整合结构变异的奶山羊体尺全基因组关联分析

doi:10.16288/j.yczz.25-293

遗传 ›› 2026, Vol. 48 ›› Issue (4): 393-406.doi: 10.16288/j.yczz.25-293

整合结构变异的奶山羊体尺全基因组关联分析

冯衍帅(), 李嘉鑫, 赵炯尧, 曹家乐, 王兴权, 姚晓婷, 傅家琪, 王喜宏()

西北农林科技大学动物科技学院，杨凌 712100

收稿日期:2025-11-06 修回日期:2026-01-14 出版日期:2026-04-20 发布日期:2026-02-05
通讯作者: 王喜宏，博士，副教授，研究方向：动物遗传育种与繁殖。E-mail: rebecca_830410@163.com
作者简介:冯衍帅，本科生，专业方向：动物遗传资源与育种。E-mail: fengyanshuai6@nwafu.edu.cn
基金资助:
国家自然科学基金项目(3257200948);国家自然科学基金项目(U23A20228);新疆维吾尔自治区重大科技专项(2024A02004-2)

Genome-wide association study of body size traits in dairy goats integrating structural variants

Yanshuai Feng(), Jiaxin Li, Jiongyao Zhao, Jiale Cao, Xingquan Wang, Xiaoting Yao, Jiaqi Fu, Xihong Wang()

College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China

Received:2025-11-06 Revised:2026-01-14 Published:2026-04-20 Online:2026-02-05
Supported by:
National Natural Science Foundation of China(3257200948);National Natural Science Foundation of China(U23A20228);Major Science and Technology Special Project of Xinjiang Uygur Autonomous Region(2024A02004-2)

摘要/Abstract

摘要：

体尺性状作为衡量体型与生长水平的重要表型特征，与生产性能密切相关。为揭示萨能奶山羊体尺性状的遗传基础并发掘潜在分子标记，本研究基于635只萨能奶山羊的低深度全基因组测序数据，依托本课题组构建的山羊参考面板进行基因型填充后，共获得14M的单核苷酸多态位点(single nucleotide polymorphism，SNP)和45K的结构变异(structural variant，SV)。本研究利用SNP估计遗传参数，分别对SNP与SV开展单性状(single-trait，ST)和多性状全基因组关联分析(multi-trait genome-wide association study，MT-GWAS)。结果显示，体高、体长和十字部高3个性状均为中等遗传力，性状间的遗传与表型均为正相关。ST-GWAS共鉴定出56个显著SNP位点和3个显著SV位点，注释到TNFSF11、HDAC4、MURC等30个候选基因；MT-GWAS检测出ST-GWAS未发现的2个显著SNP位点和2个显著SV位点，注释后新增4个候选基因(S100A11、LOC108635595、GALNTL6和FSIP2)。值得注意的是，在第10号染色体的NRXN3附近发现了体长与十字部高的重叠关联信号，共定位分析支持该区域存在共享因果变异。KEGG富集分析显示候选基因主要富集于脂肪酸生物合成及相关代谢通路。本研究表明，整合SV的MT-GWAS可提供SNP之外的关联信号，为开展分子标记辅助选择与体型精准选育提供了理论基础。

关键词: 萨能奶山羊, 体尺性状, 结构变异, 多性状全基因组关联分析, 共定位分析

Abstract:

Body size traits serve as crucial phenotypic indicators of body conformation and growth, showing a close correlation with production performance. To elucidate the genetic basis of these traits and identify potential molecular markers in Saanen dairy goats, we analyzed low-coverage whole-genome sequencing (lcWGS) data from 635 individuals. Following genotype imputation based on an in-house goat reference panel, we obtained 14 million single-nucleotide polymorphisms (SNPs) and 45 thousand structural variants (SVs). Genetic parameters were estimated using SNP data. Subsequently, single-trait (ST) and multi-trait genome-wide association studies (MT-GWAS) were conducted using both SNP and SV datasets. Results indicated that body height, body length, and rump height possess moderate heritability, with positive genetic and phenotypic correlations observed among these traits. ST-GWAS identified 56 significant SNPs and 3 significant SVs, mapping to 30 candidate genes, including TNFSF11, HDAC4, and MURC. Furthermore, MT-GWAS detected 2 significant SNPs and 2 significant SVs missed by ST-GWAS, identifying 4 additional candidate genes (S100A11, LOC108635595, GALNTL6, and FSIP2). Notably, overlapping association signals for body length and rump height were observed near NRXN3 on chromosome 10, with colocalization analysis supporting the existence of a shared causal variant in this region. KEGG enrichment analysis indicated that candidate genes were primarily enriched in fatty acid biosynthesis and related metabolic pathways. In conclusion, this study shows that integrating structural variants into MT-GWAS can reveal association signals beyond those captured by SNPs, providing a theoretical basis for marker-assisted selection and precision breeding for body conformation.

