crucial for an6viral regula6on. Monocyte-­‐derived DCs (mDCs) are major target cells in PRRSV pathogenesis; however, the plas6city of mDCs in response to ac6va6on s6muli and PRRSV infec6on remains unstudied. In this study, we polarized mDCs using the framework established in MΦs, and applied genome-­‐wide transcriptomic analysis to compare signature genes involved in mDCs ac6va6on and response to PRRSV infec6on. Our long-­‐term goal is to integrate ac6va6on status with an6viral responses in these cells and to func6onally modulate them for a prototypic cellular adjuvant/vaccine that is ideal for poten6a6ng an6viral immunity. Porcine mDCs were polarized with mediators for 30 hours, then mock-­‐infected, infected with PRRSV strain VR2332, or highly pathogenic strain (HP-­‐PRRSV), for 5 h. Total RNA was extracted from the pooled cells of four replicates, and used to construct sequencing libraries for RNA-­‐Seq procedures previously op6mized. Comparisons were made between each polarized and unpolarized groups (i.e. mediator vs. PBS), and between PRRSV-­‐infected and uninfected cells s6mulated with the same mediator. The overall similarity between samples was assessed in heat map plots calcula6ng the Euclidean distance between regularized log transformed data to allow equal contribu6on from all genes. Principal component analysis, Poisson distance and DESeq2 dispersion es6mates emphasized varia6ons in comparisons. Clustering of samples was by virus strain and then by mediator. We then asked which genes showed the most variability across all treatments as these are likely to be the genes that will provide resolu6on for clustering the samples. Many of the genes showing the most variability were related to cellular structure and innate immune response. The magnitude of differen6ally expressed gene profiles detected in HP-­‐PRRSV rJXwn06 infected mDCs as compared to VR-­‐2332 infected mDCs was consistent with the increased pathogenicity of the HP-­‐PRRSV in vivo. TRANSCRIPTOMICS -­‐ Abstract N° 61 COMPARISON AMONG CO-­‐EXPRESSION NETWORKS OF PLURIPOTENT CELL POPULATIONS FROM PORCINE, BOVINE AND MURINE EMBRYOS Gianluca Mazzoni1, Kris6ne Freude1, Vanessa Jane Hall1, Kaveh Mashayekhi2, Poul Hy:el1, Andras Dinnyes2 and Haja Kadarmideen1 Department of Veterinary Clinical and Animal Sciences, University of Copenhagen , Grønnegårdsvej 7, 1870, Frederiksberg C, DK 2 BioTalentum, Ltd, Aulich Lajos str. 26, 2100, Gödöllő, HU ù 1 Differen6ated soma6c cells can be reprogrammed in induced pluripotent stem cells (iPSCs); a cell type with great poten6als in regenera6ve medicine and in vitro disease modeling. In the pig, we have developed iPSCs, but proper culture condi6ons for maintaining pluripotency over 6me are s6ll lacking. Hence, there is a need for a more fundamental dissec6on of the pluripotency apparatus in the pig as well as in ca:le. The aim of this study is to analyze RNA-­‐
seq data to increase the knowledge about biological pathways in porcine and bovine embryonic pluripotent cell popula6ons exploi6ng the mouse data as proof of principle. In par6cular we studied cell popula6ons from three different stages of pluripotency that the cells assumed arer fer6liza6on: the inner cell mass of the blastocyst, the epithelial epiblast of blastocyst as well as the gastrula6ng epiblast. Understanding the molecular basis of these three states may allow for stable culture of pluripotent cells in pig and ca:le. Reads quality was checked with FASTQC, then the reads were pre-­‐processed using Prinseq and mapped with STAR aligner ending up with a minimum of 80% of uniquely mapped reads per sample. Post mapping quality control with Qualimap showed a minimum of 60% of reads mapped in the exonic regions. Finally the expression levels were es6mated using HTSeq. Gene co-­‐expression will be analyzed using a weighted network based method to iden6fy highly co-­‐expressed genes (module) and hub genes. Furthermore, modules with a poten6al role in pluripotency will be selected with an enrichment procedure and regulator genes iden6fied with LemonTree algorithm. Finally, the differen6al wiring of the modules among species will be evaluated to find poten6al differences in mechanisms controlling the pluripotent state in embryos of these species. Acknowledgements: We thank for the financial support from the EU project PluriSys, HEALTH-­‐2007-­‐B-­‐223485 TRANSCRIPTOMICS -­‐ Abstract N° 62 COMPARISON OF MIRNA PROFILES BETWEEN PROLIFERATING, DIFFERENTIATING AND DIFFERENTIATED SATELLITE CELLS OF BULLS OF DIFFERENT BREEDS Tomasz Sadkowski1, Anna Ciecierska1 and Alicja Majewska1 Department of Physiological Sciences, Warsaw University of Life Sciences -­‐ SGGW, Faculty of Veterinary Medicine, Nowoursynowska 159, 02776, Warsaw, PL 1 The aim of the study was to inves6gate the role of miRNAs during skeletal muscle development by comparing the miRNA expression between prolifera6ng, differen6a6ng (myotubes forming) and differen6ated (myotubes formed) satellite cells derived from skeletal muscle of beef and dairy bulls. The analyses were done on bovine satellite cells isolated from semitendinosus muscle of beef (Limousin (LIM) and Hereford (HER)) and dairy (Holstein-­‐Friesian (HF)) ca:le breeds. The cells were cultured in growth medium un6l 80% of confluency (prolifera6on stage), and in differen6a6on medium un6l 2nd (early) or 6th day (late) of differen6a6on. Microarray and real-­‐
6me PCR techniques were used for miRNA iden6fica6on and valida6on, respec6vely. Aforemen6oned analyses revealed differences in expression of 14 miRNAs at prolifera6on stage, 29 miRNAs at early differen6a6on stage and 23 miRNAs at late differen6a6on stage between the beef breeds (LIM/HF) and the dairy breed (HF). Six miRNAs from each group were chosen for real-­‐6me PCR valida6on. Further analysis showed that the differen6ally expressed miRNAs can be divided into three groups: miRNAs engaged in prolifera6on/early differen6a6on (PRO/E-­‐DIFF); in early-­‐
differen6a6on/late differen6a6on (L-­‐DIFF/L-­‐DIFF) and in all three stages of in vitro myogenesis. During all inves6gated stages the expression of miR-­‐145 was down-­‐regulated, whereas miR-­‐486 and miR-­‐660 were up-­‐regulated in beef breeds in comparison to dairy breed. Addi6onally, in PRO/E-­‐DIFF and E-­‐DIFF/L-­‐DIFF groups, 5 and 8 miRNAs, respec6vely, showed a common expression profile in the beef breeds and the same trend of changes in expression when compared with the dairy breed. Obtained results have shown strong engagement of miRNAs in in vitro myogenesis of bovine satellite cells and revealed differences in miRNA expression between beef and dairy breeds. Because most of the iden6fied miRNAs is not annotated as muscle-­‐specific, further research is needed to find their mode of ac6on and target genes in examined 6ssue. This work was supported by the grant no. 2011/03/B/NZ9/03987 from the Na6onal Science Centre (Poland). TRANSCRIPTOMICS -­‐ Abstract N° 63 DIET INDUCED MILK FAT DEPRESSION ALTERS THE MAMMARY TRANSCRIPTOME IN LACTATING DAIRY COWS Sirja Viitala1, Daniel Fischer1, Laura Ven:o1, Heidi Leskinen1, Alireza R. Bayat1, Kevin J. Shingfield2 and Johanna Vilkki1 1 Green Technology, Natural Resources Ins6tute Finland (Luke), Alimentum, 31600, Jokioinen, FI Ins6tute of Biological, Environmental and Rural Science, Aberystwyth University, Penglais Campus SY23, 3FL, Aberystwyth, GB 2 Diets that contain highly fermentable components or supplemented with plant or marine oils are known to cause milk fat depression (MFD) in lacta6ng cows. Diet induced MFD has been a:ributed to altera6ons in ruminal biohydrogena6on leading to the synthesis of specific intermediates that inhibit milk fat synthesis. However the mechanisms responsible for decreased lipogenesis in the mammary gland are not well defined. Four Finnish Ayrshire dairy cows in mid lacta6on fi:ed with rumen cannula were used in a 4x4 La6n Square with 35d experimental periods to inves6gate changes in the mammary transcriptome during MFD. Treatments comprised total mixed ra6ons with a high or low propor6on of grass silage containing 0 or 50 g/kg of sunflower oil (SO) formulated to cause variable effects on milk fat synthesis. Mammary biopsies were taken on d 1, 8, 15 and 26 of each experimental period. Treatments had no effect on milk yield, but including SO in the high concentrate diet decreased milk fat synthesis and altered fa:y acid composi6on. RNA sequencing (Illumina) of total RNA extracted from biopsies collected on d8 and d15 was performed to characterize changes in key genes and biochemical pathways associated with MFD. The Grape-­‐pipeline (CRG) was applied for mapping and quan6fica6on of reads. Differen6ally expressed genes were assigned to relevant cellular func6ons using Ingenuity Pathway Analysis (QIAGEN). The diet causing MFD decreased the expression of several genes of cholesterol and lipid metabolism. Changes were not confined to lipid and cholesterol metabolism, but also involved altera6ons in other func6onal pathways. TRANSCRIPTOMICS -­‐ Abstract N° 64 EFFECT OF DIETARY SUPPLEMENTATION OF BROILER CHICKENS WITH THE NATURAL ANTIOXIDANTS HESPERIDIN AND NARINGIN ON THE EXPRESSION OF LIPOGENESIS RELATED GENES AND FATTY ACID PROFILE Ariadne L. Hager-­‐Theodorides1, Nina A. Dragona1, Katerina Moschou2, Chris6na Kappou1, Ilias Arkoumanis1, Michael Goliomy6s1, Maria Charismiadou1, Panagio6s Simitzis1, Theofilos Massouras2 and Stelios G Deligeorgis1 1 Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, GR Food Science and Human Nutri6on, Agricultural University of Athens, Iera Odos 75, 11855, Athens, GR 2 Hesperidin and naringin, flavonoids abundant in citrus fruits, exhibit health-­‐promo6ng proper6es notably an6oxidant and modula6on of lipid metabolism. Increased an6oxidant capacity and favorable fa:y acid profile are desirable proper6es for broiler meat. In chickens hesperidin lowered plasma and egg yolk cholesterol and improved broiler meat an6oxidant capacity. Here the effects of broiler diet supplementa6on with hesperidin and naringin on the expression of the lipogenesis related genes adiponec6n, ppar-­‐γ and fa:y acid synthase (fasn) and fa:y acid profile were assessed. 