A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

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DOIResolve DOI: http://doi.org/10.1186/s13059-015-0606-4
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TypeArticle
Journal titleGenome Biology
ISSN1474-7596
Volume16
Issue1
Article number48
Subjectallele; allopolyploidy; contig mapping; gene; genotype phenotype correlation; haplotype; phylogeny; genetics; polymorphism; wheat; Triticum aestivum
AbstractBackground: 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. Results: A 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. Conclusions: Evidence 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.
Publication date
LanguageEnglish
AffiliationAquatic and Crop Resource Development; National Research Council Canada
Peer reviewedYes
NPARC number21276966
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Record identifier914c3485-aef5-4867-8887-ee61eb20f0d4
Record created2015-11-10
Record modified2016-05-09
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