A genome-wide association study unveiled quantitative trait loci for multiple rust resistance in U.S. winter wheat

1. GWAS identified two novel QTLs each for wheat resistance to leaf rust ( QLr . hwwg-4AL, QLr . hwwg-2BL ) and stripe rust ( QYr . hwwg-2AS . 1 and QYr . hwwg-4BL ). 2. U.S. hard winter wheat carry QTLs corresponding to at least six known resistance genes ( Lr74, Lr77, Lr18, Lr68, Yr17, Yr30 ). 3. Some QTLs with resistance to both rusts can be pyramided with other resistance genes to improve durable resistance to both rusts in new wheat cultivars. Leaf rust ( Puccinia triticina ) and stripe rust ( Puccinia striiformis f. sp. tritici ) are among the most prevalent foliar diseases in wheat, causing significant annual yield losses worldwide. To identify rust resistance genes in U.S. winter wheat, we conducted a genome-wide association study (GWAS) on resistance to leaf and stripe rusts in U.S. winter wheat cultivars and elite advanced breeding lines. Using simple sequence repeats (SSRs) and wheat 90K single nucleotide polymorphism (SNP) arrays, we identified two novel quantitative trait loci (QTLs), QLr . hwwg-2BL and QLr . hwwg-4AL , and four QTLs corresponding to known genes Lr74, Lr77, Lr18 and Lr68 for leaf rust resistance. We also identified five QTLs conferring stripe rust resistance, which included the three previously characterized loci Yr17/YrM1225 on the 2NS/2AS translocation, Yr30/Sr2 on 3BS, and QYr . hwwg-2BS , along with two putative novel loci, QYr . hwwg-2AS . 2 and QYr . hwwg-4BL , with the latter located in a QTL-rich region. The QTLs identified in this study will be useful for improving durable resistance to leaf and stripe rusts in new wheat cultivars using marker-assisted gene-pyramiding strategy.