基于全基因组SNP位点的晋南牛群体遗传结构分析与分子选配

doi:10.19543/j.cnki.1673-4556.20260602.007

中国畜禽种业 ›› 2026, Vol. 22 ›› Issue (6): 72-80.doi: 10.19543/j.cnki.1673-4556.20260602.007cstr: 32418.14.j.cnki.1673-4556.20260602.007

基于全基因组SNP位点的晋南牛群体遗传结构分析与分子选配

任端阳(), 李文霞, 王馨培, 王曦()

山西农业大学生态农牧研究所，山西朔州 036002

收稿日期:2026-02-26 出版日期:2026-06-26 发布日期:2026-07-06
通讯作者: 王曦 E-mail:ren457842071@163.com;wxphilip@aliyun.com
作者简介:任端阳（1990—），男，博士，研究方向：分子及数量遗传学，E-mail：ren457842071@163.com。
基金资助:
山西省现代农业产业技术体系建设项目(2025CYJSTX13-04);山西省重点研发计划项目(202402140601005);山西省科技重大专项计划揭榜挂帅项目课题(202201140601026-1);山西农业大学生物育种工程项目(YZGC131);山西畜禽遗传基因库项目子课题(2022xczx16-3);山西省博士毕业生、博士后研究人员来晋工作奖励经费科研项目(SXBYKY2024003);山西省博士毕业生、博士后研究人员来晋工作奖励经费科研项目(SXBYKY2024110);山西农业大学“引进人才科研启动工程”项目(2024BQ05);山西农业大学“引进人才科研启动工程”项目(2024BQ32)

Population genetic structure analysis and molecular mating of Jinnan cattle based on genome-wide SNP loci

Duanyang Ren(), Wenxia Li, Xinpei Wang, Xi Wang()

Institute of Ecological Agriculture and Animal Husbandry, Shanxi Agricultural University, Shuozhou, 036002, Shanxi

Received:2026-02-26 Online:2026-06-26 Published:2026-07-06
Contact: Xi Wang E-mail:ren457842071@163.com;wxphilip@aliyun.com

摘要/Abstract

摘要：

目的本研究旨在分析晋南牛保种群的遗传多样性与群体遗传结构，评估其个体间的基因组亲缘关系并进行分子选配，从而更好地保护与利用晋南牛遗传资源。方法试验使用牛20 K单核苷酸多态性（Single nucleotide polymorphism，SNP）芯片对161头晋南牛（46头公牛，115头母牛）进行基因分型，分型结果经质控后用于保种群遗传多样性、群体遗传结构分析及个体间基因组亲缘关系计算，优化公牛遗传贡献以最小化下一代的近交系数，同时维持群体遗传多样性。结果结果表明：质控后保留17070个SNP位点，个体平均观测杂合度为0.387，平均期望杂合度为0.386，SNP多态信息含量均值为0.305。纯合性片段检测共发现1907个ROH片段，平均长度为7.754 Mb，个体平均携带12.973个ROH片段，基于ROH计算的近交系数均值为0.060。依据家系进化树，该晋南牛群体可清晰划分为8个以上家系。该群体遗传多样性为0.888。基于全基因组SNP位点构建关系矩阵，个体间亲缘关系为-0.107～0.521，而将SNP位点划分为单倍型片段构建关系矩阵，个体间的亲缘关系为0～0.269，均值为0.112。通过优化公牛的遗传贡献最小化下一代的近交系数，前10头公牛的遗传贡献占全部公牛遗传贡献的57.639%。结论综上，晋南牛保种群遗传多样性丰富、近交水平较低；基于单倍型计算的亲缘关系，可为晋南牛科学选配及保种利用提供参考。

关键词: 晋南牛, 全基因组SNP芯片, 遗传多样性, 群体遗传结构, 分子选配

Abstract:

Objective This study aims to analyze the genetic diversity and population genetic structure of the conservation population of Jinnan cattle, evaluate genomic relationships among individuals, and conduct molecular mating, thereby better protecting and utilizing the genetic resources of Jinnan cattle. Method A total of 161 Jinnan cattle (46 bulls and 115 cows) were genotyped using the bovine 20 K single nucleotide polymorphism (SNP) chip. After quality control, the genotypic data were used to analyze genetic diversity, population genetic structure, and calculate genomic relationships. Genetic contributions of bulls were optimized to minimize inbreeding coefficients in the next generation while maintaining population genetic diversity. Result The results showed that after quality control, 17070 SNP loci were retained. The average observed heterozygosity of the individuals was 0.387, the average expected heterozygosity was 0.386, and the mean SNP polymorphism information content was 0.305. A total of 1,907 runs of homozygosity (ROH) were detected, with an average length of 7.754 Mb and an average of 12.973 ROH segments per individual. The average inbreeding coefficient based on ROH was 0.060. According to the family evolutionary tree, this Jinnan cattle population can be clearly divided into more than 8 families. The genetic diversity of this population is 0.888. Based on the relationship matrix constructed by whole-genome SNP loci, the genetic relationship between individuals ranges from -0.107 to 0.521.When SNPs were divided into haplotype blocks to build the relationship matrix, pairwise relationships ranged from 0 to 0.269 with a mean of 0.112. By optimizing bull genetic contributions to minimize next-generation inbreeding, the top 10 bulls accounted for 57.639% of the total genetic contribution. Conclusion In summary, the conservation population of Jinnan cattle has abundant genetic diversity and low inbreeding level. The kinship estimated based on haplotypes can provide a theoretical basis for scientific mating and conservation utilization of Jinnan cattle.

Key words: Jinnan cattle, Whole genome SNP chip, Genetic diversity, Population genetic structure, Molecular mating

中图分类号:

S823

任端阳, 李文霞, 王馨培, 王曦. 基于全基因组SNP位点的晋南牛群体遗传结构分析与分子选配[J]. 中国畜禽种业, 2026, 22(6): 72-80.

Duanyang Ren, Wenxia Li, Xinpei Wang, Xi Wang. Population genetic structure analysis and molecular mating of Jinnan cattle based on genome-wide SNP loci[J]. Chinese Livestock and Poultry Breeding, 2026, 22(6): 72-80.