240 ROSS308 broilers were divided into treatment groups that received different diets supplemented with 0.75 or 1.5g hesperidin, 0.75 or 1.5g naringin, 0.2g vitE per kg feed or unsupplemented/control diet from the 11th to 42nd day of age. Abdominal adipose 6ssue, liver, breast and thigh muscle samples were obtained from 10 animals per treatment and used for gene expression and/or fa:y acid composi6on analysis. Hesperidin and naringin did not affect the expression of the genes studied in adipose 6ssue and hesperidin did not affect gene expression in the liver (P>0.05). On the contrary, naringin significantly lowered the level of fasn (P<0.05). Breast muscle fa:y acid profile analysis showed a tendency for lower palmi6c acid content in naringin fed compared to control chickens and increased oleic acid content in hesperidin fed animals and increased total PUFA in both hesperidin and naringin fed animals (P<0.10). In the abdominal fat, a tendency for lower fat percentage, increased conjugated linoleic acids (CLA) and increased PUFA was observed in naringin fed animals compared to control and a tendency for reduced oleic acid, increased CLA (P<0.10) and significantly reduced MUFA in hesperidin fed animals (P<0.05). Increased fasn expression is associated with increased fat deposi6on therefore the observed reduc6on of fasn expression in the liver in naringin fed chickens is a puta6ve molecular mechanism of naringin affec6ng lipid metabolism and fat deposi6on in broiler meat. In addi6on palmi6c acid is the product of fasn ac6vity therefore the observed reduced levels of fasn expression are consistent with the lower palmi6c acid levels in breast muscle of naringin fed chickens. Project implemented within the framework of "Thalis -­‐ The effects of an6oxidant's dietary supplementa6on on animal product quality", MIS380231, Funding Body: Hellenic State, European Union. TRANSCRIPTOMICS -­‐ Abstract N° 65 EFFECT OF SWINE GENOTYPE (PURE IBERIAN VS DUROC CROSSBRED) ON BíCEPS FEMORIS MUSCLE TRANSCRIPTOME AT BIRTH Miriam Ayuso1, Almudena Fernández2, Yolanda Núñez2, Rita Benítez2, Beatriz Isabel1, Ana Isabel Fernández2, Ana Isabel Rey1, Antonio González-­‐Bulnes3, Juan Medrano4, Ángela Canovas4, Clemente López-­‐Bote1 and Cris6na Óvilo2 1 Producción Animal, UCM, Facultad de Veterinaria, 28040, Madrid, ES 2 Mejora Gené6ca Animal, INIA, Ctra A6, km 7.5, 28040, Madrid, ES 3 Reproducción Animal, INIA, Ctra A6, km 5.9, 28040, Madrid, ES Animal Science, University of California-­‐ Davis, One Shields Avenue, 95616, Davis, US 4 Iberian ham is a high quality dry-­‐cured pork product that may be obtained either from purebred Iberian (IB) or from crossbred Duroc X Iberian (DUxIB) pigs. There are significant differences, from early developmental stages, in produc6ve traits and meat quality between both genotypes. This experiment was conducted to inves6gate gene expression pa:erns in IB and DUxIB pigs and to iden6fy poten6al transcrip6on factors (TF) regula6ng changes in gene expression. Nine IB and 10 DUxIB pigs were sampled at birth. Carcass traits were measured and samples from Biceps femoris were drawn to study intramuscular fat (IMF) content and composi6on and to analyze the muscle transcriptome with RNAseq technology. Carcasses were lighter and shorter in IB than in DUxIB neonates (P<0.001); IB piglets showed greater IMF content and n6/n3 ra6o (P<0.05) and a trend to greater oleic acid and lower saturated fa:y acids content (P<0.1) than DUxIB. Regarding the muscle transcriptome analysis, 150 genes were found to be differen6ally expressed (DE) between IB and DUxIB (P<0.01 and Fold change>1.5); among them, 95 genes were upregulated in IB and 55 genes were upregulated in DUxIB. Some of them are closely related to lipid metabolism and muscular development biological func6ons (i.e. APOM, SLC2A4 or PVALV). Pathways analysis disclosed that upregulated genes in both groups were involved in “RXR/LXR ac6va6on”, related to cholesterol homeostasis and lipogenesis. On the other hand, pathways such as “IGF-­‐1 Signaling” or “Fa:y Acid α-­‐oxida6on” were associated to genes upregulated in IB pigs; and “nNOSSignaling in Skeletal Muscle Cells” or “Ac6n Cytoskeleton Signaling” to genes upregulated in DUxIB pigs, sugges6ng a differen6al trend for adipose and muscle 6ssue growth in IB and DUxIB pigs. Arerwards, we inves6gated poten6al TF affec6ng gene expression in IB and DUxIB pigs. The 87 iden6fied TFs are involved in pathways, such as “adipogenesis”or“Glucocor6coid Receptor Signaling”. Among them, EGR2 and FOXO1 are of especial interest because of their roles in growth, adipogenesis and myogenesis. These results contribute a be:er understanding of mechanisms underlying produc6ve and meat quality differences between purebred and crossbred Iberian pigs. TRANSCRIPTOMICS -­‐ Abstract N° 66 EFFECT OF SWINE GENOTYPE AND AGE ON LONGISSIMUS DORSI MUSCLE TRANSCRIPTOME Miriam Ayuso1, Almudena Fernandez2, Yolanda Nuñez2, Rita Benítez2, Beatriz Isabel1, Ana I Fernández2, Ana I Rey1, Antonio González-­‐Bulnes3, Juan F Medrano4, Angela Canovas4, Clemente J López-­‐Bote1 and Cris6na Óvilo2 Departamento de Producción Animal, Facultad de Veterinaria UCM, Avda Puerta de Hierro s/n, 28040, Madrid, ES 2 Departamento de Mejora Gené6ca Animal, INIA, Ctra Coruña, km 7.5, 28040, Madrid, ES 3 Departamento de Reproducción Animal, INIA, Ctra Coruña km 5.9, 28040, Madrid, ES 4 Department of Animal Science, University of California Davis, One Shields Avenue, 95616, Davis, US 1 Iberian pig produc6on is based in both purebred Iberian (IB) and crossbred Duroc X Iberian (DUxIB) pigs. These two gene6c types show important differences in growth, fa:ening and 6ssue composi6on.This studywas conducted to assess muscular gene expression profiles in16IB and 20 DUxIB newborns and to understand how this profile may be affected by age. Nine IB and 10 DUxIB piglets were slaughtered at birth, and 7 IB and 10 DUxIB were slaughtered at 4 months-­‐old. Carcass traits were measured and samples from Longissimus dorsi were taken to study intramuscular fat (IMF) content and composi6on and to analyze the muscle transcriptome with RNAseq technology. Carcasses were lighter and shorter in IB than in DUxIB neonates (P<0.001). At 4 months-­‐old, IB pigs showed greater IMF content (P<0.05). Age significantly affected expression of 4662 genesin the muscle transcriptome analysis. However, the effect of the gene6c type wassmaller than 6me effect, since only 261 genes were found differen6ally expressed (DE) between IB and DUxIB (P<0.01 and Fold change>1.5) at birth; among them, 130 genes were upregulated in IB. At 4 months, 113 genes were DE, being 88 of them upregulated in IB. Ten genes were DE at both ages. Some of the DE genes were related to lipid metabolism and muscular growthbiological func6ons (i.e.SLC2A4 or FOXO3at birth and SNCA or HDL at 4 months). Pathways analysis at birth showed an enrichment in pathways related to energy homeostasis (Aldosterone Signaling) or protein metabolism (Ubiqui6na6on Pathway), and to compound biosynthesis (serine, glicine and re6noids) or glucose metabolism (Glucose and Glucose-­‐1-­‐phosphate Degrada6on) at 4 months. Ingenuity Pathways Analysis sorware iden6fied poten6al regulators related to the DE genes observed, such as FOXO3 and EGF at birthor CTNNB1 or NFKBIA at 4 months of age. The DE genes were also employed to build networks. At birth, main networks were related to the cardiovascular system and to Connec6ve Tissue Disorders, with genes such as CDH2 or ELANE playing central roles. At 4 months, the most significant network built was related to Lipid Metabolism and showed interes6ng genes, such as SNCA or NPPC. Taken together, these results increase the knowledge about age-­‐specific genes and molecular mechanisms underlying phenotypic differences observed between purebred and Duroc-­‐crossbred Iberian pigs and highlight some candidate genes implicated in those molecular mechanisms. TRANSCRIPTOMICS -­‐ Abstract N° 67 EVALUATION OF BCL2 AND PTX3 GENES EXPRESSION IN SWINE CUMULUS CELL CULTURED IN DIFFERENT MEDIA Calin Mircu1, Oana Boldura1, Camelia Tulcan1 and Ioan Huțu1 Horia Cernescu Research Unit, Banat University of Agricultural Science and Veterinary Medicine, 119th Aradului Street, 30064, Timisoara, RO 1 The aim of study was to increase the fer6liza6on rate of swine oocyte by adding cysteine in the culture media by expression of Bcl2 and Ptx3 genes. Cumulus-­‐oocyte complexes (COC) were aspirated from 2-­‐6 mm follicles using 5 ml syringe and an 18-­‐gauge needle. The follicle content was pelleted in conical tubes. Arer sedimenta6on, the COCs were washed twice in PBS and twice in culture medium. The COCs collected were cultured in Greiner Bio-­‐One 30 mm Petri dishes in 80 µl TCM199 (Sigma, M7528) supplemented with 10 mg/ml BSA, 0.5µg/
ml FSH, 0.1 mg/ml cysteine (in group II with cysteine) and 10% (v/v) ECS covered with mineral oil for 44h at 38.50C in a humidified incubator with 5% CO2 in air. Arer culture of COCs, the cumulus cells were removed from oocyte with 24-­‐gauge needles in PBS and washed two 6mes in the same washing medium with 5 min centrifuga6on at 200G between them. The cumulus cells were frozen in liquid nitrogen and stored at -­‐800C un6l tRNA was isolated. Cumulus cells were divided into 3 groups: group I-­‐ cumulus cells before COC in vitro matura6on, group II – cumulus cells arer COC in vitro matura6on in medium without cysteine and group III – cumulus cells arer COC in vitro matura6on in medium with cysteine. The Bcl2 and Ptx3 genes expressions were evaluated by qRT-­‐PCR method. Total ARN was isolated from samples of cumulus cells, revers transcripted in cDNA and used as template in SYBR Green analysis. The ra6o for the mRNA of interest was normalized with β – Ac6n gene value of expression. Obtained data were interpreted by 2 ∆∆ C(T) method. The mean and standard devia6on were calculated. The obtained data were sta6s6cally interpreted using the ANOVA sorware. Bcl2 gene expression varies in different evalua6ve stages of oocyte but also depending on culture media composi6on while Ptx3 mRNA concentra6ons did not gave any conclusive results. There is an increase of Bcl2 gene expression in the case of mature oocyte cumulus cells compared with immature oocyte cumulus cells. In the mature oocyte cumulus cells obtained from COC complexes significant differences can be no6ced in Bcl2 gene expression from cumulus cells that were cul6vated in media supplemented with cysteine. An increased level of inhibi6on Bcl2 gene expression leads of apoptosis by a mitochondrial pathway, which leads to a no6ceable increase of oocyte fer6liza6on rate. TRANSCRIPTOMICS -­‐ Abstract N° 68 EXPRESSION ANALYSIS OF SELECTED CANDIDATE GENES IN BUFFALO OOCYTES (BUBALUS BUBALIS) BEFORE AND AFTER MATURATION WITH DIFFERENT QUALITY BASED ON MORPHOLOGICAL ASSESSMENT Ashraf El-­‐Sayed2, Dalia A. Ahmed1, Salem M. Salem1 and Ashraf H. Barkawi1 Department of Animal Produc6on, Faculty of Agriculture, Cairo university, Gamaa street, 12613, Giza, EG Cairo University Research Park (CURP), Faculty of Agriculture, Cairo University, Gamaa street, 12613, Giza, EG 1 2 The developmental competence of oocytes may be a func6on of the presence/abundance of specific transcripts in their mRNA pools, since the earlier stages of embryogenesis in mammals and other animals are regulated by maternally-­‐inherited RNAs and proteins stored within the oocyte. Inves6ga6on on the molecular characteris6cs of oocytes of varying developmental competence is cri6cal for the development of future classifica6on criteria for the selec6on of oocytes with superior developmental capacity. However, there is no available informa6on in regard to selec6on of buffalo oocytes based on the expression of molecular markers. As far as we know, this is the first study conducted to analyze gene expression of morphologically good and poor buffalo immature oocytes. Cumulus oocytes complexes (n=180) were recovered from buffalo ovaries collected from local slaughterhouses and transported in physiological saline supplemented with 50 μg/ml gentamicin at 30-­‐35°C . Based on morphological characteris6cs (number of cumulus cells enclosed the oocytes and the clearance of the cytoplasm) the oocytes were classified into good and poor. Each grade has three biological replicates with 30 oocytes each. In addi6on, 90 mature oocytes (three replicates each) resulted from immature good ones were tested for the selected transcripts. Total RNA was isolated from all samples using PicoPureTM RNA