Journal
GENOME BIOLOGY
Volume 16, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13059-015-0606-4
Keywords
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Funding
- National Research Initiative Competitive [2011-68002-30029]
- USDA National Institute of Food and Agriculture [2012-67013-19401]
- Bill and Melinda Gates Foundation grant
- Genome Prairie
- Genome Canada
- Saskatchewan Ministry of Agriculture
- Western Grains Research Foundation
- BBSRC Career Development Fellowship [BB/H022333/1]
- Doctoral Training Grant
- Howard Hughes Medical Institute
- Gordon and Betty Moore Foundation
- Kansas Agricultural Experiment Station [15-338-J]
- NSF [ACI-144054]
- BBSRC [BB/H022333/1, BB/G013004/1, BB/L011786/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/H022333/1, BB/L011786/1, BB/G013004/1] Funding Source: researchfish
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Background: 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.
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