Analysis of the genetic structure and selection signatures of Xiangyang black pigs using whole-genome resequencing data.

Xiangyang Black (XYB) is a valuable indigenous pig breed from Hubei Province, China, known for its high meat quality, disease resistance, and adaptability to the local conditions. 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. 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, with an observed heterozygosity (Ho) of 0.38 and a nucleotide diversity (pi) of 0.35 and the inbreeding coefficient based on runs of homozygosity (FROH) ranged from 0.001 to 0.090, indicating its strong potential for genetic improvement and conservation. Population structure analyses-including neighbor-joining tree, principal component analysis, and admixture analysis-revealed a distinct genetic structure and confirmed the distinct genetic status of XYB at the molecular level. A combination of three complementary methods-fixation index (Fst), nucleotide diversity (θπ) ratio, and cross-population extended haplotype homozygosity (XP-EHH)-revealed 1,080 putative selective sweep regions (covering approximately 76.1 Mb of the genome) harboring 951 candidate genes in the Xiangyang Black pig breed compared to 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). 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.