基于全基因组重测序分析西门塔尔牛遗传多样性与群体结构

doi:10.11843/j.issn.0366-6964.2025.03.020

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (3): 1189-1202.doi: 10.11843/j.issn.0366-6964.2025.03.020

基于全基因组重测序分析西门塔尔牛遗传多样性与群体结构

胡鑫¹^,²(), 游伟¹^,², 姜富贵¹^,², 成海建¹^,², 孙志刚³, 宋恩亮¹^,²^,*()

1. 山东省农业科学院畜牧兽医研究所, 山东省畜禽疫病防治与繁育重点实验室, 济南 250100
2. 农业农村部畜禽生物组学重点实验室, 济南 250100
3. 格润富德农牧科技股份有限公司, 烟台 265701

收稿日期:2024-09-26 出版日期:2025-03-23 发布日期:2025-04-02
通讯作者: 宋恩亮 E-mail:huxin19890803@163.com;enliangs@126.com
作者简介:胡鑫(1989-)，女，辽宁盘锦人，助理研究员，博士，主要从事肉牛遗传育种的研究，Tel: 0531-66655139，E-mail: huxin19890803@163.com
基金资助:
泰山产业领军人才工程专项经费；烟台市科技计划项目(2023ZDCX024)；现代农业(肉牛牦牛)产业技术体系(CARS-37)；山东省现代农业产业技术体系牛产业创新团队(SDAIT-09-03)；山东省农业科学院创新工程(CXGC2024F10)

Analysis of Genetic Diversity and Population Structure of Simmental Cattle Based on Whole Genome Resequencing

HU Xin¹^,²(), YOU Wei¹^,², JIANG Fugui¹^,², CHENG Haijian¹^,², SUN Zhigang³, SONG Enliang¹^,²^,*()

1. Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
2. Key Laboratory of Livestock and Poultry Multi-omics of Ministry of Agriculture and Rural Affairs, Jinan 250100, China
3. Green Food Agriculture and Animal Husbandry Technology Co., LTD., Yantai 265701, China

Received:2024-09-26 Online:2025-03-23 Published:2025-04-02
Contact: SONG Enliang E-mail:huxin19890803@163.com;enliangs@126.com

摘要/Abstract

摘要：

旨在对西门塔尔牛群体遗传多样性和遗传结构进行分析，为配种方案和遗传改良提供理论依据。本研究对149头西门塔尔牛的全基因组进行了重测序，并利用这些基因组数据获取的高质量单核苷酸多态性(single-nucleotide polymorphisms, SNPs)位点，对其遗传结构、连续纯合片段(runs of homozygosity, ROH)以及其亲缘关系和家系构建等方面进行了深入的分析。结果显示，149头西门塔尔牛平均测序深度为5×，质控后共鉴定到1 265 356个SNPs位点，平均最小等位基因频率为0.067，平均多态信息含量为0.083，平均观察杂合度为0.121，平均期望杂合度为0.157。亲缘关系G矩阵与状态同源(identical by state, IBS)遗传距离矩阵具有相似的结果，大部分个体间的亲缘关系呈中等水平。在149头西门塔尔牛个体中，共检测到70个基因组ROH，且ROH总长度为127 627.935 kb，其中有98.57%的ROH是长度介于在1~5 Mb之间。基于ROH计算得到的近交系数为0.000 3，提示近亲繁殖程度不高。此外，进化树分析将这149头西门塔尔牛划分成为22个不同的家系分支。综上所述，西门塔尔牛群体表现出相对丰富的多样性和适度的亲缘关系。在少数个体中观察到近亲繁殖，但种群的整体近亲繁殖水平仍然很低。

关键词: 西门塔尔牛, 低密度全基因组重测序, 群体遗传结构, 遗传多样性, 亲缘关系

Abstract:

