Published February 26, 2016
r es e a r c h h i g h l i g h t s
Segregation Bias in Doubled Haploid
Barley Population Arises Strictly during
the In Vitro Phase
Estimation of allelic frequencies is often required in breeding but
genotyping many individuals at many loci can be expensive.
Bélanger et al. have developed a genotyping-by-sequencing (GBS)
approach for estimating allelic frequencies on pooled samples (PoolGBS) and show that allelic frequencies can be cost-effectively and
accurately estimated. This Pool-GBS approach yielded allelic frequency estimates that were highly reproducible and correlated with
the true frequency derived from analysis of individual lines. PoolGBS was used to investigate segregation bias throughout barley
androgenesis. Whereas significant biases could be shown to arise
during embryo formation and plant regeneration, no strong bias was
detected among the microspores. 
Genetics Influencing Barley Root Traits
Water availability is a major limiting factor for crop production,
making drought adaptation and its many component traits a desirable attribute of barley cultivars. Robinson et al. identified a major
quantitative trait loci (QTL) influencing both seminal root angle
and root number—traits associated with increased soil moisture
extraction—in barley. Using a recently developed high-throughput
phenotyping method, a panel of 30 barley genotypes and a
doubled-haploid (DH) population (ND24260 ´ ‘Flagship’) comprising 330 lines were evaluated for seminal root angle (deviation from
vertical) and root number under controlled environmental conditions.
A high degree of phenotypic variation was observed in both populations and seven QTL were detected for seminal root traits (root angle,
two QTL; root number, five QTL). Here, we provide insight into seminal root phenotypes and provide a first look at the genetics controlling these traits in barley. 
Evaluating Marker-assisted Selection
in Lettuce
Statistical models recommended for marker-assisted selection (MAS)
differ depending on the putative number of markers underlying the
target quantitative trait and the size of their individual effects. The
predictive abilities of models for marker-assisted selection computed
Published in The Plant Genome 9.
doi: 10.3835/plantgenome2016.10.0001rh
© Crop Science Society of America
5585 Guilford Rd., Madison, WI 53711 USA
This is an open access article distributed under the CC BY-NC-ND
license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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vol . 9, no . 1 under a specific cross-validation scheme are commonly used to evaluate their relative performances. Hadasch et al. compare the predictive abilities of contending models for MAS under several contrasting
cross-validation schemes using empirical datasets on two quantitative traits with different heritabilities collected from multienvironment
trials. The predictive abilities of models for MAS were strongly
influenced by the presence of marker loci with large effects and thus
indirectly by the heritability of the target trait. The predictive abilities
of models for MAS also varied across the different cross-validation
schemes, but none of the schemes consistently produced the highest predictive abilities across all models or traits. Consequently, it is
recommended to evaluate the predictive abilities of models for MAS
under multiple cross-validation schemes that are based on sampling
genotypes, environments, or both. 
A Symphony of Genes Make
a Maize Plant
Genes provide the blueprint that results in the development of an
organism; in maize, more than 30,000 genes play a role during the
life cycle from seed germination to mature grain. In this study, we
used RNA sequencing to measure the expression of genes throughout the life of the plant. We gathered samples from various organs
such as roots, leaves, and developing seeds across time. This analysis revealed a coordinated symphony of gene expression underlying
plant growth and development and provides a framework to translate genomic information to understand basic plant processes and to
breed improved cultivars. 
Mapping Wheat Fusarium Head
Blight Resistance
Host resistance is important for control of Fusarium head blight (FHB)
in wheat. Arruda et al. used genotyping-by-sequencing on a panel of
273 soft red winter wheat lines to identify loci associated with FHB
resistance. Significant loci were identified on chromosomes 4A, 6A,
7A, 3B, 1D, 4D, and 7D. Some loci for FHB resistance were identified
in chromosome regions previously reported as harboring loci for FHB
resistance in biparental populations, especially on wheat chromosome 3B. This study provides evidence that accumulation of quantitative trait loci can result in higher levels of FHB resistance. 
