Unveiling the genetic architecture of stripe rust resistance in wheat: a region-specific GWAS in Xinjiang, China

Wheat stripe rust is a fungal disease that decreases wheat yield and quality. In this study, 300 winter wheat cultivars (lines) from different regions were infected with stripe rust and analyzed in terms of disease severity and infection type at the seedling and adult-plant stages. Additionally, a genome-wide association study was performed using the wheat 90 K SNP chip. Sixteen accessions exhibited all-stage resistance to the prevalent Pst races CYR32 and CYR34. Moreover, the enriched compressed mixed linear model detected 261 marker-trait associations at the seedling and adult-plant stages; these markers were located on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3D, 4B, 5A, 5B, 5D, 6A, 6B, 7A, and 7B. By combining this finding with a linkage disequilibrium decay distance of 1.72 Mb, 20 and 12 quantitative trait loci related to stripe rust resistance at the seedling and adult-plant stages, respectively, were identified; these QTLs explained 0.01%-20.85% of the phenotypic variation. Comparative analysis with known Yr genes or quantitative trait loci (QTLs) revealed 11 potentially novel seedling-stage resistance loci and 7 novel adult-plant resistance loci. Three of these loci were on chromosomes 2A, 3A, and 3D, which explained 16.49%-20.85%, 7.41%-19.27%, and 8.78%-18.56% of the phenotypic variation, respectively. Additionally, haplotype analysis showed that Hap2 significantly improved stripe rust resistance. Additionally, functional Kompetitive allele-specific PCR markers were developed and validated for SNP loci Kukri_c2289_635. Hence, this study provides a theoretical basis, parental materials, and molecular markers that may be useful for breeding disease-resistant wheat cultivars.