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

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.

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform

“…The ability to query homeologue-specific expression data will also complement growing knowledge about sequence diversity between homeologues. A recent genome-wide analysis between landraces and elite varieties suggested that, during domestication, positive selection was usually restricted to an advantageous mutation within a single homeologue (Jordan et al, 2015). This highlights that understanding of homeologue-specific variation in both sequence and expression will be fundamental for future advances in wheat improvement.…”

Optimizing Training Population Size and Genotyping Strategy for Genomic Prediction Using Association Study Results and Pedigree Information. A Case of Study in Advanced Wheat Breeding Lines

“…The chip used to genotype the population yielded 9,290 mapped SNPs functional for the GWAS, of which only 11.7% were located on D chromosomes. Even though this might have hampered QTL discovery in these regions, the D genome shows a reduced diversity compared to A and B [42], hence less genetic variation influencing the traits are expected to be found on the D genome.…”

The wheat pangenome: assembly and analysis

“…These results are comparable to those obtained by Jordan et al (2015) who found that 52.3% of the SNPs were non-synonimous (Jordan et al, 2015). The dataset represents the most comprehensive SNP resource available for the improvement of elite bread wheat cultivars.…”

“…Most sequencing projects focus on reference genome assembly and the discovery of SNPs, however, the importance of structural variants is becoming increasingly acknowledged , Jordan et al, 2015. Studies in several plant species reveal the existence of extensive structural variation (Gordon et al, 2014, Xu et al, 2012, Springer et al, 2009b, Hardigan et al, 2016, Li et al, 2014d.…”