Analysis of Population Structure and Selection Signals of Huchuan Mountain Pigs Based on Whole-Genome SNPs

Genetic resources constitute the cornerstone of seed-industry revitalization and sustainable agriculture. Their conservation and judicious utilization are imperative for safeguarding national seed security, enhancing livestock competitiveness, and maintaining biodiversity. The Huchuan Mountain pigs, a representative indigenous pig cluster in Southwest China, possess a unique genetic background and valuable local traits. It is a crucial source of income for local farmers and underpins regional agricultural development. However, frequent outbreaks of African swine fever and intensifying market competition have severely eroded its genetic diversity. Several populations—most notably Luopanshan, Hechuan Black, and Quxi pigs—are now critically endangered, demanding urgent conservation measures. Systematically dissecting the genetic structure, population divergence, and putative adaptive variants of the Huchuan Mountain pigs is therefore of both theoretical and practical importance for informed conservation and genetic improvement.

This study aimed to comprehensively characterize the population structure and genetic differentiation of the Huchuan Mountain pigs cluster, to identify selection signatures under contrasting conservation schemes, and to uncover candidate adaptive genes, thereby providing a robust scientific basis for the conservation and genetic enhancement of local pig resources.

Taking these six Huchuan Mountain pig populations as study subjects, whole-genome resequencing was performed. Based on high-quality SNP data, principal component analysis (PCA) and Admixture analysis were employed to evaluate genetic differences and admixture levels among populations, thereby revealing the genetic structure of each population. By constructing a phylogenetic tree, the kinship relationships and introgression events among populations were analyzed to further clarify their genetic connections. Combining the Fst (population genetic differentiation index) and π (nucleotide diversity) ratio, those selection signatures were detected to identify regions and candidate genes under selection during adaptive evolution in populations conserved under different conservation models. GO and KEGG functional enrichment analyses of these candidate genes were conducted to uncover their potential functions and biological characteristics related to adaptation, thus systematically dissecting the genetic structure and the genetic mechanisms underlying adaptive phenotypes in Huchuan Mountain pig populations.

PCA and ADMIXTURE analysis revealed pronounced genetic differentiation among populations. Yacha and Enshi Black pigs exhibited distinct genetic backgrounds, whereas Quxi and Penzhou Mountain pigs displayed extensive genetic admixture. A subset of Hechuan Black individuals clustered closely with Enshi Black pigs, and introgression signals were detected in multiple directions, especially involving Luopanshan pigs. The phylogeny tree corroborated these findings, underscoring the complex reticulate evolution within the cluster. Selection signal analysis based on Fst and θπ ratio revealed 998 highly differentiated loci corresponding to 7088 candidate genes in the nature-reserve conservation model and 616 highly differentiated loci corresponding to 3360 candidate genes in the preserving farms model. Functional enrichment indicated that genes under natural selection in the nature-reserve conservation model were predominantly associated with immune response, energy metabolism, and environmental adaptation, whereas those under artificial selection in the preserving farms model were enriched for reproductive regulation, hormone signaling, and metabolic pathways, reflecting distinct genetic adaptations under different rearing and management conditions.

The Huchuan Mountain pig cluster was characterized by intricate population structure and marked genetic differentiation. Nature-reserve conservation effectively preserved genetic diversity and adaptive potential, whereas preserving farms conservation enhanced production and reproductive performance. These findings provided the critical genomic evidence for designing complementary conservation strategies tailored to the sustainable utilization of this invaluable genetic resource.