Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Genomic signatures of selection reveal genetic mechanisms underlying economic traits in Licha black pigs

  • Jiajia Liu (Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University) ;
  • Zhe Tian (Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University) ;
  • Mubin Yu (Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University) ;
  • Wenwen Li (Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University) ;
  • Pengcheng Lv (Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University) ;
  • Tao Wang (Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University) ;
  • Yu Tian (Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University) ;
  • Shuer Zhang (General Station of Animal Husbandry of Shandong Province) ;
  • Junjie Wang (Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University) ;
  • Wei Shen (Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University)
  • Received : 2025.09.25
  • Accepted : 2025.11.26
  • Published : 2026.05.01
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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.

Keywords

Acknowledgement

This work was financially supported by the Key R&D Program of Shandong Province, China (2024LZGC002), the Key R&D Program of Shandong Province, China (2024LZGC017), Qingdao Science and Technology for the People Demonstration Project (24-1-8-xdny-5-nsh), Shandong Modern Agricultural Industry Technology System - Swine Innovation Team (Project ID: SDAIT-08-02).

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