Key words: Saanen dairy goat, body size traits, structural variation, multi-trait genome-wide association study, colocalization analysis

冯衍帅, 李嘉鑫, 赵炯尧, 曹家乐, 王兴权, 姚晓婷, 傅家琪, 王喜宏. 整合结构变异的奶山羊体尺全基因组关联分析[J]. 遗传, 2026, 48(4): 393-406.

Yanshuai Feng, Jiaxin Li, Jiongyao Zhao, Jiale Cao, Xingquan Wang, Xiaoting Yao, Jiaqi Fu, Xihong Wang. Genome-wide association study of body size traits in dairy goats integrating structural variants[J]. Hereditas(Beijing), 2026, 48(4): 393-406.

图/表 13

表1

图1

表2

图2

表3

与体尺单性状GWAS显著相关的SNP位点及其候选基因"

性状	SNP位点	P值	功能注释	候选基因
体长	Chr4:75794056	4.33×10^-7	基因间区	PMPCB(dist=8,193), NAPEPLD(dist=30,201)
	Chr5:10779060	8.22×10^-7	内含子区	PPFIA2
	Chr5:11047790	3.09×10^-7	内含子区	PPFIA2
	Chr5:12194924	1.82×10^-7	内含子区	TMTC2
	Chr10:12311274	4.56×10^-7	内含子区	NRXN3
	Chr10:12312426	2.18×10^-7	内含子区	NRXN3
	Chr11:44751547	2.65×10^-7	基因间区	SLC5A7(dist=126,991), ST6GAL2(dist=375,961)
	Chr11:44786696	8.24×10^-7	基因间区	SLC5A7(dist=162,140), ST6GAL2(dist=340,812)
	Chr11:44795378	6.39×10^-7	基因间区	SLC5A7(dist=170,822), ST6GAL2(dist=332,130)
	Chr11:44800203	4.99×10^-7	基因间区	SLC5A7(dist=175,647), ST6GAL2(dist=327,305)
	Chr11:44958684	6.82×10^-7	基因间区	SLC5A7(dist=334,128), ST6GAL2(dist=168,824)
	Chr11:44959015	6.82×10^-7	基因间区	SLC5A7(dist=334,459), ST6GAL2(dist=168,493)
	Chr11:44961348	6.58×10^-7	基因间区	SLC5A7(dist=336,792), ST6GAL2(dist=166,160)
	Chr11:44964434	9.81×10^-7	基因间区	SLC5A7(dist=339,878), ST6GAL2(dist=163,074)
	Chr11:44979777	1.49×10^-7	基因间区	SLC5A7(dist=355,221), ST6GAL2(dist=147,731)
	Chr11:44996103	7.90×10^-7	基因间区	SLC5A7(dist=371,547), ST6GAL2(dist=131,405)
	Chr11:44998997	7.90×10^-7	基因间区	SLC5A7(dist=374,441), ST6GAL2(dist=128,511)
	Chr11:45002140	1.61×10^-7	基因间区	SLC5A7(dist=377,584), ST6GAL2(dist=125,368)
	Chr11:45002439	7.83×10^-7	基因间区	SLC5A7(dist=377,883), ST6GAL2(dist=125,069)
	Chr11:45002441	9.09×10^-7	基因间区	SLC5A7(dist=377,885), ST6GAL2(dist=125,067)
	Chr14:13590853	6.22×10^-7	基因间区	TRNAS-AGA(dist=435,743), LOC102170068(dist=236,306)
	Chr20:61086551	1.72×10^-7	基因间区	LOC102178486(dist=402,357), CTNND2(dist=142,674)
	Chr20:61086826	6.01×10^-8	基因间区	LOC102178486(dist=402,632), CTNND2(dist=142,399)
	Chr20:61086867	1.50×10^-7	基因间区	LOC102178486(dist=402,673), CTNND2(dist=142,358)
	Chr20:61089002	7.41×10^-7	基因间区	LOC102178486(dist=404,808), CTNND2(dist=140,223)
