GWAS (Genome Wide Association Mapping) and linkage analysis using bi-parental mapping populations are two methods for gene discovery of leaf rust (Lr) and stripe rust (Yr) resistance. In the study, GWAS panel of 268 lines (207 accessions from the different wheat production regions of China, and 61 accessions from foreign countries) were evaluated for seedling resistance to Lr using 8 Chinese isolates and also tested for the two rusts at adult-plant stage under multiple environments and genotyped using 90K SNP chip. Genome-wide association mapping (GWAS) was performed using the mixed linear model (MLM). Results showed 22 loci including the known Lr genes viz. Lr1, Lr26, Lr3ka, LrZH22, and 17 potentially new loci were identified at the seedling stage and explained phenotypic variation ranging from 4.6 to 25.2%. GWAS identified 21 and 23 loci associated with leaf and stripe rust in the field. Of which, 7 and 6 were identified in multiple environments and BLUP data at adult plant stage, respectively. Four potentially pleiotropic APR (Adult plant resistance) locus, including Lr46/Yr29, and three new regions, QLr-2AL.1/QYr-2AL.1, QLr-2AL.2/QYr-2AL.2, and QLr-5BL/QYr-5BL.1 conferred resistance to both rusts. A total of 12 associated SNPs was successfully transformed into KASP (Kompetitive allele specific PCR) makers.
QTL mapping for wheat leaf rust were conducted for six bi-parental populations (including Zhou 8425B/Chinese Spring RIL population, Pingyuan 50/Mingxian 169 DH population, SW 8588/Thatcher RIL population, Fuyu 3/Zhengzhou 5389 F2:3 population, W014204/Zhengzhou 5389 F2:3 population, and Fundulea 900/Thatcher F2:3 population) using 55K SNP chip technology or SSR markers under Chinese environments. Results showed that 3-9 QTL for leaf rust, including the known genes Lr12, Lr22b, Lr34, Lr37, Lr46, Lr68, and LrZH22, were identified in each population, respectively. Lr12 from Chinese Spring, Lr34 from W014204, Fundulea 900 and Chinese Spring, Lr37 from SW 8588, Lr46 from Fundulea 900, Lr68 potentially present in SW8588 and Fuyu 3, and LrZH22 from Zhou 8425B, showed good resistance for leaf rust. Lr22b from Thatcher, was previously thought to be ineffective in China, contributed a large effect for leaf rust resistance in SW 8588/Thatcher RIL population. In addition, other potentially new loci viz. QLr.hebau-3DS, QLr.hebau-3AL, QLr.hebau-5AL, QLr.hebau-7BL etc. were identified. Some associated SNPs for wheat leaf rust QTL, QLr.hebau-3DS, QLr.hebau-3AL, and QLr.hebau-5AL, were developed into KASP makers. Closely linked SSR and SNP markers can be used in marker-assisted selection in breeding.