Population Structure, Genetic Diversity, and Stripe Rust Resistance in Core Subset of the USDA Winter Wheat Germplasm Collection.

Knowledge of available genetic variation and population structure is important for utilization of core collections and in understanding the genetic basis of diverse physiological, agronomic, and morphological traits. Here we report the results of genetic characterization and association mapping for resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, in 1,175 winter wheat accessions from 64 countries based on genotyping with the wheat 9K SNP iSelect assay and phenotyping of adult plants under natural disease epidemics in four environments.  Model-based assessment of population structure revealed three subpopulation groups. Group 1 is predominantly landraces from Asia, and groups 2 and 3 are mostly comprised of breeding and cultivated lines, genetic stocks and cultivars from Europe and the Americas, respectively. F_ST estimates revealed high levels of genetic differentiation between subpopulation 1 and subpopulations 2 and 3. In contrast, minor genetic differences were observed between subpopulations 2 and 3. Population structure was evident when accessions were grouped by improvement status, origin, and stripe rust reaction. Association analyses identified 99 resistance loci that were effective across all environments, including 20 with significant genome-wide adjusted p-values (FDR <0.1). Based on relative map positions of previously reported genes and QTL, 5 of the QTL identified in this study represent potentially new loci. This study highlights the importance of integrating population structure, genetic diversity, and association analyses in utilization of core collections as genetic resources for development of germplasm, identification of genes, and development of DNA markers.