中国西南地区4个山羊品种产仔数性状全基因组关联分析

doi:10.13560/j.cnki.biotech.bull.1985.2025-0982

摘要/Abstract

摘要：

目的产仔数是山羊最重要的经济性状之一。挖掘与山羊产仔数性状显著关联的遗传变异位点及相关候选基因。方法以酉州乌羊、大足黑山羊、川中黑山羊、黔北麻羊4个西南地区山羊品种为研究对象，收集保种场历史产羔记录，采集高产母羊60个和低产母羊54个血液样品，进行平均测序深度为27.10×的全基因组重测序。利用群体遗传分化指数（Fst）和全基因组关联分析（GWAS）的方法挖掘与目的性状强关联位点，通过基因注释、GO和KEGG富集分析、单倍型分析，确定最有可能的候选基因。结果共鉴定到65个候选SNP位点，分布在2号、4号和X染色体上的4个Fst显著选择区域内，预测5个与产仔数性状有关的候选基因，其中COL4A5和COL4A6基因显著富集到ECM-受体相互作用、PI3K-Akt等信号通路，注释到COL4A6基因和ETV1基因上的显著变异位点各自构成一个单倍型块，且Hape1均与其他单倍型的产仔数差异极显著（P<0.01）。结论检测到多个与产仔数性状显著关联的SNP位点，筛选出COL4A5、COL4A6、ETV1、SP3和PLS3等基因可能是影响山羊产仔数性状的候选基因，为西南地区山羊高繁殖力遗传改良和品种选育提供了新的视角。

关键词: 全基因组关联分析, 产仔数性状, 山羊, 群体遗传分化指数, 全基因组重测序

Abstract:

Objective Litter size is one of the most important economic traits in goats. This study aimed to identify genetic variants and candidate genes significantly associated with goat litter size. Method Four goat breeds from southwestern China (Youzhou Dark goats, Dazu Black goats, Chuanzhong Black goats, and Qianbei Ma goats) were used as experimental subjects. Historical lambing records from conservation farms were collected, and blood samples from 60 high-yielding and 54 low-yielding ewes were subjected to whole-genome resequencing at an average depth of 27.10×. Population genetic differentiation index (Fst) and genome-wide association study (GWAS) methods were employed to identify loci strongly associated with the target trait. The most likely candidate genes were identified through gene annotation, haplotype analysis, and GO and KEGG enrichment analyses. Result A total of 65 candidate SNPs were identified, distributed within four Fst-significant selective sweep regions on chromosome 2, 4, and X. Five candidate genes potentially associated with the litter size trait were predicted. Among them, the COL4A5 and COL4A6 genes were significantly enriched in signaling pathways such as the ECM-receptor interaction and PI3K-Akt. The significant variant sites annotated to the COL4A6 and ETV1 genes each formed a haplotype block. Furthermore, Hap1 showed highly significant differences in litter size compared to other haplotypes (P<0.01). Conclusion Multiple variant loci significantly associated with litter size traits were detected. Genes such as COL4A5, COL4A6, ETV1, SP3, and PLS3 were identified as potential candidate genes influencing goat litter size traits, which may provide new perspectives for the genetic improvement and selective breeding of high-fertility goats in southwestern China.

Key words: genome-wide association study (GWAS), litter size trait, goats, population genetic differentiation index (Fst), whole-genome resequencing

蒋婧, 吕士鹏, 陈浩林, 熊婷, 孙晓燕, 李杰, 陈灿灿, 王高富, 任航行. 中国西南地区4个山羊品种产仔数性状全基因组关联分析[J]. 生物技术通报, 2026, 42(7): 341-350.

JIANG Jing, LYU Shi-peng, CHEN Hao-lin, XIONG Ting, SUN Xiao-yan, LI Jie, CHEN Can-can, WANG Gao-fu, REN Hang-xing. Genome-Wide Association Analysis of Litter Size Trait in Four Goat Breeds in Southwest China[J]. Biotechnology Bulletin, 2026, 42(7): 341-350.

图/表 7

表1 高产仔数组和低产仔数组产仔数性状描述统计

Table 1 Descriptive statistics of litter size traits in high and low litter size groups

分组

Grouping

样本量

Sample size

最大值

Max

最小值

Min

平均值

Mean

标准差

Standard deviation

变异系数

CV （%）

高产组 High litter size group

低产组 Low litter size group

图1 群体分析结果A：SNPs在各染色体上的密度图，B：群体主成分分析图，C：群体LD衰减图，D：亲缘关系矩阵热图

Fig. 1 Results of the population analysisA: Distribution density of SNPs on each chromosome. B: PCA of populations. C: LD attenuation diagram of populations. D: Kinship matrix heatmap

图2 群体遗传分化指数和全基因组关联分析曼哈顿图及QQ图A：群体遗传分化指数Fst曼哈顿图，B：全基因组关联分析曼哈顿图，C：全基因组关联分析QQ图

Fig. 2 Manhattan plots of population genetic differentiation index (Fst) and GWAS, along with the GWAS Q-Q plotA: Manhattan plot of population genetic differentiation index (Fst). B: Manhattan plot of genome-wide association study (GWAS). C: Q-Q plot of GWAS

表2 山羊产仔数性状Fst和GWAS分析结果

Table 2 Fst and GWAS analysis results of litter size traits in goats

染色体 Chromosome	Fst显著选择区域 Fst significant selection regions	平均Fst值 Average Fst value	显著关联的变异位点数量 Number of significantly associated variant sites	相对基因位置 Location relative to gene	区域内基因 Genes in the region
2	chr2：113 280 001-113 460 000	0.04	36	Downstream	SP3
4	chr4：98 210 001-98 430 000	0.05	5	Upstream， Intron	ETV1
X	chrX：26 050 001-26 470 000	0.08	2	Upstream	PLS3
X	chrX：34 890 001-35 350 000	0.07	24	Upstream， Intron	COL4A5、COL4A6

图3 候选基因GO富集分析柱状图

Fig. 3 Bar plot of GO and KEGG enrichment analysis for candidate genes

图4 候选基因KEGG富集分析气泡图

Fig. 4 Bubble plot of KEGG enrichment analysis of the candidate genes

图5 ETV1和COL4A6基因的单倍型显著性分析A：注释到ETV1基因上的5个显著SNP的单倍型图；B：注释到ETV1基因上的主要单倍型小提琴图；C：注释到COL4A6基因上的24个显著位点的单倍型图；D：注释到COL4A6基因上的主要单倍型小提琴图

Fig. 5 Haplotype-based association analysis of ETV1 and COL4A6 genesA: Haplotype block diagram of 5 significant SNPs annotated to the ETV1 gene. B: Violin plot of the major haplotypes annotated to the ETV1 gene. C: Haplotype block diagram of 24 significant loci annotated to the COL4A6 gene. D: Violin plot of the major haplotypes annotated to the COL4A6 gene

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