Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (8): 1809-1824.doi: 10.3864/j.issn.0578-1752.2026.08.015

• ANIMAL SCIENCE·VETERINARY SCIENCE • Previous Articles    

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

LONG Xi1,2(), CHAI Jie1,2, ZHANG Liang1,2, PAN Yu1,2, TU Zhi1,2, ZHANG LiJuan1,2, ZHANG LiDan2, TANG YiTong1, GUO ZongYi1,2,*(), PAN HongMei1,2,*()   

  1. 1 Chongqing Academy of Animal Science and Veterinary Medicine, Chongqing 402460
    2 National Swine Technology Innovation Center, Chongqing 402460
  • Received:2025-07-22 Accepted:2026-03-30 Online:2026-04-21 Published:2026-04-21
  • Contact: GUO ZongYi, PAN HongMei

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Abstract:

【Background】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.【Objective】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.【Method】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.【Result】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 7 088 candidate genes in the nature-reserve conservation model and 616 highly differentiated loci corresponding to 3 360 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. 【Conclusion】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.

Key words: Huchuan Mountain pigs, re-sequencing, whole-genome SNPs, group structure, signal selection

Table 1

Sample information of 179 individuals from six breeds"

品种
Breed		 简称
Abbreviation		 样本数量
Number of samples		 采样地点
Location of samples		 保种模式
Breed conservation model		 采样时间
Sampling time
罗盘山猪
Luopanshan pig		 LP 公 Male 3 重庆市潼南区新胜镇罗盘山猪保护区
Luopanshan pig conservation area in Xinsheng town, Tongnan district, Chongqing		 保护区
Conservation area		 2022年12月
December 2022
母 Female 27
合川黑猪
Hechuan Black pig		 HC 公 Male 14 重庆市合川区龙市镇合川黑猪保护区
Hechuan black pig conservation area in Longshi town, Hechuan district, Chongqing		 保护区
Conservation area		 2022年12月
December 2022
母 Female 16
盆周山地猪
Penzhou Mountain pig		 PZ 公 Male 15 重庆市盆周山地猪涪陵保种场
Fuling conservation farm of Penzhou mountain pig in Chongqing		 保种场
Conservation farm		 2022年12月
December 2022
母 Female 15
恩施黑猪
Enshi Black pig		 ES 公 Male 11 湖北省恩施州地大农牧有限责任公司
Hubei Enshi prefecture dida agriculture and animal husbandry Co., Ltd.		 保种场
Conservation farm		 2022年12月
December 2022
母 Female 19
丫杈猪
Yacha pig		 YC 公 Male 7 四川省泸州市古蔺县兰洋生态农业专业合作社
Lanyang ecological agriculture specialized cooperative in Gulin county, Luzhou city, Sichuan		 保种场
Conservation farm		 2022年12月
December 2022
母 Female 23
渠溪猪
Quxi pig		 QX 公 Male 5 重庆市渠溪猪丰都保种场
Chongqing Fengdu conservation farm of Quxi Pig		 保种场
Conservation farm		 2022年12月
December 2022
母 Female 24

Fig. 1

Distribution of SNPs on chromosomes"

Table 2

Genetic diversity parameters analysis of Huchuan Mountain pigs"

有效等位基因数
Effective allele number		 期望杂合度
Expected heterozygosity		 观测杂合度
Observed heterozygosity		 纯合度
Homozygosity		 多态信息含量
Polymorphism information content
罗盘山猪Luopanshan pig 1.405 0.2 440 0.2 295 0.770 0.198
合川黑猪Hechuan Black pig 1.398 0.2 407 0.2 127 0.787 0.196
盆周山地猪Penzhou Mountain pig 1.446 0.2 703 0.2 625 0.737 0.220
恩施黑猪Enshi Black pig 1.467 0.2 834 0.2 830 0.717 0.231
丫杈猪Yacha pig 1.479 0.2 859 0.2 989 0.701 0.231
渠溪猪Quxi pig 1.486 0.2 948 0.3 061 0.694 0.240

Fig. 2

Principal component analysis of Huchuan Mountain pigs"

Fig. 3

Cross-validation error values at different K values"

Fig. 4

Ancestral component analysis of Huchuan Mountain pigs"

Fig. 5

Phylogenetic tree of Huchuan Mountain pigs"

Fig. 6

Gene flow analysis of six groups of Huchuan Mountain pigs A: Genetic drift and introgression network among populations. The x-axis denotes drift parameter, and the color and thickness of lines correspond to migration weight, reflecting the intensity of inter-population gene flow; B: Heatmap of genetic differentiation matrix among six pig populations. The color gradient represents standardized genetic differentiation Z-score (-1.5 SE to 1.5 SE)"

Fig. 7

Identification of candidate selected regions under different conservation models in Huchuan Mountain pigs based on joint analysis of Fst and θπ ratio The x-axis represents the log2θπ ratio) between the population conserved in nature reserves (TWO) and the population conserved in breeding farms (FOUR), while the y-axis indicates the Fst values. Blue dots represent genomic regions under selection in the population conserved under the nature reserve model, and green dots represent those under selection in the population conserved under the breeding farm model. The marginal plots on the top and right show the distribution density and cumulative percentage of log2(θπ ratio) and Fst values, respectively. The selection thresholds are defined as log2(θπ ratio)≤-1.65 or≥1.65, and Fst≥0.12"

Fig. 8

GO enrichment analysis results A: GO enrichment results of candidate selected genes in the population under the nature reserve conservation model; B: GO enrichment results of candidate selected genes in the population under the breeding farm conservation model"

Fig. 9

KEGG enrichment analysis results A: KEGG enrichment results of candidate selected genes in the population under the nature reserve conservation model; B: KEGG enrichment results of candidate selected genes in the population under the breeding"

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