基于重测序数据分析太行山羊种公羊遗传多样性及群体结构

doi:10.16431/j.cnki.1671-7236.2025.10.020

摘要/Abstract

摘要： 【目的】研究旨在通过全基因组重测序(WGS)技术对太行山羊种公羊群体的遗传多样性和群体遗传结构进行深入分析，以期为太行山羊的选育及保种提供科学依据。【方法】选取35只健康无病的成年太行山羊种公羊，采集静脉血样后提取DNA构建测序文库，利用Plink 1.9软件对太行山羊种公羊的单核苷酸多态性(SNP)数据进行质控，计算群体期望杂合度(He)、观测杂合度(Ho)、最小等位基因频率(MAF)及多态信息含量(PIC)等遗传参数，并进行连锁不平衡分析、核苷酸多样性分析、连续性纯合片段(ROH)分析、主成分分析、系统进化树构建以及群体遗传结构分析。【结果】太行山羊种公羊群体最小等位基因频率为0.1889，多态信息含量平均值为0.2760，为中度多态，期望杂合度为0.2764，观测杂合度为0.1929。35只种公羊群体共发现7 499个ROH，其中0～2 Mb的ROH数量最多，平均近交系数为0.0334。PCA和系统进化树分析显示，35只公羊个体分为四大支；群体遗传结构分析显示K=2时有较明显的分层。【结论】太行山羊种公羊群体遗传多样性较高，呈中度多态性，具备选育潜力；群体存在低至中度近交，需在育种中避免近亲交配；群体存在复杂遗传结构，呈明显分层(K=2时最显著)，可划分为多个家系。研究结果为太行山羊的保种策略和选育方向提供了理论依据。

关键词: 太行山羊; 全基因组重测序; 遗传多样性; 群体遗传结构; 家系划分

Abstract: 【Objective】 The aim of this study was to conduct a thorough analysis of the genetic diversity and population genetic structure of Taihang goat ram population through whole genome resequencing (WGS) technology,so as to provide scientific foundations for the breeding and conservation of Taihang goats.【Method】 A total of 35 healthy adult Taihang goat rams without diseases were selected,venous blood samples were collected to extract DNA for constructing a sequencing library,and the single nucleotide polymorphism (SNP) data in Taihang goat rams was subjected to quality control using Plink 1.9 software.The genetic parameters of Taihang goat ram population were calculated,including expected heterozygosity (He),observed heterozygosity (Ho),minor allele frequency (MAF),and polymorphic information content (PIC).Additionally,analysis were performed on linkage disequilibrium,nucleotide diversity,runs of homozygosity (ROH),principal component analysis (PCA),phylogenetic tree construction,and population genetic structure.【Result】 The MAF of Taihang goat ram population was 0.1889,and the average PIC was 0.2760,indicating moderate polymorphism.The He of Taihang goat ram population was 0.2764,and the Ho was 0.1929.A total of 7 499 ROH were identified in 35 rams,with the largest number of ROH ranging from 0 to 2 Mb.The average inbreeding coefficient was 0.0334.PCA and phylogenetic tree analysis revealed that 35 rams were divided into four main clades,while population genetic structure analysis showed distinct stratification when K=2.【Conclusion】 Taihang goat ram population showed relatively high genetic diversity with moderate polymorphism,demonstrating significant potential for breeding improvement.There was low-to-moderate inbreeding in the population,and inbreeding should be avoided in breeding. The population had a complex genetic structure,showing obvious stratification (most significant at K=2),and could be divided into multiple familial lineages.The results provided a theoretical basis for conservation strategies and breeding directions of Taihang goats.

Key words: Taihang goats; whole genome resequencing; genetic diversity; population genetic structure; pedigree assignment

中图分类号:

S827

姚书海, 熊金珂, 杨培福, 朱硕, 孙歆恬, 尚明玉, 鲍晶晶, 黄举鹏, 孙敬华, 张莉. 基于重测序数据分析太行山羊种公羊遗传多样性及群体结构[J]. 中国畜牧兽医, 2025, 52(10): 4742-4753.

YAO Shuhai, XIONG Jinke, YANG Peifu, ZHU Shuo, SUN Xintian, SHANG Mingyu, BAO Jingjing, HUANG Jupeng, SUN Jinghua, ZHANG Li. Genetic Diversity and Population Structure of Taihang Goat Rams Revealed by Whole Genome Resequencing[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(10): 4742-4753.

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