Mapping and Evaluation of Quantitative Trait Loci for Adult-Plant Stripe Rust Resistance in the Sichuan Wheat Cultivar Chuanmai 62

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a persistent threat to wheat production in China. The Sichuan cultivar Chuanmai 62 (CM62) has exhibited stable adult-plant resistance (APR) for over a decade. To elucidate its genetic basis, we evaluated a recombinant inbred line population (CM62 × Avocet S) across 13 environments and genotyped it using the 55K SNP array. QTL mapping identified six QTL distributed on chromosomes 1BL, 2AS, 2BL, 5AL (two loci), and 5BL. Among these, three major QTL (QYr.CM62-1BL, QYr.CM62-2AS, and QYr.CM62-2BL) were detected. Notably, QYr.CM62-2BL was the preeminent locus, explaining 8.97–50.59% of phenotypic variance and exhibiting high stability across 11 of the 13 environments; this locus is closely linked to the previously reported QYR1 region, although whether it is allelic to QYR1 remains unclear. QYr.CM62-2AS corresponded to Yr17/YrM1225, while QYr.CM62-1BL aligned with Yr29. A significant finding was the identification of QYr.CM62-5BL, a novel minor-effect QTL mapped to the rearranged 5BL·7BL segment resulting from a 5B/7B reciprocal translocation present in both parents. Furthermore, two Kompetitive Allele-Specific PCR (KASP) markers (KASP-AX-109507945 and KASP-AX-109844182) were developed for QYr.CM62-2BL. Polymorphism screening of 328 cultivars confirmed their utility for marker-assisted selection. Collectively, our results demonstrate that the durable APR in CM62 is governed by multiple additive QTL. The newly developed KASP markers, together with the novel QYr.CM62-5BL locus and prioritized candidate genes from in silico annotation of the QYr.CM62-2BL interval, provide valuable genetic resources for pyramiding resistance alleles and future map-based cloning in wheat breeding programs.