Analysis of the genetic structure and selection signature of Xiangyang Black pigs using whole-genome resequencing data

Abstract Background Xiangyang Black (XYB) is a valuable indigenous pig breed from Hubei Province, China, renowned for its excellent meat quality, strong disease resistance, and adaptability to local environments. To explore the genetic diversity, population structure, and selection signatures of XYB in the context of Chinese and Western pig breeds, we performed whole-genome resequencing on 15 pig breeds, involving 225 individuals. Results After quality control, 20,479,203 high-quality single-nucleotide polymorphisms (SNPs) were retained for subsequent analysis. Genetic diversity analysis revealed that XYB exhibited relatively high genetic diversity (Ho = 0.38, pi = 0.35) and a low inbreeding coefficient (FROH = 0.001–0.090), indicating its strong potential for genetic improvement and conservation. Population structure analyses—including neighbor-joining tree, principal component analysis, and ADMIXTURE—revealed a distinct genetic structure and verified the rationality of XYB’s status as a unique genetic resource at the molecular level. Selection signature detection using three complementary methods (Fst, θπ ratio, and XP-EHH) identified 1080 significant selected regions and 951 candidate genes in XYB compared with Western breeds. Functional annotation showed that these genes were enriched in pathways related to meat quality (e.g., FABP2, PPARG, C/EBPα, and THRSP), reproduction (e.g., GNRH1, CENPE, and CCDC112), and disease resistance (e.g., CCL17, CCL22, and CX3CL1). Conclusions Our results provide insights into the genetic basis of phenotypic traits in XYB pigs and offer a theoretical foundation for their conservation, breeding, and genetic improvement.