	Chr20:61415340	3.72×10^-7	内含子区	CTNND2
	Chr20:61492726	9.96×10^-7	内含子区	CTNND2
十字部高	Chr3:2304998	6.68×10^-7	内含子区	HDAC4
	Chr3:66499383	2.79×10^-7	内含子区	LOC102180934
	Chr10:12304101	8.49×10^-7	内含子区	NRXN3
	Chr10:12306561	4.88×10^-7	内含子区
	Chr10:12307080	8.03×10^-7	内含子区
	Chr10:12311274	6.43×10^-7	内含子区
	Chr10:12312426	3.47×10^-7	内含子区
	Chr10:12314053	8.61×10^-7	内含子区
	Chr10:12314089	7.76×10^-7	内含子区
	Chr12:69436019	2.84×10^-7	基因间区	SUCLA2(dist=158,724), HTR2A(dist=283,911)
	Chr12:73720343	3.97×10^-7	基因间区	FAM216B(dist=97,348), TNFSF11(dist=91,043)
	Chr12:73722126	9.28×10^-7	基因间区	FAM216B(dist=99,131), TNFSF11(dist=89,260)
	Chr12:73722128	9.28×10^-7	基因间区	FAM216B(dist=99,133), TNFSF11(dist=89,258)
	Chr24:39400720	4.14×10^-7	基因间区	EPB41L3(dist=32,170), TMEM200C(dist=235,434)
	Chr24:39400784	2.92×10^-7	基因间区	EPB41L3(dist=32,234), TMEM200C(dist=235,370)
	Chr24:39400805	6.29×10^-8	基因间区	EPB41L3(dist=32,255), TMEM200C(dist=235,349)
	Chr24:39401108	9.67×10^-8	基因间区	EPB41L3(dist=32,558), TMEM200C(dist=235,046)
	Chr24:39401201	9.67×10^-7	基因间区	EPB41L3(dist=32,651), TMEM200C(dist=234,953)
	Chr24:39401286	9.67×10^-8	基因间区	EPB41L3(dist=32,736), TMEM200C(dist=234,868)
	Chr24:39401294	9.67×10^-8	基因间区	EPB41L3(dist=32,744), TMEM200C(dist=234,860)
	Chr24:39401332	9.67×10^-8	基因间区	EPB41L3(dist=32,782), TMEM200C(dist=234,822)
	Chr24:39401405	9.67×10^-8	基因间区	EPB41L3(dist=32,855), TMEM200C(dist=234,749)
	Chr24:39401465	9.67×10^-8	基因间区	EPB41L3(dist=32,915), TMEM200C(dist=234,689)
	Chr24:39401492	9.67×10^-8	基因间区	EPB41L3(dist=32,942), TMEM200C(dist=234,662)
	Chr24:39401640	9.67×10^-8	基因间区	EPB41L3(dist=33,090), TMEM200C(dist=234,514)
	Chr24:39401876	1.39×10^-7	基因间区	EPB41L3(dist=33,326), TMEM200C(dist=234,278)
	Chr27:16721410	6.11×10^-7	基因间区	FUT10(dist=202,786), LOC108634069(dist=3,105)
	Chr27:16958269	4.46×10^-7	基因间区	LOC108634069(dist=219,887), NRG1(dist=28,177)
	Chr27:17912798	4.21×10^-7	基因间区	TRNAS-GGA(dist=318,811), WRN(dist=466,516)
	Chr27:17914619	2.93×10^-7	基因间区	TRNAS-GGA(dist=320,632), WRN(dist=464,695)
	Chr27:17916982	4.76×10^-7	基因间区	TRNAS-GGA(dist=322,995), WRN(dist=462,332)

表3

图3

表4

图4

图5

表5

图6

表6

图7

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性状	样本数量	最大值	最小值	平均值±标准差	变异系数(%)
体高(cm)	635	92.57	52.78	71.43±4.94	6.91
体长(cm)	635	99.88	61.82	82.83±7.76	9.37
十字部高(cm)	635	108.70	55.41	74.78±5.96	7.97

