南疆地方绵羊品种群体遗传结构解析与选择信号挖掘

doi:10.11843/j.issn.0366-6964.2025.12.016

摘要/Abstract

摘要： 旨在挖掘绵羊中与优异性状相关基因，对遗传改良与育种实践具有重要价值。本研究以93只策勒黑羊、33只皮山红羊和13只瓦格吉尔羊为对象，进行颈静脉采血、DNA提取、基因分型。用PLINK软件对基因型数据进行质量控制(质控标准为：剔除个体检出率小于90%、SNP检出率小于95%、最小等位基因频率小于5%、哈代温伯格平衡P<1×10^-6的SNPs)和主成分分析(PCA)，构建进化树、群体祖先成分分析和连锁不平衡分析(LD)，同时基于全基因组长纯合片段(runs of homozygosity,ROH)分析和群体遗传分化指数(F_ST)分析，选择前10%的ROH片段作为高频区域和F_ST值的前5%位点作为受选择区域，参考绵羊基因组Oar＿v4.0注释基因并进行GO和KEGG分析。F_ST和F_ROH结果表明，3个群体之间遗传分化水平较低，且在K=4呈现清晰的遗传背景分化。同时识别出 ACVR1、ACVR1C、UPP2、CRY1 和NR4A2 等是南疆地方绵羊品种在干旱沙漠环境中形成遗传适应性的候选基因。本研究通过群体遗传结构多样性和选择信号分析，揭示了南疆地方绵羊品种的遗传变异特征，从多维度的遗传变异视角寻找到相关优异基因，为绵羊种质资源保护、新品种培育及资源多样性提升提供了重要参考依据。

关键词: 南疆地方绵羊, 群体遗传结构, 芯片, ROH分析, F_ST分析

Abstract: The study aimed to identify genes associated with superior traits holding significant value for genetic improvement and practical breeding programmes. This study utilized 93 Qira black sheep, 33 Pishan red sheep, and 13 Waghgir sheep. Blood samples were collected from the jugular vein, followed by DNA extraction and genotyping. Genotype data quality control was performed using PLINK software (quality control standards: excluding individuals with detection rates below 90%, SNP detection rates below 95%, minimum allele frequencies below 5%, and SNPs with P<1×10^-6 for Hardy-Weinberg equilibrium). Principal component analysis (PCA) was conducted to construct evolutionary trees, analyze population ancestral components, and assess linkage disequilibrium (LD). Simultaneously, based on genome-wide runs of homozygosity (ROH) analysis and population genetic differentiation index (F_ST) analysis, the top 10% ROH segments were selected as high-frequency regions, and the top 5% loci by value were designated as selected regions. Reference was made to annotated genes in the sheep genome Oar_v4.0 for Gene Ontology (GO) and KEGG pathway analysis. The F_ST and F_ROH results indicated a low level of genetic differentiation among the 3 groups, with a clear genetic background differentiation emerging at K=4. Concurrently, genes including ACVR1, ACVR1C, UPP2, CRY1, and NR4A2 were identified as candidate genes for genetic adaptation in local sheep breeds of southern Xinjiang within arid desert environments. This study revealed the genetic variation characteristics of local sheep breeds in southern Xinjiang through analysis of population genetic structure diversity and selection signals. It identified relevant superior genes from a multidimensional perspective of genetic variation, providing important reference for sheep germplasm resource conservation, new variety development, and enhancement of resource diversity.

Key words: local sheep breeds in Southern Xinjiang, population genetic structure, chip, ROH analysis, F_ST analysis

中图分类号:

S826.2

孔令锋, 朱丽君, 厉彦浩, 彭玉薇, 寇富民, 李亮, 刘书东. 南疆地方绵羊品种群体遗传结构解析与选择信号挖掘[J]. 畜牧兽医学报, 2025, 56(12): 6116-6129.

KONG Lingfeng, ZHU Lijun, LI Yanhao, PENG Yuwei, KOU Fumin, LI Liang, LIU Shudong. Analysis of the Genetic Structure of Local Sheep Breed Populations in South Xinjiang and Mining of Selection Signals[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(12): 6116-6129.

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