Analysis of Genome-Wide Patterns of Genetic Variation Across Wheat Genome using 90,000 SNP iSelect Assay

Genome-wide analysis of genetic variation in crops is a powerful tool for dissecting the genetic basis of important agronomic traits, making phenotypic predictions and studying the history of domestication and selection. The SNP resources developed by the international wheat SNP consortium were combined to develop custom iSelect genotyping assay including 90,000 gene-associated SNPs. The SNP discovery panels were composed of diverse wheat accessions including wild emmer, durum wheat and bread wheat landraces and cultivars. To account for SNP-specific patterns of variation in genotype clustering, genotype calling procedures for tetraploid and hexaploid wheat were manually curated and trained in a panel of wheat lines including mapping populations and diversity panels. A high-density consensus genetic map has been build utilizing bi-parental and MAGIC populations. The utility of the assay for genotyping diverse populations was investigated by comparing the distribution of SNPs among populations of tetraploid and hexaploid wheat including wild relatives, cultivars and landraces. This dataset has been used to investigate the structure of wheat populations and the history of wheat breeding, and identify genomic regions subjected to selection. We uncovered strong patterns of genetic differentiation related to geographic origin of wheat accessions. However, the effects of growth habit and the level of improvement (cultivars vs. landraces) on genetic differentiation were less substantial. We have identified a number of candidate selection targets associated with wheat improvement including regions containing genes involved in the regulation of flowering, development and stress response providing valuable information for understanding the genetics of agronomic traits in wheat.