Genome-Wide Association Study and Gene Specific Markers Identified a Large Number of Genes or QTL for Resistance to Stripe Rust in U.S. Winter Wheat Cultivars and Breeding Lines

To determine stripe rust resistance genes in U.S. winter wheat cultivars and breeding lines, we analyzed a winter wheat panel of 857 cultivars and breeding lines in a genome-wide association study (GWAS) using genotyping by multiplexed sequencing (GMS) and by genotyping with molecular markers of 18 important stripe rust resistance genes or quantitative trait loci (QTL).The 31 markers for the 18 previously reported Yr genes or QTL were successfully tested in the 857 winter wheat accessions and/or reference genotypes. The presence and absence of the markers are provided in Supplementary Table S3. The GMS-GWAS analysis identified 36 loci on 15 chromosomes (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 5A, 5B, 5D, 6A, 6B, 7A, and 7B) significantly associated with stripe rust resistance in Supplementary Table S4.