Genome-Wide Linkage Mapping of QTL for Adult-Plant Resistance to Stripe Rust in a Chinese Wheat Population Lantian 25 × Huixianhong

Stripe rust, caused by <i>Puccinia striiformis</i> f. sp. <i>tritici</i> (Pst), represents a major global threat to wheat (<i>Triticum aestivum</i>. L). Planting varieties with adult-plant resistance (APR) is an effective approach for long-term management of this disease. The Chinese winter wheat variety Lantian 25 exhibits moderate-to-high APR against stripe rust under field conditions. To investigate the genetic basis of APR in Lantian 25, a set of 219 F₆ recombinant inbred lines (RILs) was created from a cross between Lantian 25 (resistant parent) and Huixianhong (susceptible parent). These RILs were assessed for maximum disease severity (MDS) in Pixian of Sichuan and Qingshui of Gansu over the 2020–2021 and 2021–2022 growing seasons, resulting in data from four different environments. Genotyping was performed on these lines and their parents using the wheat Illumina 50K single-nucleotide polymorphism (SNP) arrays. Composite interval mapping (CIM) identified six quantitative trait loci (QTL), named <i>QYr.gaas-2BS</i>, <i>QYr.gaas-2BL</i>, <i>QYr.gaas-2DS</i>, <i>QYr.gaas-2DL</i>, <i>QYr.gaas-3BS</i> and <i>QYr.gaas-4BL</i>, which were consistently found across two or more environments and explained 4.8–12.0% of the phenotypic variation. Of these, <i>QYr.gaas-2BL</i>, <i>QYr.gaas-2DS</i>, and <i>QYr.gaas-3BS</i> overlapped with previous studies, whereas <i>QYr.gaas-2BS</i>, <i>QYr.gaas-2DS</i>, and <i>QYr.gaas-4BL</i> might be novel. All the resistance alleles for these QTL originated from Lantian 25. Furthermore, four kompetitive allele-specific PCR (KASP) markers, <i>Kasp_2BS_YR</i> (<i>QYr.gaas-2BS</i>), <i>Kasp_2BL_YR</i> (<i>QYr.gaas-2BL</i>), <i>Kasp_2DS_YR</i> (<i>QYr.gaas-2DS</i>) and <i>Kasp_2DL_YR</i> (<i>QYr.gaas-2DL</i>), were developed and validated in 110 wheat diverse accessions. Additionally, we identified seven candidate genes linked to stripe rust resistance, including disease resistance protein RGA2, serine/threonine-protein kinase, F-box family proteins, leucine-rich repeat family proteins, and E3 ubiquitin-protein ligases. These QTL, along with their associated KASP markers, hold promise for enhancing stripe rust resistance in wheat breeding programs.