基于简化基因组测序的吐鲁番黑羊遗传结构分析

doi:10.16431/j.cnki.1671-7236.2025.09.020

中国畜牧兽医 ›› 2025, Vol. 52 ›› Issue (9): 4216-4225.doi: 10.16431/j.cnki.1671-7236.2025.09.020

• 遗传繁育 • 上一篇

基于简化基因组测序的吐鲁番黑羊遗传结构分析

罗春彦¹, 白锋¹, 滕文³, 阿米妮古丽·阿不来孜², 玛尔孜娅·亚森², 周喜荣², 纳扎开提·艾尼万尔¹, 买斯吐尔古丽·阿布力提甫³, 张耘滔¹, 纪新民¹, 张艳花²

1. 新疆畜牧科学院畜牧研究所, 农业农村部畜禽资源(羊)评价利用重点实验室, 新疆绒毛用羊遗传育种与繁殖重点实验室, 乌鲁木齐 830026;
2. 托克逊县风城国营牧业有限公司, 吐鲁番 838100;
3. 新疆农业大学动物科学学院, 乌鲁木齐 830052

收稿日期:2024-11-26 发布日期:2025-08-29
通讯作者: 张艳花 E-mail:181103221@qq.com
作者简介:罗春彦，E-mail：871227917@qq.com。
基金资助:
中央引导地方科技发展专项资金：羊遗传资源评价与利用实验平台建设(ZYYD2023B10)；吐鲁番市重点研发专项：吐鲁番黑羊核心群选育体系建立及优质肉产品开发(202316)；新疆自治区产业技术体系(XJARS-09-05)；新疆牧区地方肉羊选育改良计划(XJMQ-1)

Genetic Structure Analysis of Turpan Black Sheep Based on Simplified Genome Sequencing

LUO Chunyan¹, BAI Feng¹, TENG Wen³, AMINIGULI·Abulizi², MAERZIYA·Yasen², ZHOU Xirong², NAZAKAITI·Ainiwaner¹, MAISITUERGULI·Abulitipu³, ZHANG Yuntao¹, JI Xinmin¹, ZHANG Yanhua²

1. Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Sheep), Ministry of Agriculture and Rural Affairs, Xinjiang Key Laboratory of Genetic Breeding and Reproduction of Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830026, China;
2. Fengcheng State-owned Animal Husbandry Co., Ltd., Toksun County, Turpan 838100, China;
3. College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China

Received:2024-11-26 Published:2025-08-29

摘要/Abstract

摘要： 【目的】研究吐鲁番黑羊育种核心群种公羊的群体遗传结构及亲缘关系，探讨吐鲁番黑羊的遗传多样性，评估其群体遗传结构，为制定合理的选种选配方案及吐鲁番黑羊品种保护策略提供数据支持。【方法】利用简化基因组测序技术对128只吐鲁番黑羊公羊单核苷酸多态性(SNP)位点进行检测，通过PLINK 1.90、R 4.4.1软件对吐鲁番黑羊群体遗传多样性及连续纯合片段(ROH)进行计算，利用Mega 10.0软件构建系统进化树，综合评估吐鲁番黑羊的群体遗传结构。【结果】吐鲁番黑羊公羊群体平均观测杂合度为0.16，期望杂合度为0.18，次要等位基因频率为0.23，多态信息含量为0.82。通过主成分分析与系统进化树发现，128只吐鲁番黑羊被分为5个亚群。遗传距离(D值)为0.1626～0.2749，平均遗传距离为0.2635，IBS遗传距离与亲缘关系G矩阵一致，显示吐鲁番黑羊群体内大部分个体间亲缘关系较远。128个吐鲁番黑羊公羊个体共检测到2 239个ROHs，其中，0～5 Mb数量最多，占比为61.37%；基于ROH的平均近交系数为0.04，表明近亲繁殖水平较低。【结论】吐鲁番黑羊育种核心群遗传多样性丰富，大部分个体间亲缘关系较远，群体内近交程度较低，具有较好的遗传资源保护和开发利用的基础。本研究结果可为吐鲁番黑羊核心群制定育种计划及开发利用提供参考依据。

关键词: 吐鲁番黑羊; 群体遗传结构; 亲缘关系; 连续纯合片段

Abstract: 【Objective】 This study was aimed to investigate the population genetic structure and relatedness of breeding rams in the core group of Turpan Black sheep,evaluate their genetic diversity,and provide scientific data support for formulating rational breeding strategies and conservation plans. 【Method】 Single nucleotide polymorphism (SNPs) of 128 Turpan Black sheep rams were detected using simplified genome sequencing technology.Genetic diversity parameters and runs of homozygosity (ROH) were calculated using PLINK 1.90 and R 4.4.1 software.Population structure was analyzed through phylogenetic tree construction with Mega 10.0 software. 【Result】 The average observed heterozygosity (Ho),expected heterozygosity (He) and minor allele frequency (MAF) were 0.16,0.18 and 0.23,respectively,with a polymorphic information content (PIC) of 0.82.The 128 rams were clustered into 5 subpopulations based on principal component analysis (PCA) and phylogenetic analysis.The genetic distance (D-value) ranged from 0.1626 to 0.2749,with an average of 0.2635.The genetic distance and phylogenetic G matrix were consistent,indicating that the majority of individuals within the Turpan Black sheep population had distant phylogenetic relationships.A total of 2 239 ROHs were detected,of which 61.37% were 0-5 Mb in length.The average inbreeding coefficient (F_ROH) was 0.04,suggesting low inbreeding levels. 【Conclusion】 The breeding core group of Turpan Black sheep demonstrated high genetic diversity,with distant kinship among most individuals and low inbreeding levels within the population,indicating a robust foundation for genetic resource conservation and utilization.The results provided a scientific reference for developing breeding programs and sustainable utilization strategies for the Turpan Black sheep core population.

Key words: Turpan Black sheep; population genetic structure; kinship; runs of homozygosity

中图分类号:

S813.3

罗春彦, 白锋, 滕文, 阿米妮古丽·阿不来孜, 玛尔孜娅·亚森, 周喜荣, 纳扎开提·艾尼万尔, 买斯吐尔古丽·阿布力提甫, 张耘滔, 纪新民, 张艳花. 基于简化基因组测序的吐鲁番黑羊遗传结构分析[J]. 中国畜牧兽医, 2025, 52(9): 4216-4225.

LUO Chunyan, BAI Feng, TENG Wen, AMINIGULI·Abulizi, MAERZIYA·Yasen, ZHOU Xirong, NAZAKAITI·Ainiwaner, MAISITUERGULI·Abulitipu, ZHANG Yuntao, JI Xinmin, ZHANG Yanhua. Genetic Structure Analysis of Turpan Black Sheep Based on Simplified Genome Sequencing[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(9): 4216-4225.

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基于简化基因组测序的吐鲁番黑羊遗传结构分析

Genetic Structure Analysis of Turpan Black Sheep Based on Simplified Genome Sequencing

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