Population structure analysis of eight goat breeds based on super-genotyping-by-sequencing

IF 2.7 3区生物学 Q2 GENETICS & HEREDITY

Gene Pub Date : 2026-02-05 Epub Date: 2025-11-10 DOI:10.1016/j.gene.2025.149877

Xiangzhen Gou , Keyan Ma , Junxiang Yang , Ke Wang , Yuqin Ma

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引用次数: 0

Abstract

China harbors rich indigenous goat resources. However, factors such as the introduction of exotic breeds and crossbreeding have led to a decline in local populations and obscured genetic structures. Consequently, it is imperative to conduct genetic diversity and population structure assessments of key indigenous goat populations. This study employed Super-GBS sequencing technology to evaluate genetic diversity and population structure in eight goat breeds (n = 211), and further identified candidate genes associated with production traits and environmental adaptation through selection signature analysis. Ziwuling black goat (ZWL) exhibited the highest diversity, whereas Dazu black goat (DZH) showed the lowest. Pairwise F_ST revealed strong differentiation between DZH and Liaoning cashmere / Inner Mongolia cashmere goat (NMC) (0.1221) due to geographic isolation, but negligible divergence between Ziwuling cashmere (ZWLH) and Hexi cashmere (HXC) (0.0066), indicating gene flow. Population structure resolved three clades: DZH as an independent lineage, Yimeng black goat (YMH) clustering with ZWL, and multiple cashmere subgroups. Runs of homozygosity (ROH) revealed elevated inbreeding in DZH (F_ROH = 0.178) versus lower levels in cashmere breeds (0.071–0.098). Selective sweeps identified 252 genes linked to cashmere traits, including DCN, SEMA3D, FGF5, enriched in TGF-β, MAPK, and circadian rhythm pathways regulating hair follicle cycling. Comparative scans between arid-adapted NMC and subtropical DZH identified 372 genes (e.g., MTOR, ROBO2, PPP3CA) involved in thermogenesis, water reabsorption, and hypoxia response. Together, these findings highlight how artificial selection and environmental adaptation jointly shape goat genomic architecture. Conservation should prioritize populations with declining diversity (e.g., ZWLH, SXC) and implement controlled breeding to reduce inbreeding, thereby safeguarding agro-biodiversity and sustainable utilization.

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基于超基因分型测序的8个山羊品种群体结构分析。

中国拥有丰富的本土山羊资源。然而，外来品种的引进和杂交等因素导致了当地种群的减少和遗传结构的模糊。因此，对主要地方山羊种群进行遗传多样性和种群结构评估势在必行。本研究采用Super-GBS测序技术对8个山羊品种（n = 211）的遗传多样性和群体结构进行了分析，并通过选择特征分析进一步确定了与生产性状和环境适应相关的候选基因。子午岭黑山羊（ZWL）多样性最高，大足黑山羊（DZH）多样性最低。两两FST结果显示，由于地理隔离，DZH与辽宁绒山羊/内蒙绒山羊（NMC）差异较大（0.1221），而子乌岭绒山羊（ZWLH）与河西绒山羊（HXC）差异较小（0.0066），提示基因流动。种群结构划分为三个支系：DZH为独立支系，沂蒙黑山羊（YMH）与ZWL聚类，羊绒亚群多。纯合性分析（ROH）显示，DZH品种近交率升高（FROH = 0.178），而羊绒品种近交率较低（0.071 ~ 0.098）。选择性扫描鉴定出252个与羊绒性状相关的基因，包括DCN、SEMA3D、FGF5、富含TGF-β、MAPK和调节毛囊循环的昼夜节律通路。干旱适应NMC和亚热带DZH的对比扫描鉴定出372个基因（如MTOR、ROBO2、PPP3CA）参与产热、水重吸收和缺氧反应。总之，这些发现强调了人工选择和环境适应如何共同塑造山羊的基因组结构。保护应优先考虑多样性下降的种群（如ZWLH、SXC），并实施控制育种，减少近亲繁殖，从而保护农业生物多样性和可持续利用。

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来源期刊

Gene 生物-遗传学

CiteScore

6.10

自引率

2.90%

发文量

718

审稿时长

42 days

期刊介绍： Gene publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses.