High Genotypic Polymorphism and Extensive Gene Flow Drive the Population Dynamics of Potato Oomycete Pathogen, Phytophthora infestans, Across Southwestern China

Potato late blight, Phytophthora infestans, remains a major global threat to potato production due to the rapid genetic change, long-distance dispersal and fungicide resistance. To clarify the genetic structure and phenotypic characteristics of P. infestans populations in southwestern China during 2019–2025, this study analyzed 241 isolates collected from Sichuan, Chongqing, Guizhou, Yunnan and Hubei. The isolates were characterized using 14 SSR markers, together with mating-type determination, metalaxyl sensitivity assays, mitochondrial haplotype identification and virulence profiling. A total of 70 alleles and 118 multilocus genotypes were detected, with certain genotypes (SW-40, SW-48 and SW-81) broadly distributed across regions, while the simultaneous presence of numerous low-frequency genotypes reflected high overall genetic diversity. Population genetic analyses revealed weak regional differentiation and strong genetic connectivity, with most genetic variation occurring within regional populations, where self-fertile isolates, metalaxyl-resistant phenotypes and mitochondrial haplotype Ia were predominant. Cluster and principal component analyses separated the isolates into three major genetic groups, with the largest group containing most isolates and showing close genetic similarity to the Blue_13 reference genotype. These findings indicate that southwestern China harbors a highly diverse and admixed P. infestans population, likely driven by frequent pathogen movement among potato-growing regions.