Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.
Bottom Line: We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations.The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin.The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
Affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.Show MeSH
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Mentions: To ascertain the transferability of SNP markers across populations, we assessed the number of shared alleles and the degree of genetic differentiation (FST) between the wheat populations (Table 3). The majority of polymorphic SNPs were shared among populations, suggesting that the targeting of SNPs with both alleles present in at least two individuals in the discovery panel enriched the array for common SNP variants. This observation is consistent with the prevalence of SNPs of intermediate to high MAF in the populations (Figure 5a). FST variation between the populations of different geographical origin is likely caused by the usage of different founders (Table 3) and/or by allele frequency divergence during the development of locally adapted populations. For example, broad usage of landraces in the breeding programmes of Asia could have resulted in low FST between landraces and Asian cultivars (Cavanagh et al., 2013). Our analyses also confirm previous observations showing the high proportion of shared alleles between wheat cultivars as a whole and landraces (Cavanagh et al., 2013), suggesting that the majority of alleles for wheat improvement were contributed by landraces.
Affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.