Bread wheat is an allohexaploid that formed through the sequential hybridization of three species. Polyploidization, subsequent natural selection, domestication and breeding bottlenecks have reduced the genetic diversity in cultivated wheat compared to its progenitors and wild relatives. These are now widely recognized as important resources from which to harness useful traits for cultivated wheats. Various genotyping methods can be used to study genomic patterns of diversity, ancestral relationships and trait associations. A number of SNP genotyping arrays have been developed to characterize genomes of important crops and animals. Here, we assessed a collection of 385 accessions with the wheat Infinium 90k array. The collection comprises 26 different species of cultivated wheat, synthetic hexaploid wheat, progenitor species, and wild relatives where ~40% have a winter growth habit. Genotype calling, SNP clustering and filtering were performed to extract reliable and informative sets of SNPs. Principal component and clustering analyses illustrate the relationships among species and ploidy levels. Wild and cultivated emmer clustered separately and, synthetic hexaploid wheat originating from wild emmer clustered with the wild tetraploid group while those obtained from crosses with cultivated emmer clustered with durum and other cultivated Triticum species. Phenotyping for leaf rust and Fusarium head blight (FHB) was performed in the field at two locations for three years. Indoor tests for leaf rust reaction type using six races and FHB Type II resistance were also performed. A genome-wide association study was conducted for these traits comparing single and multi-locus models. Our results highlight the potential of SNP arrays for analyzing genome-wide variations in wheat and essentially create opportunities for future marker-trait association studies using wild wheat.

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