The aim was to analyze the genetic diversity and genetic structure of Simmental cattle populations to provide a theoretical basis for breeding programs and genetic improvement. In this study, 149 Simmental cattle were subjected to whole genome resequencing, and genetic structure, runs of homozygosity (ROH), and kinship and lineage construction were analyzed based on high-quality single-nucleotide polymorphisms (SNPs) sites obtained from all the genomic data. The results showed that the average sequencing depth of 149 Simmental cattle was 5×, and a total of 1 265 356 SNPs loci were identified after quality control, with an average minimum allele frequency of 0.067, an average polymorphic information content of 0.083, an average observed heterozygosity of 0.121, and an average expected heterozygosity of 0.157. The G matrix of kinship and the IBS distance matrix had similar results, and most individuals had medium level of kinship. A total of 70 genomic ROH were detected in 149 Simmental cattle with a total ROH length of 127 627.935 kb, of which 98.57% were between 1 to 5 Mb in length. The inbreeding coefficient based on ROH was 0.000 3, suggesting a low degree of inbreeding. In addition, evolutionary tree analysis classified these 149 Simmental cattle into 22 different family branches. In summary, the Simmental cattle herd showed relatively rich diversity and moderate relatedness. Inbreeding was observed in a few individuals, but the overall level of inbreeding in the population remained low.

Key words: Simmental cattle, low-density whole genome resequencing, population genetic structure, genetic diversity, kinship

中图分类号:

S823.2

胡鑫, 游伟, 姜富贵, 成海建, 孙志刚, 宋恩亮. 基于全基因组重测序分析西门塔尔牛遗传多样性与群体结构[J]. 畜牧兽医学报, 2025, 56(3): 1189-1202.

HU Xin, YOU Wei, JIANG Fugui, CHENG Haijian, SUN Zhigang, SONG Enliang. Analysis of Genetic Diversity and Population Structure of Simmental Cattle Based on Whole Genome Resequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(3): 1189-1202.

图/表 10

图 1

表 1

图 2

表 2

图 3

图 4

图 5

图 6

图 7

表 3

西门塔尔牛群家系划分结果"