isola6on kit, and then converted into cDNA via reverse transcrip6on kit. Quan6ta6ve Real-­‐Time PCR was performed using specific primers for a set of selected candidate genes regula6ng cell cycle (Cyclin B), polyamine biosynthe6c (ODC1), signal transduc6on and ac6va6on of transcrip6on (STAT3), Cell cycle regulator gene (PTTG1) and transcrip6on factor ac6vity (OCT4). Quan6ta6ve real-­‐6me PCR results showed a higher expression of all the selected genes in good compared to poor grade immature oocytes. The trend of these transcripts in mature oocytes showed up-­‐regula6on of Cyclin B and OCT4 and down-­‐regula6on of the three transcripts (ODC1, STAT3 and PTTG1) in mature compared to immature counterparts. In conclusion, we report for the first 6me the expression level of some candidate genes in buffalo oocytes with different developmental competence. Further molecular studies at large scale transcrip6onal analysis is strongly needed for this species. TRANSCRIPTOMICS -­‐ Abstract N° 69 FIRST IDENTIFICATION OF POTENTIAL GENOMIC POLYMORPHISMS WITH FUNCTIONAL EFFECTS ON FEED EFFICIENCY BY LIVER RNA-­‐SEQ IN NELLORE CATTLE Pamela A. Alexandre1, Gabriel C. M. Moreira2, Jose Bento S. Ferraz1, Miguel H. A. Santana1 and Heidge Fukumasu2 Veterinary Sciences, University of Sao Paulo, College of Animal Sciences and Food Engineering , Rua Duque de Caxias Norte, 225, 13635, Pirassununga, SP, BR 2 Animal Sciences, University of Sao Paulo, Escola Superior de Agricultura Luiz de Queiroz , Av. Pádua Dias -­‐ Vila Independencia, 13418, Piracicaba, SP, BR 1 The growing demand for food to supply the expanding human popula6on makes important to improve produc6vity and reduce the environmental impact of livestock. Feed efficiency (FE) in beef ca:le is the animal’s intrinsic ability to convert food into meat. Efficient animals eat less food and generate fewer pollutants as methane and manure to produce the same amount of meat when compared to inefficient animals, improving produc6vity and sustainability. One way to include this trait in breeding programs is the iden6fica6on of molecular markers that are associated with phenotypic varia6on among animals. In order to iden6fy func6onal genomic polymorphisms associated with FE, 98 Nellore bulls were individually evaluated in a 70-­‐d feeding trial and FE was es6mated by residual intake and body weight gain. Then, 8 animals from each extreme (high and low FE) were biopsied for liver samples. Total RNA was extracted, purified to keep only mRNA, sequenced on Illumina HiSeq 2500 and aligned with the Bos taurus UMD3.1 reference genome. SAMtools sorware was used to iden6fy small varia6ons in rela6on to the reference genome (SNPs and INDELs) which were then input on CLCbio sorware to keep only varia6ons with quality >30 and sequencing deep >4. Fisher´s exact test was used to iden6fy genotypes with significant differences in the frequency between the 2 condi6ons, which were next input on VEP online tool to predict their func6onal effects. A total of 778,631 variants were found and 223,640 were kept arer quality control. From those, 3,123 variants presented significant differences between condi6ons (p<0.05) and 37% of them corresponded to novel variants. The posi6on and consequences of these variants were 35% on downstream gene sequence, 19% synonymous SNPs, 15% on 3’UTR region, 8% missense SNPs, 8% on upstream gene sequence, 7% intronic variants, 4% intergenic variants, 2% on 5’UTR region and 1% splice region variant. From total missense variants, 51 were predicted as not-­‐tolerated by SIFT tool and those variants may have func6onal implica6ons to translated proteins. Moreover, synonymous variants can influence alterna6ve splicing and UTR variants can have regulatory roles. These preliminary results need to be further inves6gated and validated. TRANSCRIPTOMICS -­‐ Abstract N° 70 GENOMICS AND SYSTEMS BIOLOGY OF BOAR TAINT AND MEAT QUALITY IN PIGS Markus Drag1, Lise:e J. A. Kogelman1, Lene Meinert2, Hanne Maribo3 and Haja N. Kadarmideen1 Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg C, DK 2 Danish Meat Research Center, Danish Technological Ins6tute, Gregersensvej 1, 2630, Taastrup, DK 3 Danish Agriculture and Food Council, SEGES -­‐ Danish Pig Research Center, Axeltorv 3, 1609, København V, DK 1 Boar taint (BT) is an offensive odour or taste of cooked porcine meat which may occur in en6re male pigs due to skatole and androstenone accumula6on in the adipose 6ssue. To avoid BT, surgical castra6on of young piglets is performed but castra6on is undesirable due to animal welfare concerns, economic losses associated with castrated pigs and a ban on castra6on in the EU effec6ve by 2018. The main objec6ve of the study is to unravel the underlying mechanisms of BT at the genomic, transcriptomic and phenotypic levels as well as its connec6on with sensory meat quality (SMQ) in order to enable op6mized breeding strategies as alterna6ve to castra6on. Male pigs with different gene6c merit of BT were selected and 6ssues from liver and tes6s were subjected to transcriptomic profiling by stranded paired end RNA-­‐Seq which produced ~30 mio. reads per sample. The reads were subjected to quality control by FASTQC and later pre-­‐processed with Cutadapt and Trimmoma6c. The reads were mapped with STAR aligner which resulted in ~87% uniquely mapped reads per sample. Post-­‐
processing quality control with Qualimap revealed ~51% of reads mapped in the exonic region and a mean mapping quality of ~52. Gene expression levels were quan6fied by HTseq. Genotypic profiling by 60K Porcine SNPchip was performed and selected cuts from fore-­‐end, loin, ham and backfat of the pigs were subjected to SMQ assessments. Combining SNPchip, RNA-­‐seq and SMQ data will reveal causa6ve genes, co-­‐expression networks and find biomarkers for BT phenotypes. Candidate bio-­‐markers will be validated by qPCR and intended for use in op6mized breeding schemes to avoid BT without compromising SMQ in a non-­‐
castra6on scenario. TRANSCRIPTOMICS -­‐ Abstract N° 71 GOEXPRESS: AN R/BIOCONDUCTOR PACKAGE FOR THE IDENTIFICATION AND VISUALISATION OF ROBUST GENE ONTOLOGY SIGNATURES THROUGH SUPERVISED LEARNING OF GENE EXPRESSION DATA Kévin Rue-­‐Albrecht1, Paul A. McGebgan1, Belinda Hernández3, David A. Magee1, Nicolas C. Nalpas1, Andrew C. Parnell3, Stephen V. Gordon2 and David E. MacHugh1 UCD School of Agriculture and Food Science, University College Dublin, Animal Genomics, Lab, UCD Veterinary Sciences Centre, D4, Dublin, IE 2 UCD School of Veterinary Medicine, University College Dublin, UCD Veterinary Sciences Centre, D4, Dublin, IE 3 UCD School Of Mathema6cal Sciences, University College Dublin, UCD Science Centre North, D4, Dublin, IE 1 Iden6fica6on of gene expression profiles that differen6ate experimental groups is cri6cal for discovery and analysis of key molecular pathways and also for selec6on of robust diagnos6c or prognos6c biomarkers. Typically, gene set enrichment analysis (GSEA) is limited to single gene lists resul6ng from simple two-­‐group comparisons or 6me series experiments. We introduce GOexpress, a sorware package for scoring and summarising the capacity of gene ontology (GO) categories to simultaneously classify samples from mul6ple experimental groups. GOexpress integrates gene expression data (e.g. from microarray or RNA-­‐seq experiments) and experimental factor informa6on with gene ontology annota6ons to derive a ranking of genes and GO terms using a supervised learning approach. The default random forest algorithm facilitates compe66ve scoring of expressed genes to evaluate their rela6ve importance in classifying predefined groups of samples. GOexpress enables rapid iden6fica6on and visualisa6on of ontology-­‐related gene panels that robustly classify groups of samples and supports both categorical (e.g. infec6on status or treatment) and con6nuous (e.g. 6me point or drug concentra6on) experimental factors. The use of standard Bioconductor extension packages and publicly-­‐available GO annota6ons facilitates straighŒorward integra6on of GOexpress within exis6ng computa6onal biology pipelines. Here we illustrate the features of GOexpress using an RNA-­‐seq data set generated from bovine alveolar macrophages s6mulated across an infec6on 6me course with two different but closely related mycobacterial pathogens: (a) Mycobacterium bovis, the causa6ve agent of tuberculosis in ca:le and (b) M. tuberculosis, the causa6ve agent of human tuberculosis, which does not cause disease in ca:le. TRANSCRIPTOMICS -­‐ Abstract N° 72 HARDERIAN GLAND TRANSCRIPTOME RESPONSE OF TWO DISTINCT INBRED LINES TO COMBINED STRESSORS OF NEWCASTLE DISEASE VIRUS AND HEAT PEROT SAELAO1, Ying Wang1, Ali Nazmi1, Rodrigo Gallardo1, David Bunn1, Susan Lamont2 and Huaijun Zhou1 1 Animal Science, University of California, Davis, One Shields ave, 3310 Meyer Hall, CA, Davis, US Animal Science, Iowa State University, Iowa State University, 2255 Kildee Hall, 50011, Ames, US 2 Newcastle disease virus (NDV) and heat stress are two major factors impac6ng poultry in Africa. Although vaccines can provide protec6on against NDV infec6on, gene6c approaches can provide an alterna6ve method for enhancing host immune response to NDV infec6on especially in adverse climates. The objec6ve of this study was to iden6fy genes and signaling pathways associated with NDV resistance within the harderian gland, a secondary lymphoid organ and the ini6al infec6on site of NDV, while under intense heat stress within gene6cally dis6nct inbred chicken lines. Between the two lines, Fayoumi birds appeared to be more resistant to NDV than Leghorn birds based on tear viral 6ters, measured at 2 and 6 DPI, and an6bodies measured from serum while under constant heat exposure (35C, 65% humidity) star6ng from two weeks of age. Total RNA extracted from the harderian gland at 2 dpi from 16 samples (4 per group: Fayoumi infected and uninfected, Leghorn infected and uninfected) were used to iden6fy differen6ally expressed genes (DEG) with a FDR < 0.05 associated with NDV infec6on and heat stress. Preliminary analysis using DESeq2 has iden6fied 202 and 249 DEG in Fayoumi and Leghorn respec6vely. Only 51 DEG were shared between the two lines and the magnitude of fold change appears to be significantly higher in Fayoumi than Leghorn (P < 0.05). Two genes, ZP1 and PLS2, showed opposite expression pa:erns between the two lines with both genes up regulated in Fayoumi and down regulated in Leghorn. GO analysis shows nine significantly enriched in pathways in Leghorn related to Toll-­‐like receptor signaling and cell cycle/division pathways, while Fayoumi demonstrated only two enriched pathways, leukocyte migra6on and axon guidance. Further analysis comparing results with collaborators at Iowa State University working on understanding NDV resistance in the absence of heat stress, will pave the way to poten6ally iden6fying genes associated with disease resistance to NDV while under extreme environmental condi6ons. TRANSCRIPTOMICS -­‐ Abstract N° 73 IDENTIFICATION OF REGULATORY CANDIDATE GENES FOR PORCINE PRODUCTIVE TRAITS USING AN EGWAS APPROACH Angel Mario Mar6nez Montes1, Anixa Muiños Bühl1, Almudena Fernández Muñoz1, Mª Carmen Rodríguez Valdovinos1, Carmen Barragán Alcaide1, Yolanda Nuñez Moreno1, Rita María Benítez Yáñez1, Josep Maria Folch2, Noelia Ibañez Escriche4 and Ana Isabel Fernández Ávila1 Mejora Gené6ca Animal, Ins6tuto Nacional de Inves6gación y Tecnología Agraria y Alimentaria INIA, Crta. de la Coruña, km 7,5, 28040, Madrid, ES 2 GENÓMICA DE PLANTAS Y ANIMALES, Centro de Inves6gación en Agrigenómica CRAG, Campus UAB Edifici CRAG, 08193, Bellaterra, ES 3 Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Campus UAB , 08193, Bellaterra, ES 4 Genè6ca y Mejora Animal, Inves6gación y Tecnología Agroalimentarias IRTA, Torre Marimon, 08140, Caldes de Montbui, ES 1 This work has been focused on the use of eGWAS approach to iden6fy genomic regions and poten6al candidate genes associated with traits of interest in pig produc6on (weight, backfat thickness, % intramuscular fat and cut yields). Data from 102 individuals belonging to an experimental backcross ((F1 Iberian x Landrace)x Landrace) genotyped with Porcine 60K SNP BeadChip and gene expression data measured in intramuscular fat with the Affymetrix porcine expression microarray were used. First, those gene expression probes (820) showing significant correla6ons (p-­‐val<0.001, corr: 0.32-­‐0.66) with at least one of the produc6ve traits, were selected for further analyses. eGWAS was conducted using the GenABEL R package, including sex and batch as fixed effects in the model. A correc6on for mul6ple test was performed using “qvalue” package (FDR<0.05). The results revealed a total of 881 eTAS (SNPs associated with gene expression levels) associated with 42 transcripts, considering consecu6ve eTAS as eQTLs containing poten6al expression regulators. Six of these eQTLs overlapped with the C.I. of four QTLs previously described for growth and fat deposi6on. We iden6fied four genes poten6ally responsible for these eQTLs: MGLL (lipid metabolism), TRIB3 (inhibi6on of insulin signaling), TXNRD3 (adipocyte differen6a6on through Wnt signaling pathway) and PDIA4 (HSP90 ac6vity in muscle differen6a6on). A previous RNA-­‐Seq study in the same material allowed us to iden6fy SNPs in these candidate genes (PDIA4;c374G>A, MGLL;c88218G>A,TXNRD3-­‐1;c25928T>C, TXNRD3-­‐2;c25947A>T, TRIB3;c72819A>G), genotyped in the backcrossed individuals and used to perform associa6on studies. The results of the analyses revealed significant associa6ons between SNPs at MGLL and TXNRD3 genes with TXNRD3 expression levels and between PDIA4 SNP and expression levels of BUB1B gene. Also the TXNRD3 and PDIA4 SNPs showed significant effects on weight (TXNRD3-­‐1: -­‐2.89±1.11, TXNRD3-­‐2: 2.63±1.25, PDIA4: -­‐2.34±1.334), and TRIB3 SNP on ham weight (-­‐0.60±0.24). Associa6on analyses performed together with the F2 Iberian x Landrace genera6on of the same experiment confirmed the significant effects on weight of TXNRD3-­‐2 SNP (5.48±2.22). The analyses conducted provide interes6ng eQTLs with poten6al effects on growth, fatness and conforma6on traits. Moreover, results obtained support the interest of TXNRD3 as poten6al gene involved in pig growth through gene expression regula6on. TRANSCRIPTOMICS -­‐ Abstract N° 74 IL-­‐22 AS A MAJOR CYTOKINE ORCHESTRATING THE BOVINE RESISTANCE AGAINST TICK INFESTATION Daniela D Moré1, Mauricio A Mudadu1, Wilson Malago Junior1, Claudia G C Gomes2, Fernando F Cardoso2 and Luciana C A Regitano1 Molecular Gene6cs, Embrapa Southeast Livestock, Rodovia Washington Luiz km 234 , 13560, Sao Carlos, BR Animal Science, EMBRAPA South Animal Husbandry and Sheep, BR 153 Km 603 -­‐ Caixa Postal 242, 96401, Bage, BR 1 2 Tick infesta6on is an important problem in livestock scenario, once is responsible for significant impairment of health, with consequences in animal welfare and produc6on. To understand the transcriptomic profile under 6ck infesta6on, gene expression of Braford ca:le with contras6ng phenotype, i.g. resistant (R) and suscep6ble (S) to infesta6on, were compared previously (pre) and arer (pos) infesta6on. For that, paired-­‐end RNA-­‐Seq reads were aligned to reference genome through TopHat2 sorware and the transcripts were counted to perform differen6al expression analysis using R packages SummarizedOverlaps and EdgeR. The analysis was performed comparing the gene expression arer 6ck infesta6on to before 6ck infesta6on (pos minus pre). Genes were considered differen6ally expressed (DE) when p-­‐value≤0.05 and FDR≤5%. Arer that, DE genes lists were filtered to keep DE genes exclusives for each comparison and with -­‐1≤logFC≥1. Finally, DE genes were func6onally enriched by Ingenuity Pathways Analysis (IPA-­‐Qiagen), and considered sta6s6cally significant when -­‐2≤z-­‐score≥2. Regarding differen6al expression analysis, Rpos-­‐pre comparison showed 124 DE genes, with logFC varying from 4.34 to -­‐1.89, most of them related to immune and inflammatory response. More interes6ng is that R animals showed a specific cytokine profile, including an increased expression of IL-­‐22, that can help the host fight against the parasite, by leading to a harmful skin inflamma6on and/or by promo6ng 6ssue repair. The expression of other genes induced by IL-­‐22, as IL-­‐6, IL-­‐20, CSF, LBP, SAA and HP, are also increased arer 6ck infesta6on, which can explain the profile observed in the enrichment analysis. Moreover, R animals show a decreased expression of IL-­‐37, a potent inhibitor of innate immune response. When DE genes from R animals were func6onally enriched, we could see six main func6onal categories ac6vated, showing z-­‐score between 2.015 and 3.24, that means none of them was inhibit. Among these categories, migra6on and ac6va6on of different types of cells were the func6ons more strongly ac6vated. Addi6onally, neovasculariza6on, angiogenesis, inflammatory response, fa:y acid metabolism and transport of molecules were also found ac6vated, showing possible mechanisms by which R animals assemble this complex trait. TRANSCRIPTOMICS -­‐ Abstract N° 75 LONG-­‐SOUGHT LEPTIN EMERGES FROM CHICKEN GENOME’S DARK-­‐SIDE: EXPRESSION PATTERN OF GC-­‐
RICH AVIAN LEP FITS AUTO/PARACRINE RATHER THAN ENDOCRINE FUNCTION Eyal Seroussi1, Yuval Cinnamon1, Sara Yosefi1, Olga Genin1, Julia Gage-­‐Smith1, Nima Rafa62, Susanne Bornelöv2, Leif Andersson2 and Miriam Friedman-­‐Einat1 1 Ins6tute of Animal Science, Agricultural Research Organiza6on, Volcani Center, 50250, Bet-­‐Dagan, IL Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala biomedicinska centrum BMC, Husarg. 3, 75123, Uppsala, SE 3 Department of Animal Breeding and Gene6cs , Swedish University of Agricultural Sciences, Ulls väg 26, 75007, Uppsala, SE 4 Department of Veterinary Integra6ve Biosciences, Texas A&M University, TX 77843-­‐4458, College Sta6on, US 2 More than 20 years arer characteriza6on of the key regulator of mammalian energy-­‐balance, lep6n, we iden6fied the genuine lep6n (LEP) genes of chicken (Gallus gallus) and duck (Anas platyrhynchos). The extreme GC-­‐content (~70%), the loca6on in a genomic region with low-­‐
complexity repe66ve and palindromic sequence elements, the rela6vely low sequence conserva6on and low level of expression has hampered the iden6fica6on of these genes un6l now. In vitro expressed chicken and duck lep6ns specifically ac6vated signaling through the chicken lep6n-­‐receptor in cell culture. In situ hybridiza6on demonstrated expression of LEP mRNA in the granular and Purkinje cells of the cerebellum, medullar hypothalamus, cor6cal pituitary, and in embryonic limb-­‐buds, somites and branchial arches sugges6ng a role in adult brain func6on and during embryonic development. The expression pa:erns of LEP and the lep6n receptor (LEPR) were explored in chicken, duck and in quail (Coturnix japonica) using RNA-­‐seq experiments available in the Short Read Archive (SRA) and, by qPCR. In adipose 6ssue, LEP and LEPR were scarcely transcribed and this expression was not correlated to adiposity. Nevertheless, LEP and LEPR expression were detected in 6ssues involved in energy homeostasis including pituitary, cerebellum, hypothalamus and adrenal gland indica6ng that lep6n signaling may have a role in the control of energy balance also in birds. Co-­‐expression of LEP and LEPR, low levels of LEP expression and undetectable levels of circula6ng lep6n strongly suggest an autocrine/paracrine mode of ac6on for bird lep6n instead of being a circula6ng hormone as in mammals. THIS WORK HAS BEEN ACKNOWLEDGED WITH THE FIRST PLACE IN THE POSTER COMPETITION
TRANSCRIPTOMICS -­‐ Abstract N° 76 MICRORNAS EXPRESSION IN HYPOTHALAMIC-­‐
PITUITARY-­‐GONADAL AXIS IN GOAT Emanuele Capra1, Stefano Frabni2, Barbara Lazzari1, Beatrice Coizet2, Debora Groppeb2, Pietro Riccaboni2, Alesssandro Pecile2, Silvana Arrighi3, Stefania Chessa1, Bianca Cas6glioni1, Andrea Talen62, Le6zia Nicoloso2, Alessia Giordano2, Davide Prave:oni3, Paola Crepaldi2, John L. Williams4, Giulio Pagnacco2 and Alessandra Stella1 Is6tuto di biologia e biotecnologia Agraria, Consiglio Nazionale delle Ricerche UOS di Lodi, Via Einstein, 26900, Lodi, IT 2 Dipar6mento di Scienze Veterinarie e Sanità Pubblica, Università degli Studi di Milano, Via Celoria, 10, 20133, Milano, IT 3 Dipar6mento di Scienze Veterinarie per la Salute, la produzione animale e la sicurezza alimentare, Università degli Studi di Milano, Via Celoria, 10, 20133, Milano, IT 4 School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, 5371, Adelaide, AU 1 Reproduc6on is an event that requires the coordina6onof peripheral organs with the central nervous system, each event is accompanied by posi6ve and nega6ve hormonal regula6on along the Hypothalamic-­‐Pituitary-­‐Gonadal (HPG) axis. MicroRNAs (miRNAs), a class of small non-­‐coding RNA molecules, play important roles in gene expressions by targe6ng messenger RNAs for post-­‐transcrip6onal cleavage or transla6onal inhibi6on, affec6ng physiology in mammals. In order to be:er understand molecular pathways involved in HPG axis regula6on, we evaluate the transcriptomic and miRNA profile changes in hypothalamus, pituitary and ovary from 3 Saanen goats using Illumina high-­‐throughput technology. Reads were mapped on the Capra hircus reference genome and expression levels of both coding and non coding RNAs were assessed. We found 818 miRNAs belonging to known (436) and novel (382) classes, 67 of which are differen6ally expressed in the three 6ssues. Transcriptomic profiling revealed 2223, genes that were differen6ally expressed between hypothalamus and pituitary, 2117 between pituitary and ovary and 3823 between hypothalamus and ovary. This study reveals for the first 6me a complete large and small RNA profile of the HPG axis in goat. The characteriza6on of these RNAs could contribute to a be:er understanding of the molecular mechanisms of reproduc6ve physiology and development in this species. Acknowledgement The research was funded by GenHome project. TRANSCRIPTOMICS -­‐ Abstract N° 77 MIRNAS AS REGULATORS OF GENE EXPRESSION MODULATE ENERGY METABOLISM OF SKELETAL MUSCLE Siriluck Ponsuksili1, Pun6ta Siengdee1, Nares Trakooljul1, Eduard Murani1, Manfred Schwerin1 and Klaus Wimmers1 Ins6tute for Genome Biology, Leibniz Ins6tute for Farm Animal Biology, Wilhelm-­‐Stahl-­‐Allee 2, 18196, Dummerstorf, DE 1 MiRNA func6on iden6fica6on has become one of the ac6ve research fields in muscle biology addressing muscle development, growth and metabolism. This study aims at the iden6fica6on of miRNAs and mRNAs associated with meat quality at adult stage. The experiment integrated miRNA and mRNA expression of M. longissimus dorsi from performance-­‐tested crossbred pig [PI×(DL×DE)] samples together with network analysis by using weighted gene co-­‐expression network analysis (WGCNA). We iden6fied the nega6ve miRNA-­‐mRNA co-­‐expression networks which revealed several biological pathways underlying the difference of meat proper6es and muscle traits (i.e. glucose metabolic process, mitochondrial ribosome and oxida6ve phosphoryla6on). Finally, miRNAs impacted on muscle metabolism were validated exemplarity by in vitro cell culture experiments. C2C12 in vitro model studies revealed that miRNAs modulate in cellular ATP produc6on and energy metabolism processes during myogenic differen6a6on. Correla6on analyses were performed between ATP level, miRNA and mRNA microarray expression profiles during C2C12 differen6a6on. Among 14 significant miRNAs represen6ng cellular ATP regulators involved in mitochondrial energy metabolism, miR-­‐423-­‐3p was iden6fied as a novel regulator for cellular ATP/energy metabolism via targe6ng the group of mitochondrial energy metabolism genes (Cox6a2, Ndu¶7, and Ndufs5). The present study further adds a comprehensive knowledge on the systems perspec6ve of the skeletal muscle miRNAs and their target genes regula6on networks that influence on myogenesis and adult skeletal muscle and meat proper6es. TRANSCRIPTOMICS -­‐ Abstract N° 78 POST-­‐WEANING BLOOD TRANSCRIPTOMIC DIFFERENCES BETWEEN YORKSHIRE PIGS DIVERGENTLY SELECTED FOR RESIDUAL FEED INTAKE Jack Dekkers1, Dan Ne:leton2, Nguyen Yet2, Haibo Liu1 and Christopher Tuggle1 1 Animal Science, Iowa State University, 2255 Kildee Hall, 50011, Ames, US Sta6s6cs, Iowa State University, 1121 Snedecor Hall, 50011, Ames, US 2 Background: Improving feed efficiency (FE) of pigs by gene6c selec6on is of economic, social and environmental significance. Residual feed intake (RFI) is an increasingly accepted measure of feed efficiency. However, currently, in order to incorporate RFI into animal breeding programs, feed intake must be recorded on individual pigs. Thus, convenient, predic6ve biomarkers for feed efficiency are greatly desired. In addi6on, molecular mechanisms underlying pig feed efficiency are largely unknown. In this study, we aimed to iden6fy differen6ally expressed genes (DEGs) and differen6ally correlated genes (DCGs) from whole blood of young pigs of extremely low and high RFI from low and high RFI lines, respec6vely, to explore the molecular basis of RFI in whole blood and generate a list of candidate predic6ve biomarkers for RFI for further valida6on in the future. Results: Using RNA sequencing (RNA-­‐seq) technology, we iden6fied 454 DEGs (q ≤ 0.05) between the two divergent groups composed of 15 low and 16 high RFI pigs. Gene ontology-­‐
biological process (GO-­‐BP) term analysis suggested that genes involved in small molecule biosynthe6c process and signaling were overrepresented among genes with higher and lower expression levels in the low RFI group than in the high RFI group, respec6vely. Genes func6oning in the proteasome complex and mitochondrion were significantly enriched among genes up-­‐regulated in the low RFI group. Weighted gene co-­‐expression network analysis revealed 4 differen6al co-­‐expression modules between low and high RFI groups. GO-­‐BP terms such as lipid metabolic process, lipid biosynthe6c process, steroid biosynthe6c process and response to s6mulus were overrepresented among the two modules most significantly associated RFI group. A total of 239 DCGs, involved in 170 pairwise gene-­‐to-­‐gene correla6ons, were iden6fied between the high and low RFI groups. Conclusions: The iden6fied DEGs, differen6al co-­‐expression gene modules, and DCGs provide further molecular insights into the basis of RFI. The discovered transcriptomic differences between pigs with divergent RFI phenotypes could be used as a star6ng list for developing predic6ve biomarkers for FE in pigs in the future. This study is supported by the Agriculture and Food Research Ini6a6ve compe66ve grant: NIFA-­‐AFRI-­‐2011-­‐68004-­‐30336 from the USDA Na6onal Ins6tute of Food and Agriculture. TRANSCRIPTOMICS -­‐ Abstract N° 79 RNA-­‐SEQ ANALISYS OF BROILER LIVER TISSUE REVEALS THE BENEFICIAL EFFECTS OF ORIGANUM VULGARE DIETARY SUPPLEMENTATION Marcella Sabino1, Andrea Verini-­‐Supplizi1, Stefano Capomaccio1, Lorenzo Bomba2, Gabriella Cobellis1, Mar6na Torricelli3, Paolo Ajmone-­‐Marsan2, Ka6a Cappelli1 and Massimo Trabalza-­‐
Marinucci1 1 Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126, Perugia, IT 2 Is6tuto di Zootecnica, Università Ca:olica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, IT Is6tuto Zooprofilabco Sperimentale Umbria e Marche, Is6tuto Zooprofilabco Sperimentale Umbria e Marche, Via Gaetano Salvemini, 1, 06126, Perugia, IT 3 Many studies report the an6microbial, immunomodula6ng and an6oxidant ac6vi6es of aroma6c plants and their supplementa6on in animal diets produces beneficial effects on animal health. We evaluated the effects of 0.2% oregano (Origanum vulgare L.) aqueous extract dietary supplementa6on on broiler liver transcriptome. Two thousand Ross 308 broilers were randomly divided in two groups and fed either a control diet (CTRL) or an oregano supplemented diet (ORE) for 52 days. Body weight and feed conversion efficiency were recorded at 10 d intervals. At slaughtering, 6ssue samples from the pectoralis major were collected to assess the meat oxida6ve status. Total RNA isolated from liver 6ssue from CTRL (n=10) and ORE (n=10) was sequenced using an Illumina HiSeq 1500 with paired end 100 bp chemistry. Arer trimming and quality control, reads were aligned with TopHat2 the chicken reference genome (galGal4). The read counts for each transcript were retrieved using featureCounts and the differen6ally expressed features were inferred using edgeR. A significant increase in growth rate up to 42 days of age of the birds, a higher feed-­‐conversion efficiency and an improved meat oxida6ve status were observed in the ORE group (p<0.01). Two hundred and nine differen6ally expressed genes were retrieved comparing ORE with CTRL: 58 genes were up-­‐regulated and 151 were down-­‐regulated. Among the up-­‐regulated genes in the ORE, noteworthy are IGF1, WNT4 and COL18A1, known to be involved in growth and collagen synthesis. Enrichment analysis revealed as the most significant (p<0.05 arer Bonferroni correc6on) KEGG pathways "Arginine and proline metabolism", "Pyruvate metabolism", "Propanoate metabolism", "Biosynthesis of amino acids" and "Insuline signalling pathway". Of par6cular interest were PPARG1A, FASN and SOCS1 genes that belong to la:er one and down-­‐regulated in the ORE compared to the CTRL group. They play roles key in adipogenesis and in nega6ve regula6on of cytokine signalling. In conclusion, the liver transcriptome analysis revealed that the dietary treatment with an oregano aqueous extract highly influenced the expression of genes involved in aminoacid and lipid metabolisms in broiler. These results may be related to the improved performance and meat oxida6ve stability evidenced in the ORE group. Sponsored by: Fondazione Cassa Risparmio Perugia -­‐ Verini Supplizi A.: FITODERIVATI, QUALITA' DELLE CARNI AVICOLE E BENESSERE ANIMALE: APPROCCIO NUTRIGENOMICO. TRANSCRIPTOMICS -­‐ Abstract N° 80 SERPINA1 GENE EXPRESSION IN OVINE MILK DURING LACTATION Cinzia Marchitelli1, Alessandra Crisà1, Francesco Napolitano1 and Bianca Moioli1 Animal Produc6on Research Centre, Council for Agricultural Research and Economics, Via Salaria 31, 00015, Monterotondo, IT 1 The serine protease inhibitor, clade A, member 1 (SERPINA1) gene encode for the alpha-­‐1-­‐
an6trypsin (AAT), protein, a member of the serine protease inhibitor (serpin) superfamily proteins. AAT is a 52kD glycoprotein synthesized primarily in the liver, but also expressed in, and secreted by, extra-­‐hepa6c 6ssues, intes6nal enterocytes, macrophages, monocytes, neutrophils and pulmonary alveolar cells. The major role of AAT is to protect 6ssue against proteoly6c diges6on by neutrophil elastase. Addi6onally, the AAT protein is produced by the mammary gland and acts as a protease inhibitor for the survival of other biologically ac6ve milk proteins. The concentra6ons of AAT in human milk are very high during the first week of lacta6on, with concentra6ons fall during subsequent weeks. AAT is also present in bovine, porcine, ovine and goat milk. Possible roles of AAT in the immune response was postulated both for the inhibi6on of lymphocyte and neutrophil chemotaxis and for the regula6on of the expression of pro-­‐inflammatory and an6-­‐inflammatory mediators. In goat SERPINA1 gene has been found up-­‐regulated during early stages of bacterial infec6on Also associa6on of polymorphisms of the AAT gene with milk produc6on traits in dairy ca:le was demonstrated. Based on the mul6ple role played by the SERPINA1 gene in other species, the aim of this study was to inves6gate the differen6al expression in milk of SERPINA1 gene in two sheep breed (Sarda e Gen6le di Puglia) during lacta6on (60, 90, 120d) by using qPCR. RNA was extracted from sheep milk soma6c cells of a total of 71 samples at three lacta6on points (60, 90, 120d) and was reverse transcribed to cDNA. The geNormplus analysis was assessed to screen the op6mal set of reference genes among 7 different housekeeping. The SERPINA1 expression analyses were performed considering the three most stable reference genes (ATP, SDH and RPS9) by using the qBaseplus sorware. We did not find any significant expression difference between the two breeds, and between three 6me points. Moreover any associa6on of SERPINA1 expression with milk produc6on traits was observed. Our findings confirm the results obtained in pig, goat and cow lacta6ng mammary gland, where SERPINA1 expression was not significantly affected by 6me. An high concentra6on of AAT was also found in bovine milk at the beginning of mas66s, and SERPINA1 was proposed as an useful marker in the early diagnosis of inflamma6on. TRANSCRIPTOMICS -­‐ Abstract N° 81 SNP CALLING ON TRANSCRIPTOME APPLIED IN GENOME ENABLED PREDICTIONS Mohammad Hossein Banabazi1, Ardeshir Neja6 Javaremi1, Ikhide G. Imumorin2, Mostafa Ghaderi Zefrei3 and Seyed Reza Miraei Ash6ani1 Animal Science, University of Tehran, Faculty of Agricultural Science & Engineering, College of Agriculture & Natural Resources (UTCAN), Daneshkadeh St., , 4111, Karaj, IR 2 Animal Science, Cornell University, College of Agriculture and Life Sciences, 14853, New York, US 3 Animal Science, University of Yasouj, Faculty of Agriculture, 74934, Yasouj, IR 1 The next genera6on sequencing (NGS) plaŒorms facilitate to produce high-­‐throughput data in a 6me and cost saving way. Besides, there is a kind of computa6onal capabili6es that allow to analysis of high volume omics data in post genomics level. So, the integrated data may resolve some limita6ons against genomics and learn more about the mechanisms involved in filling of phenotype-­‐genotype gap. This can led to more real predic6ons for animal ranking and finally their more gene6c improvements due to increasing of selec6on accuracy and reliability. Among of the omics levels, transcriptome can likely fill the gap between phenotype and genotype. A variety of transcriptomics data are produced using different techniques that RNA-­‐Seq is more quan6ta6ve and accurate than