Genome-wide association study identifies candidate genes for stripe rust resistance in wheat across multiple environments

Stripe rust, caused by Puccinia striiformis f. sp. tritici , threatens wheat production. To investigate resistance expressed at the adult-plant stage, 120 wheat accessions were evaluated in four field environments at three sites during 2022–2024. Genotyping with a wheat 50 K liquid-phase SNP chip yielded 54,636 retained markers. Genome-wide association analysis used a mixed linear model incorporating population structure and kinship, with disease severity in each environment and across-environment best linear unbiased predictions (BLUPs) analyzed as five phenotypic datasets. Disease severity varied continuously, and broad-sense heritability was 0.90. Twelve recurrent marker records, representing 11 unique physical positions, were detected on chromosomes 1 A, 6B, and 7B at P < 0.001 in at least three phenotypic datasets, including BLUP. These marker records were grouped into five provisional association regions using subgenome-specific linkage disequilibrium (LD) decay distances. Seven candidate genes were prioritized on the basis of functional annotation. Haplotype analysis of four selected SNP-containing blocks identified haplotypes associated with lower disease severity. AX-111,091,126 was detected in 23YL, 24TS, and BLUP; Hap1 in its block showed lower severity than Hap3 under BLUP. A KASP assay developed for this SNP distinguished A/G genotypes in an independent panel of 221 wheat accessions. The recurrent associations, candidate genes, and favorable haplotypes provide targets for further genetic validation. The AX-111,091,126 KASP assay offers a genotyping tool for evaluating the associated allele in wheat resistance breeding.