Work

Genomic signatures of selection reveal genetic mechanisms underlying economic traits in Licha black pigs

Year: 2025

Type: article

Abstract: OBJECTIVE: The Licha black pig (LC) is a Chinese indigenous breed that is nationally protected, recognized for its superior meat quality and strong environmental adaptability. However, the population has experienced a rapid decline due to extensive crossbreeding with commercial lines. Understanding the genetic basis of economically important traits is crucial for conservation and genomic improvement. METHODS: Whole-genome resequencing was performed on 120 LC pigs and combined with genomic data from 285 pigs representing 32 global populations, including wild boars, commercial breeds, and other Chinese indigenous pigs. Population structure was investigated using phylogenetic trees, principal component analysis, ADMIXTURE and TreeMix analysis. Selection signatures were identified through four complementary approaches (FST, θπ ratio, XP-CLR, and Tajima's D). Candidate genes were examined through functional enrichment analysis, protein structure prediction, and cross-referencing with trait association and tissue-specific expression databases. Phenotypic data on body size and teat number were also collected in LC pigs for targeted genotype-phenotype analysis. RESULTS: Phylogenetic analyses showed clear stratification among global pig populations, with Chinese indigenous breeds significantly separated by the Qinling-Huaihe Line. LC pigs formed a distinct genetic cluster between northern Chinese and European breeds. Selective sweep analyses identified several candidate genes under positive selection, including SOCS6 and ATP2B4 (skeletal muscle development), RASAL2 (adipogenesis), and DOCK2 (male fertility). Trait-focused analyses identified ZNRF3 as a major locus for body size, with a missense mutation (g.46228935G>A; Gln→Arg) predicted to influence Wnt/β-catenin signaling. Signals of selection in ADGRB3, a gene potentially involved in teat patterning and mammary gland vascularization, were associated with variation in teat number. CONCLUSION: Our genomic analyses provide new insights into the genetic architecture of economically important traits and environmental adaptation in the LC. These findings provide a foundation for genomic-informed selective breeding and present valuable molecular tools for the genetic improvement and sustainable utilization of this indigenous genetic resource.

Source: Animal Bioscience

DOI: 10.5713/ab.250712