性状	体高	体长	十字部高
体高	0.30(0.09)	0.89(0.07)	0.99(0.04)
体长	0.66(0.02)	0.30(0.09)	0.80(0.03)
十字部高	0.76(0.02)	0.53(0.03)	0.31(0.09)

性状	SV位点	P值	功能注释	候选基因
体高与体长	Chr27:5673517~5673646:Del	2.61×10^-7	基因间区	OXSM(dist=36,583), LOC102179912(dist=100,529)
	Chr2:125485023~125486184:Del	2.57×10^-6	基因间区	TRNAC-GCA(dist=111,235), FSIP2(dist=273,642)
	Chr2:125486425~125487483:Del	2.83×10^-6	基因间区	TRNAC-GCA(dist=112,637), FSIP2(dist=272,240)

整合结构变异的奶山羊体尺全基因组关联分析

Genome-wide association study of body size traits in dairy goats integrating structural variants

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性状	SNP位点	P值	功能注释	候选基因
体长与十字部高	Chr3:101866590	6.68×10^-7	基因间区	S100A11(dist=36,011), LOC108635595(dist=12,239)
	Chr4:75794056	5.75×10^-7	基因间区	PMPCB(dist=8,193), NAPEPLD(dist=30,201)
	Chr8:4796225	3.33×10^-7	内含子区	GALNTL6
	Chr10:12304101	4.68×10^-7	内含子区	NRXN3
	Chr10:12306561	9.64×10^-7	内含子区
	Chr10:12307080	7.54×10^-7	内含子区
	Chr10:12311274	2.03×10^-7	内含子区
	Chr10:12312426	9.78×10^-8	内含子区
	Chr10:12314089	8.34×10^-7	内含子区
	Chr11:44979777	7.12×10^-7	基因间区	SLC5A7(dist=355,221), ST6GAL2(dist=147,731)
	Chr20:61086826	3.57×10^-7	基因间区	LOC102178486(dist=402,632), CTNND2(dist=142,399)
	Chr20:61086867	8.46×10^-7	基因间区	LOC102178486(dist=402,673), CTNND2(dist=142,358)
	Chr24:39400805	3.21×10^-7	基因间区	EPB41L3(dist=32,255), TMEM200C(dist=235,349)
	Chr24:39401108	5.13×10^-7	基因间区	EPB41L3(dist=32,558), TMEM200C(dist=235,046)
	Chr24:39401201	5.13×10^-7	基因间区	EPB41L3(dist=32,651), TMEM200C(dist=234,953)
	Chr24:39401286	5.13×10^-7	基因间区	EPB41L3(dist=32,736), TMEM200C(dist=234,868)
	Chr24:39401294	5.13×10^-7	基因间区	EPB41L3(dist=32,744), TMEM200C(dist=234,860)
	Chr24:39401332	5.13×10^-7	基因间区	EPB41L3(dist=32,782), TMEM200C(dist=234,822)
	Chr24:39401405	5.13×10^-7	基因间区	EPB41L3(dist=32,855), TMEM200C(dist=234,749)
	Chr24:39401465	5.13×10^-7	基因间区	EPB41L3(dist=32,915), TMEM200C(dist=234,689)
	Chr24:39401492	5.13×10^-7	基因间区	EPB41L3(dist=32,942), TMEM200C(dist=234,662)
	Chr24:39401640	5.13×10^-7	基因间区	EPB41L3(dist=33,090), TMEM200C(dist=234,514)
	Chr24:39401876	8.47×10^-7	基因间区	EPB41L3(dist=33,326), TMEM200C(dist=234,278)
	Chr27:16958269	8.73×10^-7	基因间区	LOC108634069(dist=219,887), NRG1(dist=28,177)

性状	SV位点	P值	功能注释	候选基因
体高	Chr27:5673517~5673646:Del	1.71×10^-7	基因间区	OXSM(dist=36,583), LOC102179912(dist=100,529)
体长	Chr27:5673517~5673646:Del	9.59×10^-6	基因间区	OXSM(dist=36,583), LOC102179912(dist=100,529)
十字部高	Chr8:90354905~90354906:Ins	2.11×10^-6	基因间区	MURC(dist=222,374), PLPPR1(dist=340,536)
十字部高	Chr8:104253014~104253015:Ins	7.12×10^-6	基因间区	LOC102179477(dist=142,855), TRNAC-GCA(dist=107,314)

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