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

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (12): 6116-6129.doi: 10.11843/j.issn.0366-6964.2025.12.016

南疆地方绵羊品种群体遗传结构解析与选择信号挖掘

孔令锋¹^,²(), 朱丽君¹^,², 厉彦浩¹^,², 彭玉薇¹^,², 寇富民¹^,², 李亮³^,*(), 刘书东¹^,²^,*()

1. 塔里木大学动物科学与技术学院, 新疆生产建设兵团塔里木畜牧科技重点实验室, 阿拉尔 843300
2. 农业农村部环塔里木畜草资源利用重点实验室, 阿拉尔 843300
3. 新疆维吾尔自治区畜牧总站, 乌鲁木齐 830004

收稿日期:2025-05-06 出版日期:2025-12-23 发布日期:2025-12-24
通讯作者: 李亮,刘书东 E-mail:1027223848@qq.com;285247786@qq.com;liushudong63@126.com
作者简介:孔令锋(2001-)，男，河南邓州人，硕士生，主要从事动物遗传与育种研究，E-mail: 1027223848@qq.com
基金资助:
中央引导地方发展基金项目(ZYYD2025CG13)；新疆维吾尔自治区重大科技专项项目(2024A02004-4-4)；羊精液低温长效保存关键技术创新与产业化应用(ZYYD2025CG13)；自治区牧区地方肉羊品种选育推广技术体系(MQTX-11)

Analysis of the Genetic Structure of Local Sheep Breed Populations in South Xinjiang and Mining of Selection Signals

KONG Lingfeng¹^,²(), ZHU Lijun¹^,², LI Yanhao¹^,², PENG Yuwei¹^,², KOU Fumin¹^,², LI Liang³^,*(), LIU Shudong¹^,²^,*()

1. Key Laboratory of Animal Husbandry Science and Technology, Tarim, Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Aral 843300, China
2. Key Laboratory of Circum-Tarim Livestock and Grass Resources Utilization of Ministry of Agriculture and Rural Affairs, Aral 843300, China
3. Xinjiang Uygur Autonomous Region General Animal Husbandry Station, Urumqi 830004, China

Received:2025-05-06 Online:2025-12-23 Published:2025-12-24
Contact: LI Liang, LIU Shudong E-mail:1027223848@qq.com;285247786@qq.com;liushudong63@126.com

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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染色体 Chromosome	位点 SNP	开始位置/bp Start	结束位置/bp End	基因 Gene	功能 Functionality
2	150 789 074	150 771 782	150 827 796	ACVR1	细胞分化、增殖和发育
2	151 043 304	151 006 414	151 059 864	ACVR1C	细胞生长、分化和凋亡
2	150 464 151	150 448 681	150 488 062	UPP2	核酸(DNA和RNA)的合成与代谢
3	175 354 733	175 346 824	175 432 659	CRY1	昼夜节律调控，控制生物钟
2	151 987 092	152 145 600	152 150 521	NR4A2	神经系统发育和功能的基因表达
22	10 457 354	10 440 163	10 458 396	FAS	参与程序性细胞死亡，维持免疫系统平衡
13	77 752 092	77 752 054	77 755 968	CEBPB	免疫和炎症反应，细胞分化与增殖
6	70 220 482	70 189 729	70 234 609	KIT	造血干细胞和生殖细胞发育
1	197 830 345	197 828 371	197 840 091	BCL6	调控B细胞发育和免疫反应
6	64 562 045	645 513 65	64 633 399	GABRG1	参与脑内抑制性神经传递
13	52 472 749	52 472 620	52 474 694	PDYN	疼痛调制、应激反应相关
8	34 948 004	34 947 842	35 404 386	GRIK2	神经系统功能相关
6	69 765 215	69 735 815	69 771 929	PDGFRA	细胞生长、分裂，胚胎发育和组织修复相关
15	4 102 698	3 849 041	4 129 967	PDGFD	细胞生长和血管生成
13	35 117 601	35 117 185	35 118 653	BAMBI	细胞生长分化、发育相关
6	70 601 487	70 562 534	70 607 422	KDR	血管生成、发育

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南疆地方绵羊品种群体遗传结构解析与选择信号挖掘

Analysis of the Genetic Structure of Local Sheep Breed Populations in South Xinjiang and Mining of Selection Signals

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