others. It's called digital expression. In this study, we supposed that SNPs covered by transcribed genomic regions are probably more suitable for genome enabled predic6ons. The number of reads mapped to these regions (as coverage p-­‐values) may be as a measure for selec6ng SNPs. In this study, the SNPs called on transcriptome sequences (RNA-­‐Seq). In addi6on, SNPs were picked out from a Illumina BovineHD BeadChips based on a threshold for their coverage on transcriptome and then applied in genome enabled predic6ons for residual feed intake (RFI) traits. Among of 22626 SNPs called on our RNA sequences, only 2571 SNPs (list1) were included in Illumina BovineHD BeadChips. With P-­‐value threshold = 0.0001, coverage level was es6mated in 120129 regions with minimum length = 50 bp. The maximum length of high covered regions was 10746 bp. 120091 regions were high coverage and the rest that is mitochondrial and nonchromosomal sequences were low. 6037 SNPs filtered from Illumina BovineHD BeadChips (list2) were localized on genomic regions with high transcriptomic coverage. These were included 2387 SNPs that had been already called by SNP discovery analysis. Arer quality control for use, our proposed SNP lists reduced to 1459 and 4399, respec6vely. Compared with full HD list (including 606096 qualified SNPs) and random subsets with the same number of SNPs, our proposed SNP lists could not sta6s6cally improve predic6on accuracies es6mated using 5-­‐fold cross-­‐valida6on in 842 Holstein heifers. This may be resulted from low density of the filtered SNPs throughout of whole genome. Genotyping of all discovered SNPs using whole genome sequences for animals that have performance records can be TRANSCRIPTOMICS -­‐ Abstract N° 82 THE LONG NON-­‐CODING RNA TRANSCRIPTOME OF THE BOVINE MAMMARY GLAND AND POTENTIAL REGULATORY ROLES IN FATTY ACID SYNTHESIS Eveline M. Ibeagha-­‐Awemu1, Ran Li1 and Pier-­‐Luc Dudemaine1 Dairy and Swine Research and Development Centre, Agriculture and Agri-­‐Food Canada, 2000 Rue College, J1M 0, Sherbrooke, CA 1 Advances in high throughput RNA sequencing have enabled the discovery of an abundant class of non-­‐coding RNA species including long non coding RNA (lncRNA). LncRNAs are >200 nt long and play roles in transcrip6onal/post-­‐transcrip6onal gene regula6on. Few studies have characterized the lncRNA repertoire in bovine. In this study, we used RNA-­‐Seq to study the lncRNA repertoire of the bovine mammary gland and their involvement in mammary gland adapta6on to a diet rich in α-­‐linolenic acid. Twelve Holstein dairy cows (35±10kg milk; 150±50 DIM) were fed a total mixed ra6on (control diet) for 28 days (Day1-­‐28)(control period, CP) followed by a treatment period (TP)(Day29-­‐56) consis6ng of control diet+5% linseed oil (LSO) (57% α-­‐linolenic acid) in a complete randomized block design. Milk samples were collected weekly for the determina6on of fat percentage (FP) and individual fa:y acids (FAs). Mammary gland biopsies were performed on 6 cows on Day 14(CP) and 56(TP). Mammary gland transcriptome was analyzed using RNA-­‐Seq. Milk FP decreased (P<0.0001) during TP as compared to CP. The contents of C4:0, C8:0, C14:0, C16:0 and C14:1 decreased (P≤0.0003) while C18:1n11t, C20:3n3, C20:5n3, C22:5n3, CLA10t12c and CLA9c11t increased (P≤0.035) during the TP. Sequencing of 18 libraries generated a total of 590 million raw paired reads. 87.2% of reads mapped to unique/mul6ple posi6ons on bovine genome UMD3.1. Of these, 96.5% mapped to unique posi6ons. Arer removing reads represen6ng other RNA species (mRNA, miRNA, snoRNA, snRNA, rRNA), 14513451 reads were used as input for lncRNA discovery. Reads were evaluated for their coding poten6al using Coding-­‐Non-­‐Coding Index and Coding Poten6al Assessment Tool programs. Reads that passed filter were compared with known bovine lncRNA annota6on from a domes6c lncRNA database (ALDB). About 4227 lncRNAs, 338 known and 3889 novel were iden6fied. Using RPKM normaliza6on, 18 lncRNAs were highly expressed (average RPKM 20.58-­‐3850.78). Majority of lncRNAs were composed of one transcript (79.37%) followed by two (10.39%). A total of 26 lncRNAs were differen6ally regulated (FDR≤0.05) (8 up-­‐ and 18 down) by treatment. Our study is the first to characterize the lncRNA repertoire of the bovine mammary gland. LncRNA is highly expressed sugges6ng poten6al regulatory roles in milk FA synthesis. This data may form the base for future elucida6on of the regulatory roles of lncRNA in mammary lipogenesis and biology. TRANSCRIPTOMICS -­‐ Abstract N° 83 TRANSCRIPTIONAL PROFILING OF MAMMARY GLAND AND MILK FATTY ACID COMPOSITION IN RESPONSE TO DIETS SUPPLEMENTED WITH FLAX AND HEMP SEED IN DAIRY GOATS Stefania Chessa1, Paola Cremonesi1, Emanuele Capra1, Barbara Lazzari1, Giovanna Ba:elli3, Federica Turri1, Stefania Colombini2, Luca Rapeb2 and Bianca Cas6glioni1 Is6tuto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Einstein s.n.c., 26900, Lodi, IT 2 Dipar6mento di Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia, Università degli Studi di Milano, via Celoria 2, 20133, Milano, IT 3 Is6tuto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, via Celoria 2, 20133, Milano, IT 1 Aim of this study was to evaluate the effects of diets enriched with polyunsaturated fa:y acids (FA), using flax (F) and hemp seed (H) supplementa6on, on milk FA composi6on and mammary gland gene expression of lacta6ng goats. A total of 18 Alpine goats were equally divided into three groups (F, H and control group C) depending on rela6onships among individuals, casein genotypes and produc6on level. The chemical composi6on of the administered diets, in terms of neutral detergent fibre (NDF), starch, and ether extract (EE), were as follows, for C, L and H, respec6vely: 416, 422 and 433 g NDF/kg DM; 172, 132 and 132 g starch/kg DM; 26, 63 and 56 g EE/kg DM. The experiment focused on two 6me points during lacta6on: T0, when all the goats were fed the same diet (about 45 days in milk, DIM); T1, when the animals were fed the three different diets (about 150 DIM). At these two 6me points, a total of 150 mL of milk was collected for both milk fa:y acid composi6on analysis and RNA extrac6on from milk soma6c cells. The FA composi6on was determined by gas chromatography. The concentra6on of milk fat at T1 increased of almost one percentage point between the animals subjected to the supplemented diet with F and H respect to the control group. The treatment with flax and hemp seed caused a clear and significant decrease in the concentra6on of all the saturated fa:y acids, in par6cular short and medium chain fa:y acids, with a more pronounced effect on milk of goats supplemented with flax seed. Massive, parallel, high-­‐throughput, RNA-­‐seq was used to generate the caprine milk transcriptome. In total, we obtained from 14.951.867 to 34.867.432 uniquely mapped reads that covered 88.93% of the current annotated transcripts, which represented 12.436 mRNA transcripts, across all the samples. Among the three dietary treatment groups, no differen6ally expressed genes (p < 0.05, false discovery rate q < 0.05) were found for the control group at the two 6me points, whereas 133 and 491 genes resulted differen6ally expressed in T1 with respect to T0 in the F and H groups respec6vely. This study inves6gated the complexity of the response of goat mammary gland to different diets. Further integrated analysis of differen6al gene expression and genome analysis will permit the iden6fica6on of candidate key genes for enhancing milk FA composi6on in goat. TRANSCRIPTOMICS -­‐ Abstract N° 84 TRANSCRIPTOME RESPONSE OF SMALL INTESTINE OF ASCARIDIA GALLI INFESTED AND NON-­‐INFESTED VILLAGE CHICKENS FROM TWO AGRO-­‐ECOLOGICAL ZONES OF SOUTH AFRICA Dikeledi Petunia Malatji2, Este VanMarle-­‐Koster1 and Cathrine Farai Muchadeyi2 Department of wildlife ad Animal Science, Faculty of Natural and Agricultural Science, University of Pretoria, Pretoria, South Africa, University of Pretoria, Private bag X20, Hatfield , 0028, Pretoria, ZA 2 Biotechnology PlaŒorm, Agricultural Research Council, Onderstepoort, Private Bag X05, Onderstepoort, 0110, Pretoria, ZA 1 Nematodes of the genus Ascaridia are known to infect many species of birds and cause fatal diseases. Ascaridia galli damages the intes6nal mucosa of chickens leading to blood loss and secondary infec6on and occasionally the obstruc6on of small intes6nes due to high worm burden. Analysis of differences in gene expression profiles associated with infesta6on or pathology status can provide an understanding into the molecular gene6c architecture of host immune response. Very li:le informa6on is available on the gene6c resistance to gastrointes6nal parasites par6culary in village chickens popula6ons. This study was aimed at inves6ga6ng the gene expression profiles in chickens from two different agro-­‐ecological zones of South Africa that were infected by the Ascaridia galli parasite. The small intes6ne from non-­‐
infected chickens did not show any presence of parasite and did not display any detectable histological changes whereas the naturally A. galli infected intes6nes displayed hypertrophy of the intes6nal villi with accumula6on of inflammatory cells and necrosis of the crypt of Lieberkühn gland. Total RNA was isolated from small intes6nes of infected and non-­‐infected village chickens. High-­‐quality RNA of the small intes6ne was sequenced using Illumina HiSeq 2500 and generated between 3908924 and 3994946 reads. Using the open-­‐access Tophat program, an average of 83.50% of trimmed and quality controlled reads were mapped to the reference chicken genome (gallus.galgal4.74). Cuffdiff was then used to analyze differen6ally expressed genes (DEG) in infected vs non-­‐infected chickens. A total of 16383 DEG were detected between any two-­‐way comparisons of the intes6nes. Of the 3061 detected in Limpopo chickens, 1608 were up-­‐regulated while 1452 were down regulated Of the 130 from KwaZulu-­‐Natal province, 11 were up-­‐regulated and 119 down-­‐regulated. Gene ontology analysis of DEG revealed an enrichment of immune response, defense response, inflammatory response and cell signaling genes. Phospha6dylinositol signaling system pathway and T cell receptor signaling pathway were among the most significantly impacted pathways. The iden6fica6on and func6onal annota6on of differen6ally expressed genes open a major step towards understanding the molecular network underlying resistance of chickens to Ascaridia galli parasites. TRANSCRIPTOMICS -­‐ Abstract N° 85 WHOLE TRANSCRIPTOME ANALYSES OF IMMUNE SYSTEM CELLS AFTER COMPETITION IN ANGLO-­‐
ARABIAN RACES HORSES: INSIGHTS ON TRANSCRIBED EXONS, INTRONS AND REPEATS Stefano Capomaccio1, Andrea Giontella1, Andrea Verini-­‐Supplizi1, Silvia Sorbolini1, Ma:eo Picciolini3, Francesca Crucianelli3, Giovanni Paolo Biggio1, Raffaele Cherchi2, Maurizio Silvestrelli1 and Ka6a Cappelli1 Dipar6mento di Medicina Veterinaria, Centro di Studio del Cavallo Spor6vo, Via San Costanzo, 4, 06126, Perugia, IT 2 AGRIS Sardegna, Servizio Ricerca per la Qualità e Valorizzazione delle Produzioni Equine, Piazza Borgia, 4, 07014, Ozieri (SS), IT 3 POLO GGB, Polo d’Innovazione Genomica, Gene6ca e Biologia, Piazzale Gambuli, 06132, Perugia, IT 1 The horse is probably the best animal model for inves6ga6ng genomic response to exercise-­‐
