Population Genomics and Virulence Analyses Reveal Migration Pathways of Puccinia striiformis f. sp. tritici Between Southeastern Tibet and Sichuan

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is one of the most damaging diseases of wheat in China. Southeastern Tibet has recently been identified as an important source of Pst inoculum; however, the population genetic relationships and dispersal pathways connecting this region to Sichuan remain unclear. In this study, 220 Pst isolates collected from southeastern Tibet and Sichuan in 2025 were characterized using 19 Chinese differentials, 18 Yr single-gene differentials, and a 5K genotyping-by-target sequencing platform to assess virulence diversity, population structure, and potential migration pathways. Virulence analyses identified 66 previously described and 76 additional races using the Chinese differentials, while 148 races were distinguished using the Yr single-gene differentials. None of the isolates exhibited virulence against Yr5 or Yr15 . Population genetic analyses revealed that the Qamdo (CD) population in eastern Tibet exhibited the highest genetic diversity and substantial admixture. Strong genetic connectivity between Qamdo and populations in southeastern Tibet and Sichuan suggested extensive regional gene flow. Close genetic relationships between Qamdo and populations from Garzê (SCGZ), Jiangyou (SCJY), and Guangyuan (SCGY) further indicated that Qamdo may serve as a bridge for pathogen dispersal. These findings support the potential contribution of oversummering Pst populations in southeastern Tibet to inoculum sources in Sichuan and highlight the epidemiological significance of the Nyingchi–Qamdo–Sichuan corridor. This study provides insights into regional Pst migration and informs resistance breeding and stripe rust management strategies.