Identification of stripe rust resistance loci in Gansu wheat landraces using genome-wide association analysis

Stripe rust severely threatens global wheat production. Identifying and using favorable resistance loci from landraces can increase the genetic diversity and durability of resistance in modern wheat cultivars. In this study, we phenotyped 376 wheat landraces from Gansu for stripe rust resistance through seedling inoculation with race CYR34 and multiyear field trials across six environments. Genotyping was performed using a 16 K SNP array and known gene markers. In total, seven significant quantitative trait loci located on chromosomes 2A, 2D, 3B, 3D, 4B, and 7A were detected at the seedling stage. Four significant and stable QTLs, including the known pleiotropic adult plant resistance gene Yr18, were identified at the adult plant stage. Among them, Yr.hzau.4B was stably detected at both ASR and APR, explaining 9.46% and 11.58% of the phenotypic variation, respectively. Haplotype analysis revealed that, compared with materials carrying the unfavorable haplotype, wheat landraces harboring the favorable Yr.hzau.4B haplotype presented a reduction of 0.6 grading units in the average infection type for ASR and a 32.4% decrease in DS for APR. Additive interaction analysis further indicated a decreasing trend in both IT and DS with an increasing number of favorable haplotypes. Additionally, a KASP molecular marker for Yr.hzau.4B was developed and validated in an independent population. Integrated candidate gene analysis revealed 29 putative resistance-related genes, encompassing gene families such as kinases and transporters. This study identified new resistance gene loci and developed breeder-friendly molecular markers. These compounds can be used to improve stripe rust resistance in wheat and provide useful resources for the breeding of wheat resistance.