Genetic Relationships of Puccinia striiformis f. sp. tritici Populations from Eastern Xizang and Neighboring Epidemic Regions Revealed by 20K Genotyping-by-Target Sequencing

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive airborne disease of wheat in China. Xizang has long been regarded as a relatively isolated epidemic region because of major geographic barriers, but the genetic relationships between Pst populations in eastern Xizang and neighboring epidemic regions remain unclear. In this study, 356 Pst isolates collected from eastern Xizang, eastern Qinghai, Gansu, and Shaanxi in 2024 were analyzed using virulence phenotyping and 20K genotyping-by-target sequencing. Virulence assays of 196 isolates on 25 Yr differential lines identified 159 virulence phenotypes, including several recurring phenotypes shared between eastern Xizang and eastern Qinghai. Genotyping yielded 4,285 high-quality, linkage-disequilibrium-pruned SNPs and revealed pronounced population structure within eastern Xizang. Zuogong–Basu isolates formed a distinct genetic group, whereas Mangkang isolates were more heterogeneous and partially overlapped with isolates from eastern Qinghai, Gansu, and Shaanxi. Pairwise FST estimates indicated lower differentiation between eastern Xizang and eastern Qinghai (FST = 0.074) than between eastern Xizang and Gansu or Shaanxi (FST = 0.098–0.106). Differentiation between Mangkang and eastern Qinghai (FST = 0.076) was also lower than that between Zuogong–Basu and eastern Qinghai (FST = 0.117). TreeMix and D-statistic analyses provided additional evidence of historical genetic exchange among several populations, including eastern Xizang and eastern Qinghai. These results show substantial internal differentiation within eastern Xizang and indicate that its Pst population is not completely isolated from neighboring epidemic regions, providing a genetic basis for coordinated regional surveillance and stripe rust management.