图/表 8

图1

图2

图3

图4

图5

图6

图7

图8

参考文献 29

[1]	蒋洪茂. 我国黄牛肉用性能研究报告(下)[J]. 黄牛杂志, 1996, 22(4): 28-31.
	JIANG H M. Research report on the performance of Chinese yellow beef (Ⅱ)[J]. China Cattle Science, 1996, 22(4): 28-31.
[2]	呙明鹏, 孟源, 王宏浩, 等. 晋南牛不同生长阶段体重和体尺性状遗传参数估计[J]. 畜牧兽医学报, 2023, 54(4): 1452-1464.
	GUO M P, MENG Y, WANG H H, et al. Estimation of genetic parameters of body weight and body size traits in Jinnan cattle at different growth stages[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1452-1464.
[3]	钟梓奇, 谢鑫峰, 王子轶, 等. 分子标记在畜禽保种中应用的研究进展[J]. 中国畜禽种业, 2024, 20(3): 3-10.
	ZHONG Z Q, XIE X F, WANG Z Y, et al. Research progress on application of molecular markers in livestock and poultry conservation[J]. The Chinese Livestock and Poultry Breeding, 2024, 20(3): 3-10.
[4]	王曦, 张元庆, 贺东昌, 等. 晋南牛与部分地方黄牛之间遗传多样性分析[J]. 畜牧兽医学报, 2015, 46(6): 911-923.
	WANG X, ZHANG Y Q, HE D C, et al. Analyses of genetic diversity among Jinnan cattle and three other Chinese indigenous cattle breeds[J]. Acta Veterinaria et Zootechnica Sinica, 2015, 46(6): 911-923.
[5]	艾尼卡尔·艾尔肯, 马凯伦, 王丹, 等. 新疆褐牛体型性状基因组育种值与表型值相关性案例分析[J]. 中国畜牧杂志 2026:1-12.
	AINIKAER·A E K, MA K L, WANG D,et al. Correlation analysis between genomic estimated breeding values and phenotypic values of body conformation traits in Xinjiang brown cattle[J]. Chinese Journal of Animal Science, 2026: 1-12.
[6]	尚燕燕. 基于基因组信息制定新疆褐牛选配方案[D]. 乌鲁木齐: 新疆农业大学, 2025.
	SHANG Y Y. Developing a Mating Scheme for Xinjiang Brown Cattle Based on Genomic Information[D]. Urumqi: Xinjiang Agricultural University, 2025.
[7]	刘晨龙, 卢丹, 周泉勇, 等. 利用高密度SNP芯片分析杭猪的群体遗传结构[J]. 畜牧兽医学报, 2022, 53(8): 2502-2513.
	LIU C L, LU D, ZHOU Q Y, et al. Analysis of population genetic structure of Hang pigs by high density SNP chip[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2502-2513.
[8]	阳文攀, 黄畅, 李细林, 等. 东乡花猪遗传多样性与分子选配分析[J]. 中国畜牧杂志, 2025, 61(8): 124-129.
	YANG W P, HUANG C, LI X L, et al. Genetic Diversity and Molecular Mating Analysis of Dongxiang Spotted Pigs [J]. Chinese Journal of Animal Science, 2025, 61(8): 124-129.
[9]	范广轩, 王天骄, 董依萌, 等. 基于SNP位点的吉林梅花鹿分子系谱构建及群体遗传结构分析[J]. 畜牧兽医学报, 2024, 55(9): 3925-3935.
	FAN G X, WANG T J, DONG Y M, et al. Molecular genealogy construction and population genetic structure analysis of Jilin Sika deer based on SNP loci[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(9): 3925-3935.
[10]	马龙刚, 刘楠, 尼玛群宗, 等. 基于SNP芯片信息分析西藏四个本地牛种的血统组成[J]. 畜牧兽医学报, 2024, 55(10): 4377-4390.
	MA L G, LIU N, NI M, et al. Study on the genetic composition of four local Tibetan cattle breeds based on SNP chip analysis[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(10): 4377-4390.
[11]	蔡保, 郭宪. 中国黄牛全基因组测序研究进展[J]. 中国畜禽种业, 2024, 20(10): 17-30.
	CAI B, GUO X. Research progress on whole genome sequencing of Chinese cattle[J]. The Chinese Livestock and Poultry Breeding, 2024, 20(10): 17-30.
[12]	童雄, 罗威, 闵力, 等. 基于全基因组SNPs分析陆丰黄牛和雷琼牛的群体结构与遗传多样性特征[J]. 中国农业科学, 2023, 56(14):2798–2811.
	TONG X, LUO W, MIN L, et al. Population structure and genetic diversity of Lufeng cattle and Leiqiong cattle based on genome-wide SNPs[J]. Scientia Agricultura Sinica, 2023,56(14):2798-2811.
[13]	刘爽. 基于基因组测序解析固原黄牛关键性状的遗传特征[D]. 银川: 宁夏大学, 2025.
	LIU S. Genetic characterization of key traits in Guyuan cattle based on genome sequencing[D]. Yinchuan: Ningxia University, 2025.
[14]	李倩, 金海, 张刘, 等. 平凉红牛和西门塔尔牛基因组选择特征分析[J/OL]. 中国畜牧兽医, 2026: 1-12. (2026-04-23). .
	LI Q, JIN H, ZHANG L, et al. Genomic selection signal characteristics analysis of Pingliang red and Simmental cattle[J/OL]. China Animal Husbandry & Veterinary Medicine, 2026: 1-12. (2026-04-23). .
[15]	王宏浩, 任小康, 张毅, 等. 基因芯片技术在晋南牛种公牛选育中的应用[J]. 畜牧兽医学报 2021, 52(10):2803-2813.
	WANG H H, REN X K, ZHANG Y, et al. Application of gene chip technology in Jinnan bull breeding[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(10):2803-2813.
[16]	戎艳花, 贾雪纯, 李鹏飞, 等. 晋南牛遗传结构特征及选择信号分析[J]. 中国畜牧兽医, 2024, 51(1):160–171.
	RONG Y H, JIA X C, LI P F, et al. Analysis of genetic structure characteristics and selection signal in Jinnan cattle[J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(1): 160-171.
[17]	PURCELL S, NEALE B, TODD-BROWN K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses[J]. American Journal of Human Genetics, 2007, 81(3): 559-575.
[18]	PARADIS E, SCHLIEP K. Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R[J]. Bioinformatics, 2019, 35(3): 526-528.
[19]	YANG J, LEE S H, GODDARD M E, et al. GCTA: a tool for genome-wide complex trait analysis[J]. American Journal of Human Genetics, 2011, 88(1): 76-82.
[20]	YANG J, BENYAMIN B, MCEVOY B P, et al. Common SNPs explain a large proportion of the heritability for human height[J]. Nature Genetics, 2010, 42(7): 565-569.
[21]	WELLMANN R. Optimum contribution selection for animal breeding and conservation: the R package optiSel[J]. BMC Bioinformatics, 2019, 20(1): 25.
[22]	CENDRON F, LEDESMA-RODRÍGUEZ A, MASTRANGELO S, et al. Genome-wide analysis of the Siboney de Cuba cattle breed: genetic characterization and framing with cattle breeds worldwide[J]. Frontiers in Genetics, 2024, 15: 1302580.
[23]	马钧, 樊安平, 王武生, 等. 全基因组重测序解析秦川牛保种群遗传多样性和遗传结构[J]. 遗传, 2023, 45(7): 602-616.
	MA J, FAN A P, WANG W S, et al. Analysis of genetic diversity and genetic structure of Qinchuan cattle conservation population using whole-genome resequencing[J]. Hereditas, 2023, 45(7): 602-616.
[24]	刘思宇, 张曼, 张岩, 等. 基于重测序数据评估南阳牛保种效果[J]. 畜牧兽医学报, 2024, 55(9): 3876-3886.
	LIU S Y, ZHANG M, ZHANG Y, et al. Evaluation of the conservation effect in Nanyang cattle based on resequencing data[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(9): 3876-3886.
[25]	张岩, 魏稚彤, 虎业浩, 等. 基于全基因组重测序评估郏县红牛保种群遗传多样性与群体结构[J]. 中国畜牧兽医, 2024, 51(7): 2933-2942.
	ZHANG Y, WEI Z T, HU Y H, et al. Genetic diversity and population structure analysis of Jiaxian red cattle based on whole genome sequencing[J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(7): 2933-2942.
[26]	PURFIELD D C, BERRY D P, MCPARLAND S, et al. Runs of homozygosity and population history in cattle[J]. BMC Genetics, 2012, 13: 70.
[27]	WANG J. Marker-based estimates of relatedness and inbreeding coefficients: an assessment of current methods[J]. Journal of Evolutionary Biology, 2014, 27(3): 518-530.
[28]	Do C, Waples R S, Peel D, et al.NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data[J]. Molecular Ecology Resources, 2014, 14(1):209-214
[29]	刘贤, 茹宝瑞, 李志明, 等. 南阳牛和郏县红牛群体威胁程度评价及保护利用途径[J]. 家畜生态学报, 2022, 43(9): 93-96.
	LIU X, RU B R, LI Z M, et al. Evaluation of Threatened Degree of Nanyang Cattle and Jiaxian Red Cattle Populations and Strategies for Protection and Utilization[J]. Acta Ecologiae Animalis Domastici, 2022, 43(9): 93-96.