Wheat–Fusarium graminearum Interaction
Fusarium head blight (FHB) is a disease affecting wheat and other
small-grain cereals caused by the fungal pathogen Fusarium graminearum that can lead to yield loss and reduced grain quality. The
trichothecene mycotoxin deoxynivalenol (DON) accumulates during
1 of 3
infection, increases pathogen virulence, and decreases grain quality. The Fhb1 locus on wheat chromosome 3BS confers resistance
to the spread of infection and is associated with resistance to DON
accumulation. Hofstad et al. examined DON accumulation, FHB
resistance, and the whole-genome transcriptomic response using
RNA-seq in a near-isogenic line pair carrying the resistant and
susceptible alleles for Fhb1 under several treatments. The results
show that the rachis is a key location for conferring resistance to
the spread of infection. Additionally, transcriptome analysis showed
a set of Fhb1- and DON-responsive genes that may play a role in
FHB resistance. 
transPLANT Provides Triticeae
Genomic Resources
The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare
L.), remained uncharacterized for a long time because of their high
repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analysis strategies,
several of these have recently been deciphered. transPLANT (http://
www.transplantdb.eu) is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale
research in the life sciences. Since the Triticeae data are intrinsically
complex, heterogenous, and distributed, the transPLANT consortium
has undertaken efforts to develop common data formats and tools
that enable the exchange and integration of data from distributed
resources. Here we present an overview of the individual Triticeae
genome resources hosted by transPLANT partners, introduce the
objectives of transPLANT, and outline common developments and
interfaces supporting integrated data access. 
Genomic Selection in Perennial
Ryegrass Breeding
Genomic selection may be an effective strategy for genetic improvement in a perennial ryegrass breeding program. Lin et al. investigated the potential of genomic selection using stochastic simulation.
They indicate that genomic selection enabled selection for plot traits
at multiple stages in a breeding program, including seedlings. This
resulted in up to fourfold the genetic gain achieved with genomic
selection when compared with conventional breeding. However, the
proposed genomic program also resulted in more inbreeding. 
Transcriptome Analysis Reveals Annual
Bluegrass Origin
Annual bluegrass (Poa annua L.) is one of the most widespread
weed species in the world. As a young allotetraploid, annual
bluegrass has occupied diverse environments from the Antarctic
area to subtropical regions. Chen et al. reported a comprehensive
transcriptome comparison between annual bluegrass and its two
putative progenitors, P. supina and P. infirma. High similarities
were found in nucleotide sequences and homeologous polymorphisms between P. annua and the two proposed parents. Comparison of chloroplast and mitochondrion genes further confirmed P.
infirma as the maternal parent. Fewer nucleotide percentage
differences were observed between P. infirma and infirma homeologs than between P. supina and supina homeologs, indicating
a higher nucleotide substitution rate in supina homeologs than
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in infirma homeologs. Gene ontology enrichment analysis suggested
the more compatible cytoplasmic environment and cellular apparatus for infirma homeologs as the major cause for this phenomenon. 
Expanding Maize Diversity with Teosinte
During the domestication of corn (maize) from its wild ancestor
(teosinte), humans selected plants that were more reliable, easier to
harvest, and better tasting, thus causing dramatic transformations in
plant, ear, and seed characteristics. However, domestication also
greatly reduced genetic diversity in modern maize, compared with
teosinte, a reduction that may ultimately limit maize productivity. Liu
et al. created a collection of over 900 new maize lines that carry
small amounts of the teosinte DNA in their genome. After determining
which chromosomal regions from teosinte are present in each line,
and evaluating these lines for plant, ear, and kernel traits, the authors
identified numerous chromosomal regions involved in the complex
genetic network regulating several traits that contribute to yield.
This collection of lines was also used to validate and refine genetic
studies, thus improving the process for gene discovery in maize and
enabling the use of teosinte alleles in maize improvement. 
Expanded Histidine Decarboxylases
are Functionally Diverged in Tomato
Pyridoxal phosphate (PLP)-dependent enzymes are involved in plant
N metabolism. Kumar et al. clearly demonstrated the expansion
of class II PLP_deC family genes during evolution of higher plants.
While two subclasses, glutamate decarboxylase and aromatic
L-amino acid decarboxylase, are relatively conserved in their gene
complement, the third subclass, histidine decarboxylase, is clearly
expanded in Solanaceae and legumes. Further functional characterization of these genes in two fleshy fruited species (tomato and
pepper) and a dry fruited species (Arabidopsis) suggests that the
expansion of histidine decarboxylases in Solanaceae, especially
tomato, has occurred to perform different functions during fruit development and ripening. 
Genomic Selection Accelerates
Intermediate Wheatgrass Domestication
Intermediate wheatgrass is a perennial wild relative of bread wheat,
providing substantial environmental services relative to annual grain
crops. The domestication and improvement of intermediate wheatgrass will provide both ecosystem services and an economic return
to farmers. Plant improvement is being revolutionized by sequencing
technologies. Using next-generation sequencing technologies, Zhang
et al. discovered genome-wide markers. By combining genome-wide
markers and statistical models, genome wide prediction equations
were developed for agronomic traits such as seed size, grain yield,
and biomass, and high predictive ability was observed. Using these
prediction equations, the breeding lines can be evaluated in the
greenhouse based on their genome wide marker data. Substantial
resources required for planting, weeding, harvesting, threshing, and
measuring will be saved and the selection efficiency and capacity
will be dramatically increased. 
