Abstract
BackgroundBread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines.ResultsA sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies.ConclusionsEvidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0606-4) contains supplementary material, which is available to authorized users.
Highlights
Bread wheat is an allopolyploid species with a large, highly repetitive genome
We produced roughly 4.7 billion paired-end reads (4.5 billion whole exome capture (WEC) reads and 0.2 billion genotyping by sequencing (GBS) reads), and 62% of WEC reads and 51% of GBS reads uniquely mapped to the chromosome survey sequence (CSS) contigs of the individual chromosomes (Figure S3 and Tables S2, S3 in Additional file 1), using alignment parameters optimized to separate reads from the different wheat genomes (Figures S4 and S5 in Additional file 1)
The sequence-based diversity map reported here is an important step towards the detailed characterization of DNA sequence polymorphism in the complex allopolyploid genome
Summary
Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. Despite being a useful genotyping tool, these arrays are incapable of capturing the entire spectrum of DNA sequence variation and allele frequencies in wheat populations, and providing unbiased information that may help directly identify causal variants affecting phenotypes. Achieving this goal requires obtaining sequence data on a genome-scale from a diverse population of lines. To date, this has only been performed on limited samples of wheat lines used to discover SNPs in the parental lines of mapping populations [17], or for SNPbased array design [18]. The recent release of the chromosome-specific wheat genome assemblies [27,28] can help to alleviate the problems associated with variant calling in the allopolyploid genome, and allow us to describe the chromosomal distribution of variants and their potential effect on gene function
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