induced stress, due to its natural ap6tude for athle6c performance and the rela6ve homogeneity of its gene6c background. In order to fully characterize the exercise-­‐induced stress transcriptome during gallop races we applied RNA-­‐sequencing technique with Illumina PE chemistry. Six 3 years old Anglo-­‐Arabian Race Horses sex matched were recruited for monitoring the transcrip6onal landscape by comparing transcrip6on levels in PBMCs collected at rest and arer a 2000-­‐meter compe66on. Arer data quality control and alignment to the reference genome, we observed a shir of transcribed ma:er from coding to non-­‐coding regions, confirming that the acute stress response to exercise involves differen6al expression of not yet annotated features. Gene expression was indeed inves6gated separa6ng exon and intron compartments to fully exploit our data. Peculiar biological processes and molecular func6ons involved in the response to sprint were mined with String-­‐db. Network analysis and Gene Ontology enrichment revealed mechanisms known to be ac6vated by stress (e.g., chemokine-­‐type cytokines, Toll-­‐like receptors, and kinases), as well as "nucleic acid binding" and "signal transduc6on ac6vity" func6ons. A large number of transcripts, corresponding to intergenic as well as intronic regions associated with new transcrip6onal elements, were iden6fied. Notably, we observed a post-­‐race increase of reads mapping to repeats, especially LINE1 elements in intergenic and intronic regions. Our results are consistent with the hypothesis that transposable elements (TE) and intronic sequences may serve as transcrip6onal units capable of enriching transcriptomes with limited genomic resources, such under stress condi6ons, through intron reten6on phenomenon, crea6ng fusion transcripts and up-­‐regula6ng small RNAs transcrip6on from TE templates. Using an improved annota6on for full-­‐length LINE1 elements we also found that 9 full-­‐length loci are over expressed arer the race. This suggests that great effort induced by an intensive bout of exercise may -­‐ in principle -­‐ ac6vate LINE1 elements retrotransposi6on, as already demonstrated in some human and mouse 6ssues and in certain sporadic cancers. This research was supported by the Italian Ministry of Agriculture, grant INNOVAGEN, and by AGRIS Sardegna. OTHER -­‐ Abstract N° 86 ARCTIC ARK. HUMAN-­‐ANIMAL ADAPTATIONS TO THE ARCTIC ENVIRONMENT: NATURAL AND FOLK SELECTION PRACTICES (ARC-­‐ARK) Juha Kantanen1, Florian Stammler2, Nasser Ghanem1, Anna Gossman-­‐Stammler2, Nuccio Mazzullo2, Jaana Peippo1, Tiina Reilas1, Päivi Soppela2, Ilma Tapio1 and Mervi Honkatukia1 1 Green technology, Natural Resources Ins6tute Finland (Luke), Mylly6e 1, 31600, Jokioinen, FI Arc6c Centre, University of Lapland, Pohjoisranta 4, PO Box 122, 96101, Rovaniemi, FI 2 The Arc6c is oren seen as a biodiversity-­‐poor region, where animal husbandry is solely based on herding of reindeer (Rangifer tarandus). However, in northern Europe and Siberia, also breeding of special autochthonous ca:le (Bos taurus) and horse (Equus caballus) breeds has a long tradi6on (for example, Northern Finnca:le, Yaku6an ca:le, Mezen horse and Yaku6an horse). The Arc6c Ark project funded by the Academy of Finland studies animals’ adapta6on to the Arc6c as a complex human-­‐environmental process. Old tradi6ons of ‘folk selec6on’, rather than those implemented by ins6tu6ons have been shaping Arc6c animals’ valuable traits. Each of the ethnic groups studied in this project (Finns, Sámi, Nenets, Pomors, Russians, Sakha, Eveny) have myths and legends connected to orally transmi:ed narra6ves of domes6ca6on and selec6on of their animals. This kind of cultural adapta6on assistance is mostly due to symbio6c domes6city, an in6mate human-­‐animal partnership. As a result of natural and folk selec6on, reindeer and Arc6c ca:le and horse breeds show metabolic, morphological and reproduc6ve adjustments. We inves6gate how indigenous and non-­‐indigenous socie6es raise reindeer, ca:le and horse breeds in Finnish Lapland, Archangelsk and Eveno-­‐Bytantaj in Russia. The methods come from gene6cs, ecology and anthropology disciplines. In the animal genomics analyses we focus on animals’ metabolic adapta6on and structural and func6onal genome varia6ons. We use modern genomic approaches for the analyses: whole-­‐genome sequencing of animals and gene expression analyses of host animals and their rumen microbiota. In the social-­‐anthropological studies we compare across regions reindeer herders' and animal farmers’ knowledge of the environment and desired animal characteris6cs that facilitate a sustainable Arc6c livelihood. The data of these two disciplines shall be integrated through approaches of ecological anthropology. The close associa6on between animals and humans over many centuries in the Arc6c allows us to iden6fy the human and nature footprints in animal adapta6ons as well as the importance of different animal species for the resilience of Arc6c cultures and economies. OTHER -­‐ Abstract N° 87 DATA INTEGRATION AND NETWORK RECONSTRUCTION WITH MUSCLE METABOLOME AND MEAT QUALITY DATA IN PIG TO HIGHLIGHT NEW BIOMARKERS FOR PORK QUALITY ASSESSMENT Julia Welzenbach1, Chris6ne Große-­‐Brinkhaus1, Chris6ane Neuhoff1, Chris6an Loor1, Karl Schellander1 and Ernst Tholen1 Animal gene6cs, Ins6tut of Animal science, Endenicher Allee 15, 53115, Bonn, DE 1 Aim of this study was the elucida6on of underlying biochemical processes and iden6fica6on of poten6al key molecules of meat quality traits drip loss, pH1, pH24 and meat color. An untargeted metabolomics approach detected the profiles of 400 annotated and 1597 unreported metabolites in 97 Duroc × Pietrain pigs. The levels of metabolites are helpful in order to understand the complex biological mechanisms of the underlying meat quality traits. Addi6onally in animal selec6on metabolite biomarkers might be used for predic6on of economical a:rac6ve phenotypes. Four different sta6s6cal methods, namely correla6on analysis, principal component analysis (PCA), random forest regression (RFR) and weighted network analysis (WNA) were applied to iden6fy significant rela6onships between muscle metabolites and meat quality traits and to handle with the sta6s6cal “large p, small n” problem. Despite obvious differences regarding the sta6s6cal approaches, parameters and command variables, the four applied sta6s6cal methods revealed similar results. These lead to the conclusion that meat quality traits pH1, pH24 and color were strongly influenced by processes of p.m. energy metabolism like glycolysis, pentose phosphate pathway and pyruvic acid metabolism whereas drip loss was significant associated with metabolites of lipid metabolism like glycerophospho-­‐, sterol-­‐ and prenol lipids that are products of membrane degrada6on. In order to predict meat quality accurately and to clarify the complex molecular background of drip loss in more detail further inves6ga6ons to select the most suitable sta6s6cal method are needed. Based on comprehensive understanding of drip loss selected metabolites might be be:er indicator than the measured phenotype itself. Due to increasing challenges in evalua6on of omics data, further analysis with increased popula6on size and sta6s6cal power is needed to select the most suitable sta6s6cal methods in predic6on of func6onal traits in pigs. As a further step metabolomics data will be combined with proteomics and transcriptomics data and analyzed in an integrated GWAS. OTHER -­‐ Abstract N° 88 DECONSTRUCTING THE PIG SEXOME: METABOLOMICS IN HEAVY PIGS DISCOVERS SEX RELATED DIMORPHISMS IN METABOLIC BIOMARKERS AND PATHWAYS Samuele Bovo1, Gianluca Mazzoni1, Daniela Giovanna Calò2, Giuliano Galimber62, Flaminia Fanelli3, Marco Mezzullo3, Giuseppina Schiavo1, Emilio Scob1, Annamaria Manisi2, Antonia Bianca Samorè1, Francesca Bertolini1, Paolo Trevisi1, Paolo Bosi1, Stefania Dall'Olio1, Uberto Pago:o3 and Luca Fontanesi1 Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna , Viale Fanin 46, 40127, Bologna, IT 2 Department of Sta6s6cal Sciences “Paolo Fortuna6”, University of Bologna , Via delle Belle Ar6 41, 40126, Bologna, IT 3 Department of Surgical and Medical Sciences, Endocrinology Unit, University of Bologna , Via Massaren6 9, 40138, Bologna, IT 1 In all livestock species, for many traits that can be expressed in both males and females, the sex of the animals is the first biology-­‐derived affec6ng factor. To evaluate this ques6on, many pig produc6on systems can be considered interes6ng case studies because males are surgically castrated a few days arer birth. Castra6on of the males is needed to avoid boar taint of the meat. This prac6ce has also other effects on several performance and carcass traits. Compared to intact gilts, surgically castrated males deposit more fat and have a less efficient feed conversion ra6o. The exploding field of systems biology, which integrates different orthogonal datasets has the poten6al to describe the complexity of the biological processes differen6a6ng castrated males from en6re gilts. In this study we used a targeted metabolomic approach coupled with metabolomic and enrichment pathway analyses to discover sex related dimorphisms in metabolic biomarkers. A total of 597 performance tested Italian Large White pigs (403 gilts and 194 castrated males) were analysed for about 200 plasma metabolites of several biochemical families (amino acids, biogenic amines, hexoses, acylcarni6nes, sphingomyelins, phospha6dylcholines and lysophospha6dylcholines). Sparse Par6al Least Square Analysis Discriminant Analysis (sPLS-­‐DA) iden6fied 85 metabolites contribu6ng to dis6nguish the two groups of pigs. Castrated males and en6re gilts were characterized by 5 and 11 significant metabolomic pathways, respec6vely. One of them (glycine, serine and threonine metabolism) had the largest impact factor among all pathways. This study produced a first metabolomic view in pigs and iden6fied several biomarkers with different levels between castrated males and en6re gilts. Our results could be useful to design sex-­‐specific breeding prac6ces and diets to improve performance traits in pigs. OTHER -­‐ Abstract N° 89 MILK'S MICROBIOTA DURING THE PERIPARTURIENT PERIOD IN HOLSTEIN COWS: POSSIBLE IMPLICATION ON ANIMAL HEALTH AND MILK QUALITY Paola Cremonesi1, Federica Riva2, Emanuele Capra1, Vi:orio Tedde3, Maria Filippa Addis3, Laure:a Turin2, Claudia Pollera2, Marco Severgnini4, Joel Filipe2, Giulio Curone2, Noemi Viscon62, Daniele Vigo2 and Bianca Cas6glioni1 Is6tuto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Einstein s/n, 26900, Lodi, IT Dipar6mento di Scienze Veterinarie e Sanità Pubblica, Università degli Studi di Milano, via Celoria 10, 20133, Milano, IT 3 R&D -­‐ Proteomics Lab, Porto Conte Ricerche S.r.l., S.P. 55 Porto Conte -­‐ Capo Caccia, km 8.400, 07041, Alghero, IT 4 Is6tuto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, via Fratelli Cervi 93, 20090, Segrate, IT 1 2 Dairy ca:le are exposed to a high risk for disease during periparturient period and this period is oren associated with the peak incidence of produc6on problems, metabolic disorders, infec6ous diseases, metri6s and mas66s. The aim of this study was to compare the milk's microbiota during the periparturient period in order to assess the possible implica6on on animal health and milk