家系名称Family name	性别Gender	个体号Individual number
家系1 Family 1	公	G231964
家系1 Family 1	母	M211829	M211471	M200990
家系2 Family 2	公	3777	G231304	G231485	G231527	G231592	G231847
		G231852	G231884	G231265	G231594	G231914	G231501
		G231582	G231591	G231851	G231866	G231541	G231540
		G231838	G231966	G231915	G231817	G231970	G231492
		G231466	G231640	G231932	G231503	G231590	G231507
		G231885	G231895	G231855	G231443	G231801	G231524
家系2 Family 2	母	M200343	M200592	M180098	210133	M210158	M211330
家系3 Family 3	公	G231161	G231207	G231515	G231566	G231570	G231588
		G231589	G231600	G231615	G231618	G231626	G231638
		G231648
家系3 Family 3	母	M211611	M190268	M190393	M190352	M190366	M190216
		M201391	M211829	M200650	M200990	M200640	M211812
		M200197	M200323	M210123	M201260	M201387
家系4 Family 4	公	G231607	G231809	G231823	G231829	G231840	G231854
		G231874	G231881	G231899	G231902	G231903	G231905
		G231917	G231923	G231933	G231938	G231951	G231954
		G231967	G231969	G231971
家系4 Family 4	母	M211812	M190216	M211772	M211829	M191691	M200197
家系5 Family 5	公	G231924	G231937
家系5 Family 5	母	M200640	M191691	M190352	M190268
家系6 Family 6	公	G231419	G231587	G231932	G231592
家系6 Family 6	母	M200343	M211330	210133	M200686	M210248	M200592
		M210158
家系7 Family 7	公	G231265	G231466	G231492	G231501	G231503	G231582
		G231591	G231817	G231838	G231877	G231884	G231485
		3777	G231558	G231914	G231507	G231439	G231640
		G231544	G231592	G231847	G231852	G231590	G231609
		G231304	G231575	G231895	G231527	G231540	G231467
		G231624	G231851	G231583	G231808	G231541	G231802
		G231601	G231915	G231885
家系7 Family 7	母	M200343	M200197	M180098
家系8 Family 8	公	G231467	G231541	G231624	G231817	G231852	G231808
		G231885	G231527	G231794	G231970	G231838	G231966
		G231802	G231915
家系8 Family 8	母	M200197
家系9 Family 9	公	G231439	G231914	G231866	G231265	G231507	G231800
		G231966	G231592	G231304	G231503	G231885	G231817
		G231871
家系9 Family 9	母	M200343
家系10 Family 10	公	G231575	G231866	G231540	G231884	G231501	G231558
		G231485	G231439
家系10 Family 10	母
家系11 Family 11	公	G231507	G231524	G231855	G231592	G231265	G231439
		G231851	G231914	G231852	G231471	G231847
家系11 Family 11	母	M200592	M200343	M180098
家系12 Family 12	公	G231544	G231594	G231885	G231582	G231808	G231877
		G231265	G231443	G231915	G231592	3777	G231541
		G231852	G231884	G231914	G231601	G231640
家系12 Family 12	母	M200343
家系13 Family 13	公	G231583	G231915	G231941	G231966	G231584	G231838
		G231640	G231802	G231877	G231594	G231884	G231527
		G231624	G231482	G231913	G231439
家系13 Family 13	母
家系14 Family 14	公	G231558	G231265	G231540	G231575	G231617
家系14 Family 14	母	M201164
家系15 Family 15	公	G231471	G231800	G231762	G231507	G231895	G231794
		G231801	G231947	G231439	G231640
家系15 Family 15	母
家系16 Family 16	公	G231584	G231590	G231601	G231895	G231583	G231492
		G231592	G231847	G231970	G231884	G231802	G231885
		G231482	G231800	G231540	G231947	G231501	G231838
家系16 Family 16	母	M200343
家系17 Family 17	公	G231620	G231802	G231640	G231624	G231617	G231601
		G231583	G231877
家系17 Family 17	母	M201164
家系18 Family 18	公	G231640	G231762	G231871	G231970	G231592	G231620
		G231583	G231265	G231800	G231885	G231591	G231471
		G231609	G231914	G231852	G231541	G231590	G231527
家系18 Family 18	母	M200343
家系19 Family 19	公	G231801	G231800	G231852
家系19 Family 19	母
家系20 Family 20	公	G231482	G231540	G231941	G231913	G231601	G231591
		G231527	G231838	G231575	G231558	G231851	G231895
		G231617
家系20 Family 20	母	M201164	M180098
家系21 Family 21	公	G231808	G231913	G231541	G231794	G231877	G231838
		G231544	G231624	G231482	G231966
家系21 Family 21	母
家系22 Family 22	公	G231609	G231617	G231794	G231851	G231871	G231817
		G231492	G231802	G231540	G231558	G231541	G231808
		G231624	G231800	G231838	G231507	G231524	G231304
家系22 Family22	母	M200343	M200592	M201164	M180098
其他Others		M210274	M200695	220235	211609	M210916	M210586
		M210751	M181734	M220118	M211423	M211712	M182050
		M181232	M180517	M180374	M181080	M181429	M191452
		M180020	M200095	M201284

表 3

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质量控制标准Quality control standard	SNPs标记数Number of SNPs
标记总数Total number of SNPs	29 421 284
最小等位基因频率 < 0.01的标记SNPs with MAF < 0.01	8 115 966
哈代-温伯格平衡检验P< 10^-6的标记 SNPs notin Hardy-Weinberg equilibriumP< 10^-6	296 458
SNP检出率 < 0.90 SNPs with call rate <0.90	10 760 983
R²>0.2的标记SNPs with R²>0.2	7 535 078
通过质量控制的SNP数SNPs used after quality control	1 265 356

遗传多样性指标 Indicators of genetic diversity	平均值 Average value
最小等位基因频率MAF	0.067
多态性信息含量PIC	0.083
有效等位基因数Ne	1.138
多态标记比例P_N	0.284
观察杂合度H_O	0.121
期望杂合度H_E	0.157

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基于全基因组重测序分析西门塔尔牛遗传多样性与群体结构

Analysis of Genetic Diversity and Population Structure of Simmental Cattle Based on Whole Genome Resequencing

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