Genomic insights into population structure, genetic diversity, and key traits of Jiangxi indigenous pigs

Jiangxi indigenous pigs are a vital genetic resource in China, known for their unique coat colors, high-quality meat, and resilience to environmental stressors. However, their genetic diversity is increasingly threatened by habitat loss, African swine fever, and the introduction of exotic breeds. This study systematically analyzed the population structure, genetic diversity, and selective sweeps in 342 individuals from eight Jiangxi pig breeds using whole-genome sequencing. Population structure analysis revealed distinct genetic clusters for each breed, with some populations, such as Gandong Black, Ganzhongnan Spotted and Hang pigs, showing internal instability and low genetic diversity in breeds like Leping Spotted and Yushan Black (YS) pigs. Selective sweep analysis identified key genes associated with economically important traits: EDNRB and DKK1 were strongly linked to coat color variation, while FGF2 was implicated in white abdominal patterns. For meat quality, PPFIBP1 and SERPINE2 were highlighted in YS pigs, influencing muscle development, fat metabolism, and tenderness. These findings provide crucial insights into the genetic basis of economically significant traits, emphasizing the need for tailored conservation strategies. The study establishes a genomic foundation for sustainable breeding and conservation efforts to safeguard Jiangxi indigenous pigs.