Population Genomics of Allopolyploid Wheat.

Crops experience strong selection aimed at developing varieties adapted to local abiotic and biotic stress factors. To investigate the impact of selection on variants distributed among homoeologous genomes and to build a foundation for understanding genotype-phenotype relationships in wheat, we performed population-scale re-sequencing of a diverse panel of lines using the 107 Mb whole exome capture assay. We catalogued SNPs and small-scale indel polymorphisms from the low-copy fraction of the genome, described their patterns of chromosomal distribution and inter-variant association, and identified variants that may have an impact on gene function based on the available annotation. A developed haplotype map was shown to be a valuable tool for imputing genotypes and increasing the power and precision of trait mapping in GWAS.  Contrasting patterns of variation and linkage disequilibrium were found among the wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Our data helped us gain insights into historic selective events and identify candidate selection targets associated with the regions harboring genes controlling important agronomic traits also validated in the GWAS. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given line suggesting that directional selection in wheat rarely acted on multiple parallel advantageous mutations across homoeologous regions. A favored variant at any one of the homoeologous regions appears could provide sufficient fitness benefit. Additional advantageous variants in other homoeologs probably either contributed little benefit, or were unavailable in populations subjected to selection. Our study highlights the importance of allopolyploidy in the evolution of wheat’s adaptive potential by increasing the likelihood of beneficial allele recovery and broadening the set of possible selection targets.