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Amaranth Genome Sequence
The grain amaranths are emerging pseudocereals native to
the Americas. While the grain amaranths have been cultivated for
centuries in the Americas, they have been underutilized since the
Spanish conquest, when they were replaced by Old World crops.
However, in the last few decades, the grain amaranths have
begun to reclaim some of their importance, largely as a result of a
renewed recognition of their superior nutritional qualities and tolerance of extreme abiotic stresses. In this study, Clouse et al. present
a high-quality draft genome sequence and BioNano physical map
of the grain amaranth species Amaranthus hypochondriacus. The
genome assembly consisted of 377 Mb in 3,518 scaffolds with
an N50 of 371 kb. Annotation of the genome identified 23,059
protein-coding genes. Resequencing analysis supported the classification of A. hybridus as the progenitor species of the grain amaranths, while a Ks (synonymous substitution rate) analysis estimate
the age of amaranth’s most recent polyploidization event to have
occurred between 36.7 to 67.9 Ma. 
Rbs1, Rbs2, and Rbs3 Fine Map
to Same Region
Brown stem rot (BSR) of soybean is difficult to control and causes significant yield loss. Genetic resistance has been found to be the best
method to combat this disease; however, the locations of BSR resistance genes are not well defined. Rincker et al. report the fine mapping of the three named resistance genes (Rbs1, Rbs2, and Rbs3) to
intervals ranging from 0.34 to 0.04 Mb on chromosome 16. These
narrowed intervals will improve efficiency of marker-assisted selection and facilitate the cloning of resistance genes. Across sources,
resistance was fine mapped to intervals inclusive of a 0.04 Mb
region, which provides evidence that one locus provides resistance
to BSR in these sources. 
Mining SNPs in Wheat Repeats
In hexaploid wheat, transposable elements represent a major obstacle for genomic studies but are also a source of genome-specific
molecular markers. Cubizolles et al. report on the development of
a high-throughput SNP discovery approach based on sequence
capture of transposable element-based markers. This method was
applied to wheat chromosome 3B, leading to the design of more
than 39,000 SNPs. The authors demonstrated that these SNPs can
be efficiently scored with the KASPar genotyping technology and
are useful tools for genetic diversity and genome-wide association
studies. 
Genetic Dissection of Kernel Morphology
Kernel shape and size in wheat determine grain and milling yield,
so understanding the genetic basis of these traits is of immense
value towards improving grain and milling yield. Kumar et al.
found that kernel length and width in wheat are under independent
genetic control and common as well as independent loci for kernel
length, width, and area contribute to thousand kernel weight. This
information provides wheat breeders the opportunity to increase
grain volume, thousand kernel weight, and ultimately yield. It was
also observed that the positive alleles for several major loci were
contributed by the non-adapted parent, suggesting that not all of
the genetic variation for kernel shape/size from wild/non-adapted
germplasm is available in the modern wheat varieties and improved
breeding germplasm. Thus, both adapted and non-adapted germplasm has considerable potential toward enhancing the gene pool
for kernel shape and size for the continued genetic improvement of
wheat. The closely linked markers associated with major and stable
QTL identified by Kumar et al. could be of immense value in marker
assisted breeding programs aimed to improve kernel shape and size
and ultimately yield in wheat. 
Transcriptional Interplay of Cucurbit
Downy Mildew
The emergence of Pseudoperonospora cubensis, the casual agent
of cucurbit downy mildew, in the United States remains the primary threat limiting cucumber production. In the current study
by Burkhardt and Day, the authors use next-generation sequencing
approaches to define the temporal changes in resistance and susceptibility during pathogen infection of cucumber. Through this work,
it was observed that the primary transitions underpinning resistance
and susceptibility are associated with the initial stages of host infection. Indeed, the current work suggests that a combination of factors,
including a delayed defense response in the host, coupled with
rapid manipulation of host signaling processes by the pathogen,
contribute to increased infection and disease. As one mechanism
driving this association, the authors present the first comprehensive
analysis of host and pathogen miRNA coexpression dynamics, suggesting that the reciprocal targeting of the transcriptional responses
in cucumber and P. cubensis play a key role in the outcome of this
interaction. 
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