Genetic evidence of population admixture with European pigs and Southern Chinese pigs in Chinese indigenous Diqing Tibetan breed

BACKGROUND: The Chinese native Diqing Tibetan pig has a long history of domestication and is distributed in the southernmost region of China compared to other Tibetan breeds. In this study, we performed whole-genome sequencing of the Diqing Tibetan pigs. By integrating previously published data, we explored the genetic structure, population diversity, and genetic introgression from commercial European pigs and Southern Chinese domestic pigs into Diqing Tibetan pigs. We further examined the potential genetic influences of European pig introgression and inferred the historical events of admixture with Southern Chinese breeds. RESULTS: Our analysis revealed various instances of population admixture between Diqing Tibetan pigs and European pigs, as well as redundant introgression from South Chinese pigs when compared to other Tibetan pig populations. The introgression from European pigs significantly increased the population diversity in Diqing Tibetan pigs, which may influence fertility. Additionally, the introgression from European pigs affected the proportion of introgression from Southern Chinese pigs, with the most pronounced effect near the PSCK2 gene, which is associated with body size. Regarding ancestral genetic components from Southern Chinese pigs, we discovered a significant level of redundant proportion in Diqing Tibetan pigs compared to other Tibetan breeds. This admixture may have occurred at multiple time points from different breeds, with the Diannan small ear breed in Yunnan Province of China potentially serving as a recent primary contributor to the introgression into Diqing Tibetan breed. CONCLUSION: Our study reveals that the Diqing Tibetan breed has been shaped by admixture from European and multiple Southern Chinese sources, where European introgression increased diversity and reshaped Southern ancestry, while Southern introgression itself derives from distinct Southern Chinese pig breeds.