Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a highly destructive airborne disease capable of long-distance spore transmission, cross-regional colonization, and widespread epidemics. This pathogen poses a severe threat to global wheat production, including China, where it causes substantial yield losses. To investigate the population structure, source, and dispersal pathways of Pst in the Ili region of Xinjiang, we genotyped 310 (2021) and 268 (2022) Pst isolates from 144 wheat fields using 18 kompetitive allele-specific PCR (KASP)-SNP markers. Genetic diversity analysis identified 162 and 115 multilocus genotypes in 2021 and 2022, respectively, with higher diversity in Gongliu, Qapqal, and Zhaosu compared with other regions. Population structure analysis revealed substantial gene flow between the winter Pst population in Qapqal and the spring Pst population in Xinyuan, as well as between the spring Pst populations in Zhaosu and Tekes. In contrast, the Tekes population showed minimal gene flow with other groups. Bayesian information criterion (BIC) and discriminant analysis of principal components (DAPC) delineated distinct clusters within the spring wheat Pst populations from Zhaosu and Tekes, alongside significant genetic exchange between the 2021 and 2022 populations. Furthermore, the Ili Pst population showed significant differentiation from global counterparts (Ecuador, Ethiopia, Italy, Mexico, and the United States). Integrating genetic structure analysis with high-altitude airflow trajectories, we identified two major Pst migration routes in the Ili region, mainly from Qapqal to Xinyuan, and secondarily from the spring wheat-growing areas of Zhaosu to Xinyuan.

Wheat powdery mildew, caused by the obligate biotrophic fungus Blumeria graminis f. sp. tritici ( Bgt ), is a devastating disease responsible for substantial global yield reductions. Host resistance offers the most sustainable management strategy, yet its durability is continually undermined by high evolutionary potential of the pathogen, driven by sexual recombination and rapid mutation. To decipher long-term virulence dynamics, we conducted a comparative analysis of Bgt populations in the Northwestern Himalayas over two decades (1994–1998 and 2015–2019). Pathotype profiling of 285 isolates on a common set of nine differential lines revealed a significant shift in virulence structure over time. While the mean virulence complexity per isolate increased in the contemporary population, indicating enhanced pathogenic capability, overall pathotype diversity decreased, suggesting a selective sweep toward fewer, more aggressive lineages. Marked changes in virulence frequency were observed with severe efficacy erosion for Pm1a (virulence increased from 6 to 63%) and Pm8 , while virulence against Pm2 , Pm3a , and Pm3b declined significantly. Notably, genes Pm2 and Pm4a demonstrated complete and durable effectiveness throughout the study period. Our results identify these as stable resistance donors and underscores the continuous adaptation of Bgt populations. This study provides critical insights for designing durable resistance gene pyramids and underscores the necessity of continuous virulence surveillance to sustain wheat production in the face of evolving pathogen threats.