Population Genetic Differentiation and Runs of Homozygosity Analysis of Bursaphelenchus xylophilus in Southwest China

Background: Pine wilt disease (PWD), caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus), is a devastating forest disease. It has been reported in five provincial-level regions in Southwest China (Chongqing, Guizhou, Sichuan, Yunnan, and Tibet), threatening local pine forest ecosystems. Methods: To unravel the population genetic variation and population differentiation of PWN isolates in this region, we purified eighty-one isolates for whole-genome resequencing and bioinformatics analysis, identifying candidate genes associated with runs of homozygosity (ROH). Results: Population structure analysis clustered the 81 isolates into three distinct genetic groups (Groups 1, 2, and 3). Notably, Group 1 exhibited fewer and shorter ROH segments compared to Groups 2 and 3, indicating higher genetic diversity and a different inbreeding history. Functional annotation of genes overlapping ROH regions revealed that Group 1 contained a subset of the genes identified in Groups 2 and 3, primarily enriched in specific molecular function categories. Conclusions: The PWN populations in Southwest China exhibit genetic differentiation, forming three distinct groups. Group 1 shows a reduced ROH burden and lower inbreeding levels, whereas Groups 2 and 3 display more extensive ROH patterns that may reflect historical demographic processes or potential adaptive selection. The differential distribution of ROH-associated genes across groups suggests possible variation in historical demographic processes and could suggest possible directional selection. These findings contribute to understanding the population history and genomic characteristics of PWN in Southwest China, providing insights that could support disease management strategies.