Genetic structure and virulence profiling of Puccinia striiformis reveal complex pathotype diversity associated with predominant MLG-10 and MLG-12 lineages in Xinjiang

Puccinia striiformis f. sp. tritici ( Pst), the causal agent of wheat stripe rust, continues to threaten global wheat production through the emergence of new virulent races. Xinjiang is a major wheat-producing border region connecting China with Central Asia and serves as an important epidemiological corridor for pathogen dispersal. Although previous studies have described Pst virulence diversity in this region, the relationship between genetic lineages and virulence phenotypes remains poorly understood. A total of 115 Pst isolates collected from major wheat-growing regions of Xinjiang were analyzed using 17 SSR markers and virulence patternson 25 Yr isogenic lines and 19 Chinese differential cultivars. Genetic and phenotypic data were integrated to evaluate population structure, multilocus genotype diversity, and pathotype variation. High virulence frequencies [> 80%] were detected against Yr1 , Yr2 , Yr6 , Yr9 , Yr17 , Yr18 , Yr27 , Yr28 , Yr29 , Yr44 , and YrA , indicating widespread resistance breakdown during the 2023 cropseason. In contrast, Yr5 , Yr8 , Yr10 , Yr15 , Yr32 , and YrTr1 remained highly effective, with virulence frequencies below 10%. A total of 36 multilocus genotypes (MLGs) were identified, revealing substantial genetic diversity within the Xinjiang Pst population. Among these, MLG-10 and MLG-12 were the Predominant in this region and exhibited the most complex virulence profiles, with broad virulence across multiple Yr genes. The prevalent race CYR34 was detected across multiple MLGs, with higher frequencies observed in the predominant MLG-10 and MLG-12, highlighting the distribution of this virulence phenotype across diverse genetic backgrounds. These findings provide the first comprehensive SSR-based characterization of Pst populations in Xinjiang and establish a baseline for future surveillance of pathogen population dynamics. The identified associations between dominant multilocus genotypes and virulence profiles may support future studies on resistance breeding and regional disease surveillance.