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

基于全基因组SNP位点的晋南牛群体遗传结构分析与分子选配

Population genetic structure analysis and molecular mating of Jinnan cattle based on genome-wide SNP loci

RichHTML

PDF (PC)

摘要/Abstract

引用本文

使用本文

图/表 8

参考文献 29

相关文章 4

Metrics

本文评价

推荐阅读 0

[1]	王宏浩, 王曦, 车雷杰, 吕怀信, 闫琪, 明仕清. 晋南牛的保种、选育与利用[J]. 中国畜禽种业, 2023, 19(7): 97-101.
[2]	李苗, 张岱阳, 王泽昭, 车雷杰, 张晓贝, 葛菲, 陈燕. 晋南牛的生长性能、屠宰性能及肉品质测定分析[J]. 中国畜禽种业, 2023, 19(7): 29-36.
[3]	巴桑旺堆, 平措占堆, 鲜莉莉, 洛桑顿珠, 王登云, 俄广鑫, 张强. 查吾拉牦牛遗传资源概况与保护利用现状[J]. 中国畜禽种业, 2023, 19(6): 4-9.
[4]	武师良, 王昱彤, 党婉怡, 韩迪, 王占红, 张晓鹰, 杨秋凤, 豆兴堂, 张立斌, 张树义, 尚嵩洋, 邹丽娜, 赵艳娇, 张庆治, 方坤. 基于SSR分子标记的辽西地区驴群体遗传多样性分析[J]. 中国畜禽种业, 2023, 19(5): 27-31.