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
Mentions: The ability of the clustering algorithms implemented in the polyploid version of GS to detect clusters of any shape allowed for the identification of alleles (clusters with low signal intensity) resulting from either the deletion of single-copy genes in the wheat genome or the divergence of genotyping probe annealing sites (Figure 4). A total of 1660 single-locus SNPs showed evidence for alleles. We investigated the molecular basis of allele origin by comparing the sequences of SNP probes detecting these alleles in wheat cultivar Chinese Spring with the genomic sequence of this cultivar. Based on the comparison of flanking sequences of 94 SNP assays detecting the alleles in cultivar Chinese Spring, 46 assays did not have annealing sites in the genome. This result suggests that about 50% of alleles result from gene deletions and remaining are the consequence of sequence divergence at the SNP probe annealing sites.
Affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.