Genetic diversity, relationships, and positive selection genes of four Wujin pig populations: unraveled through whole-genome resequencing.
5 affiliations
- 1Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
- 2Yunnan Provincial Livestock Station, Kunming, 650506, China.
- 3Bijie Academy of Agricultural Sciences, Bijie, Guizhou Province, 551700, China.
- 4Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China. [email protected].
- 5Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China. [email protected].
Abstract
Background
Wujin pigs (WJPs) is an important indigenous pig resource in southwest China, traditionally classified into four subpopulations: Dahe pig (DHP), Kele pig (KLP), Liangshan pig (LSP), and Zhaotong pig (ZTP). Nevertheless, research on the population genetic characteristics of WJPs based on genome-wide variations remains scarce. In particular, the genetic relationships among the four WJPs have yet to be clearly elucidated. This study conducted genome resequencing on 120 WJPs from the four populations (30 individuals per population). By integrating genomic data from 30 Asian wild boars (AWBs) and 90 pigs from three commercial breeds (30 each of Duroc, Landrace, and Yorkshire), their population structure, genetic diversity, genetic relationships, and selection signatures were investigated.Results
A total of 66,878,082 autosomal single nucleotide polymorphisms (SNPs) were detected in the 240 pigs, and 26,142,708 high-quality SNPs were retained for subsequent analysis. The results showed that DHPs, KLPs, LSPs, and ZTPs were four distinct populations of WJPs, with unique population structure and higher genetic diversity compared to AWBs and the three commercial breeds. Among the four WJPs, DHPs had relatively slower linkage disequilibrium (LD) decay, lower genetic diversity, and higher inbreeding coefficient (FROH) values than ZTPs, LSPs, and KLPs. A greater genetic distance and higher differentiation degree were observed between DHPs and the other three WJPs, while a smaller genetic distance and lower differentiation were found between ZTPs and LSPs. Furthermore, five important selected regions containing 50 published QTLs were identified. Totals of 111 candidate genes were annotated within these regions, and nine of the genes under selection were found to be associated with immune response (TICAM1, JAK2, CD274, and IL33), nervous system development (KDM4B and KDM4C), cardiovascular system regulation (RLN2), reproduction (MAP2K2), and fat deposition (EGR2).Conclusion
Our findings enhance the understanding of the genomic characteristics of WJPs, reveal that DHPs may form a relatively independent population within this breed, and identify nine candidate genes related to immunity, adaptation, reproduction, and fat deposition, which provide a valuable foundation for the conservation, breeding, and sustainable utilization of WJPs.
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BibTeX
@article{zhu2026genetic,
title = {{Genetic diversity, relationships, and positive selection genes of four Wujin pig populations: unraveled through whole-genome resequencing.}},
author = {Yixuan Zhu and Chengliang Xu and Jinhua Lai and Xiaoyi Wang and Lixing Wang and Ligang Lu and Qiang Chen and Shuyan Wang and Mingli Li and Shaoxiong Lu},
journal = {BMC genomics},
year = {2026},
month = aug,
doi = {10.1186/s12864-026-13259-9},
url = {https://europepmc.org/article/MED/42972229},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Genetic diversity, relationships, and positive selection genes of four Wujin pig populations: unraveled through whole-genome resequencing.
AU - Yixuan Zhu
AU - Chengliang Xu
AU - Jinhua Lai
AU - Xiaoyi Wang
AU - Lixing Wang
AU - Ligang Lu
AU - Qiang Chen
AU - Shuyan Wang
AU - Mingli Li
AU - Shaoxiong Lu
PY - 2026
DA - 2026/08/06
JO - BMC genomics
DO - 10.1186/s12864-026-13259-9
UR - https://europepmc.org/article/MED/42972229
AB - Background Wujin pigs (WJPs) is an important indigenous pig resource in southwest China, traditionally classified into four subpopulations: Dahe pig (DHP), Kele pig (KLP), Liangshan pig (LSP), and Zhaotong pig (ZTP). Nevertheless, research on the population genetic characteristics of WJPs based on genome-wide variations remains scarce. In particular, the genetic relationships among the four WJPs have yet to be clearly elucidated. This study conducted genome resequencing on 120 WJPs from the four populations (30 individuals per population). By integrating genomic data from 30 Asian wild boars (AWBs) and 90 pigs from three commercial breeds (30 each of Duroc, Landrace, and Yorkshire), their population structure, genetic diversity, genetic relationships, and selection signatures were investigated.Results A total of 66,878,082 autosomal single nucleotide polymorphisms (SNPs) were detected in the 240 pigs, and 26,142,708 high-quality SNPs were retained for subsequent analysis. The results showed that DHPs, KLPs, LSPs, and ZTPs were four distinct populations of WJPs, with unique population structure and higher genetic diversity compared to AWBs and the three commercial breeds. Among the four WJPs, DHPs had relatively slower linkage disequilibrium (LD) decay, lower genetic diversity, and higher inbreeding coefficient (FROH) values than ZTPs, LSPs, and KLPs. A greater genetic distance and higher differentiation degree were observed between DHPs and the other three WJPs, while a smaller genetic distance and lower differentiation were found between ZTPs and LSPs. Furthermore, five important selected regions containing 50 published QTLs were identified. Totals of 111 candidate genes were annotated within these regions, and nine of the genes under selection were found to be associated with immune response (TICAM1, JAK2, CD274, and IL33), nervous system development (KDM4B and KDM4C), cardiovascular system regulation (RLN2), reproduction (MAP2K2), and fat deposition (EGR2).Conclusion Our findings enhance the understanding of the genomic characteristics of WJPs, reveal that DHPs may form a relatively independent population within this breed, and identify nine candidate genes related to immunity, adaptation, reproduction, and fat deposition, which provide a valuable foundation for the conservation, breeding, and sustainable utilization of WJPs.
SN - 1471-2164
ER -