quality. Milk samples were collected from each quarters of six pluriparous Holstein cows at 340 ± 60 days of lacta6on (T1), at the day arer calving (T2) and between 7 to 10 days arer calving (T3). To determine the udder health status, a standard bacteriological analysis on milk samples were performed; moreover, SCC was obtained by an automated fluorescent microscopic soma6c cell counter. For the microbiome analysis, the bacterial DNA was extracted from the pool of the quarters for each animal using a protocol previously described (Cremonesi et al., 2005) with some modifica6ons and the 16S rRNA gene (V3-­‐V4 region) was analyzed by Miseq (Illumina). Milk proteins were evaluated by SDS-­‐PAGE and by densitometric analysis for assessment of total protein profiles. In addi6on, the presence of the inflamma6on markers cathelicidin and S100A9 was es6mated by western immunoblobng. Tests were done for all quarters and for the three lacta6on stages. Moreover, the expression of CD45 and KRT5 messengers in the isolated milk cells was analyzed in order to assess the modifica6on of leukocyte/exfoliated epithelial cell ra6o during peripartum, while the expression of IL-­‐1b and TNFa mRNA in the isolated milk cells was studied for their capability to produce cytokines. Finally, the expression of PTX3 transcript in the milk fat globules was analyzed in order to evaluate its modula6on and to check the ac6va6on of the mammary epithelial cells. Bacteriological analysis showed the absence of contagious bacteria such as Staph. aureus and S. agalac6ae. An interes6ng modifica6on of the leukocyte/exfoliated epithelial cell ra6o during peripartum was observed with an up-­‐regula6on of PTX3 in the colostrum. Moreover, this study describes the rela6ve changes in milk protein abundance along lacta6on and according to composi6on of the microbial flora. These data have also been integrated with informa6on on protein markers of inflamma6on. To our knowledge, this is the first 6me that mammary gland metagenome was studied during the periparturient period. OTHER -­‐ Abstract N° 90 PHYLOGENETIC NETWORK AND ENTEROTYPES OF THE GUT MICROBIOTA OF 60-­‐DAYS OLD PIG Yuliaxis Ramayo-­‐Caldas1, Nuria Mach1, Patricia Lepage2, Florance Levenez2, Cathrine Denis1, Gaetan Lemonnier1, Jean-­‐Jacques Leplat1, Yvon Billon5, Mustapha Berri6, Joel Dore2, Claire Rogel-­‐Gaillard1 and Jordi Estelle1 1 GABI, INRA, Domaine de Vilvert, 78352, Jouy en Josas, FR 2 MICALIS, INRA, Domaine de Vilvert, 78352, Jouy en Josas, FR 3 UMR ISP, INRA, Val del Loire, 37380, Nouzilly, FR 4 DSV-­‐IRCM-­‐LREG, CEA, Domaine de Vilvert, 78352, Jouy en Josas, FR 5 UE967 GEPA, INRA, Le Magneraud, 17700, Le Magneraud, FR UMR1282 ISP, Universite de Tours, Tours, 37000, Tours, FR 6 The intes6nal microbiota is a complex ecosystem that has in6mate symbio6c interac6ons with the host and contributes to its health and well-­‐being. However, the ecological interac6ons among the microbiota communi6es are s6ll far from being understood. In this study we report the first phylogene6c network applied to the gut microbiota of pigs. Fecal microbiota of 518 healthy piglets (60 day-­‐old) was characterized by 16S rRNA gene sequencing . Two networks were constructed at genera and opera6onal taxonomic unit levels. The predicted interac6ons within each network produced robust pa:erns of co-­‐occurrence and co-­‐exclusion, and were dominated by phylogene6c assorta6vity. Similar to humans, pig gut microbiota interac6ons show a strong co-­‐exclusion between the Prevotella and Ruminococcus genera. Furthermore, two enterotype-­‐like clusters in the pig microbiota were iden6fied. According to differen6al abundance analyses at func6onal level, KEGG orthology groups associated with Prevotella-­‐
dominated enterotype were found to belong to pathways rela6ng to carbohydrate metabolism. Significant effects of enterotype-­‐like cluster on body weight at 60 days of age and average daily gain during weaning period were observed. Author List Abdel-­‐Shafy
H
1
Addis
M
89
Aguiar
T
27
Ahmed
D
68
Ajmone-­‐Marsan
P
9, 22, 24, 31, 79
Al-­‐Tohamy
A
1
Alber6ni
E
15
Alexandre
P
69
Almeida
J
4
Amaral
A
4
Andersson
L
75
Anis
G
35
Arkoumanis
I
64
Arrighi
S
13, 76
Ayuso
M
65, 66
Bahbahani
H
29
Balbo Zavarez
L
12
Baldi
F
26
Ballester
M
52
Banabazi
M
81
Barkawi
A
68
Barragán Alcaide
C
73
Barufab Grisolia
A
3
Ba6sta
L
38
Ba:elli
G
83
Baumgard
L
32
Bayat
A
63
Bedada
Z
34
Belo
A
4
Benítez
R
5, 65, 66
Benítez Yáñez
R
73
Berri
M
90
Berry
D
8
Bertolini
F
88
Bessa
R
4
Be:encourt
C
4
Biageb
M
39
Biffani
S
9
Biggio
G
85
Billon
Y
52, 90
Blecha
F
60
Bocchini
M
15
Boldura
O
67
Bolormaa
S
31
Bomba
L
9, 31, 79
Bonin
M
26
Bornelöv
S
75
Borowska
A
37
Boschiero
C
11
Bosi
P
88
Boussaha
M
25
Bovo
S
88
Bressan
M
4
Browne
J
58
Bueno
R
26
Bunn
D
72
Calò
D
88
Cañon
J
23
Canovas
A
65, 66
Capomaccio
S
9, 79, 85
Cappelli
K
9, 79, 85
Capra
E
13, 54, 76, 83, 89
Cardoso
F
74
Carvalheiro
R
27
Carvalho
M
26, 30
Cas6glioni
B
13, 76, 83, 89
Cavani
C
55
Ceccobelli
S
15, 39
Chamberlain
A
31
Charismiadou
M
64
Cherchi
R
85
Chessa
S
13, 76, 83
Chillemi
G
59
Ciecierska
A
53, 62
Cieslak
J
37
Cinar
M
33
Cinnamon
Y
75
Ciullo
M
39
Clarke
L
7, 43
Cobellis
G
79
Coizet
B
13, 22, 76
Colli
L
9, 31
Colombini
S
83
Consor6um
T
31
Cou6nho
L
17
Corrêa Ledur
M
11
Correia
C
58
Cou6nho
L
56
Crapaldi
P
13
Cremonesi
P
54, 83, 89
Crepaldi
P
22, 76
Crisà
A
59, 80
Cromie
A
8
Crucianelli
F
85
Curcio
L
39
Curone
G
89
D'Andrea
M
20
Da Silva
T
38
Da Silva Ba6sta
L
21
Da Silva Costa
M
27
Daetwyler
H
31
Dalastra Lauren6
M
21
Dall'Olio
S
88
Da:a
A
7
Davoli
R
55
De Andrade
R
38
De Paula Nogueira
G
57
De Sousa Sussai
T
12
De Souza
M
49
Decker
J
56
Dekkers
J
78
Deligeorgis
S
64
Denis
C
90
Di Lorenzo
P
15, 39
Dias de Andrade
R
21
Dimauro
C
20
Dinnyes
A
61
Dore
J
90
Drag
M
70
Dragona
N
64
Du
Y
14
Duarte Pacheco
A
21
Dudemaine
P
82
Dunner
S
23
Dzama
K
10
Edea
Z
32
El-­‐Halawany
N
1
El-­‐Sayed
A
68
Estelle
J
90
Estellé
J
52
Estonba
A
40
Eufemi
E
9
FAANG Consor6um
-­‐
43
Falcao da Costa
H
57
Fanelli
F
88
Farries
G
18
Fernandez
A
66
Fernández
A
5, 65, 65, 66
Fernández Ávila
A
73
Fernández Muñoz
A
73
Ferraz
J
26, 30, 69
Ferrè
F
59
Ferreira da Silva
T
21
Filipe
J
89
Finlay
E
48
Fischer
D
63
Flicek
P
7, 43
Florêncio de Athayde
F
44
Flynn
P
8
Folch
J
73
Fonseka
G
36
Fontanesi
L
88
Frabni
S
13, 22, 76
Freua
M
30
Freude
K
61
Friedman-­‐Einat
M
75
Frodsham
R
36
Fukumasu
H
69
Gage-­‐Smith
J
75
Galimber6
G
88
Gallardo
R
72
Galvão Tavarez Pereira
A
27
Gama
L
4
Gama-­‐Carvalho
M
4
Garcia
J
3, 9, 12, 21, 24, 27, 38, 44
Gaspa
G
20
Genin
O
75
Ghaderi Zefrei
M
81
Ghanem
N
86
Gil
I
23
Giontella
A
85
Giordano
A
13, 76
Gliozzi
T
54
Gobbo
S
57
Goliomy6s
M
64
Gomes
C
74
González-­‐Bulnes
A
5, 65, 66
Gootwime
E
45
Gordon
S
58, 71
Gormley
E
58
Gossman-­‐Stammler
A
86
Gough
K
18
Griebel
P
51
Griffin
D
36
Groppeb
D
13, 76
Große-­‐Brinkhaus
C
33, 87
Guan
L
51
Guan
Y
51
Guerrero-­‐Bosagna
C
11
Hager-­‐Theodorides
A
64
Hall
V
61
Hamill
R
2
Hano:e
O
19, 29
Hayes
B
31
Heiffer
C
10
Henrique da Silva
V
11
Henrique de Rezende Neves
H
27
Hernández
B
71
Hill
E
18
Honkatukia
M
86
Horodyska
J
2
Huțu
I
67
Hy:el
P
61
Ibañez Escriche
N
73
Ibeagha-­‐Awemu
E
82
Imumorin
I
81
Iriondo
M
40
Isabel
B
65, 66
J da S Diniz
W
17
Janisch
S
50
Johnson
N
7
Jue:emann
T
7
Kadarmideen
H
30, 61, 70
Kantanen
J
86
Kappou
C
64
Katz
L
18
Kearney
F
8
Kim
K
32, 34
Ko
E
41
Kogelman
L
70
Krischek
C
50
Kuczynska
B
37
Kul
S
28
Lamont
S
72
Langa
J
40
Lasagna
E
15, 39
Lauren6
M
38
Lawal
R
19
Lawrie
M
36
Lazzari
B
13, 54, 76, 83
Lehmann Cou6nho
L
11
Lemonnier
G
52, 90
Lepage
P
90
Leplat
J
90
Leskinen
H
63
Letaief
R
25
Levenez
F
90
Li
R
82
Liang
G
51
Lima
A
17, 56
Lindenberg Sarmento
J
27
Liu
H
78
Lombardi Lopes
F
57
Loor
C
33, 87
López-­‐Bote
C
5, 65, 66
Luczak
M
37
M de Souza,
M
17
M El Sayed
N
44
Maccio:a
N
9, 20
Mach
N
90
MacHugh
D
58, 71
Mackowski
M
37
MacLeod
I
31
Magee
D
58, 71
Maione
S
47
Majewska
A
62
Malago Junior
W
74
Malatji
D
84
Malmuthuge
N
51
Manisi
A
88
Manzano
C
40
Marchitelli
C
80
Marcondes
M
21, 38
Marconi
G
15
Marczak
L
37
Maribo
H
70
Maroilley
T
52
Maroni Nunes
C
21, 44
Mar6nez Montes
A
73
Mashayekhi
K
61
Massouras
T
64
Mátlová
V
46
Mazzoni
G
61, 88
Mazzoni
M
55
Mazzullo
N
86
McClure
J
8
McClure
M
8
McGebgan
P
18, 71
McGivney
B
18
McLoughlin
K
58
Meade
K
48
Medrano
J
65, 66
Meinert
L
70
Mercat
M
52
Mezzullo
M
88
Milanesi
M
9, 12, 22, 24, 31
Miller
L
60
Miraei Ash6ani
S
81
Mircu
C
67
Moioli
B
59, 80
Moré
D
74
Moreira
G
69
Moreira
O
4
Moroldo
M
52
Morozini Padula
R
12
Moschou
K
64
Mourão
G
56
Muchadeyi
C
84
Muchadeyi
F
10
Mudadu
M
17, 56, 74
Muiños Bühl
A
73
Mullen
M
8
Müller de Oliveira
F
44
Murani
E
14, 50, 77
Mwacharo
J
29
Nalpas
N
58, 71
Napolitano
F
80
Naraballobh
W
50
Nardone
A
9, 22
Nazmi
A
72
Negrini
R
9
Neja6 Javaremi
A
81
Ne:leton
D
78
Neuhoff
C
33, 87
Nicolazzi
E
9, 22, 47
Nicoloso
L
13, 76
Novák
K
46
Nunes
C
38
Núñez
Y
5, 65, 66
Nuñez Moreno
Y
73
O'Farrelly
C
48
O’Connor
R
36
Oliveira
P
17, 56
Oliveira Jr
G
26
Oliveira Junior
G
30
Oster
M
14
Óvilo
C
5, 65, 66
Ozmen
O
28
Pacheco
A
38
Pagnacco
G
13, 22, 76
Pago:o
U
88
Parnell
A
71
Pawlak
P
37
Pecile
A
13, 76
Pedroso
A
57
Peippo
J
86
Peiro
J
57
Pér6lle
F
11
Petracci
M
55
Pezzob
G
39
Picciolini
M
85
Pilla
F
20
Pizzi
F
54
Pollera
C
89
Ponsuksili
S
14, 50, 77
Prave:oni
D
13, 76
Przydatek
E
53
Puppel
K
37
Rafa6
N
75
Ramayo-­‐Caldas
Y
90
Rapeb
L
83
Rasero
R
47
Rauschkolb Katsuda Ito
P
44
Reecy J
17
Regitano
L
17, 49, 56, 74
Reilas
T
86
Renata da Silva Romero
A
3
Rendo
F
40
Rey
A
65, 66
Reyer
H
2
Rezende
F
26
Ribamar Nunes
J
11
Riccaboni
P
13, 76
Richardson
D
7, 43
Riva
F
89
Rocha
D
25
Rodríguez Valdovinos
M
73
Rogel-­‐Gaillard
C
52, 90
Rosov
A
45
Ross
J
32
Rothschild
M
32
Rubin
C
9
Rue-­‐Albrecht
K
71
Ruiz
O
40
Sá
J
4
Sabino
M
79
Sacchi
P
47
Sadkowski
T
53, 62
Saelao
P
72
Salem
S
68
Samorè
A
88
Sang
Y
60
Santana
M
26, 30, 69
Santana do Carmo
A
27
Santos-­‐Silva
J
4
Sar6
F
15, 39
Sartore
S
47
Schellander
K
33, 87
Schiavo
G
88
Schnabel
R
56
Schwerin
M
77
Scob
E
88
Sebas6ani
C
39
Seibert
J
32
Seroussi
E
45, 75
Sevane
N
23
Severgnini
M
89
Shaughnessy
R
58
Shawky
A
1
Shingfield
K
63
Shirak
A
45
Siengdee
P
77
Silva Cipriano
R
12
Silvestrelli
M
85
Simitzis
P
64
Sirri
F
55
Soglia
D
47
Soglia
F
55
Sölkner
J
27
Sonia
B
35
Soppela
P
86
Sorbolini
S
20, 85
Souza
M
56
Stachowiak
A
37
Stammler
F
86
Stella
A
13, 54, 76
Streeter
I
43
Talen6
A
13, 22, 76
Tapio
I
86
Taylor
J
17, 56
Tedde
V
89
Teodoro Caminhas
M
12
Tesfaye
D
33
Tholen
E
33, 87
Tizioto
P
17, 56
Tomokane
T
38
Torrecilha
R
21, 38
Torricelli
M
79
Trabalza-­‐Marinucci
M
79
Trakooljul
N
14, 50, 77
Trevisi
P
88
Trey Belew
A
44
Tuggle
C
78
Tulcan
C
67
Turin
L
89
Turri
F
54, 83
Uddin
M
33
Utsunomiya
A
3, 12
Utsunomiya
Y
3, 9, 12, 21, 24, 27, 38, 44
Vajana
E
31
Valen6ni
A
9, 22
van Kaam
J
9, 22
VanMarle-­‐Koster
E
84
Vaquerizas
J
49
Varley
P
2
Ven:o
L
63
Ventura
R
26, 30
Verini-­‐Supplizi
A
79, 85
Vieira do Nascimento
A
3
Vigo
D
89
Viitala
S
63
Vilkki
J
63
Villani Miguel
M
57
Villarreal-­‐Ramos
B
58
Viscon6
N
89
Vordermeier
H
58
Wang
M
10
Wang
Y
72
Waters
S
8
Weld
R
8
Welzenbach
J
87
Whelan
A
58
Whiston
R
48
Wicke
M
50
Wilder
S
7
Williams
J
9, 13, 22, 76
Wimmers
K
2, 14, 50, 77
Wodas
L
37
Yet
N
78
Yoon
D
41
Yosefi
S
75
Yumie Tomokane
T
21
Zambonelli
P
55
Zappaterra
M
55
Zerbino
D
7
Zerlo6ne
A
49
Zhang
R
33
Zhou
H
72

Ellis Wasson, Aristocracy and the modern world. Basingstoke and

The animal kingdom

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