吐鲁番黑羊体重和体尺性状全基因组关联分析

doi:10.11843/j.issn.0366-6964.2025.09.016

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (9): 4315-4327.doi: 10.11843/j.issn.0366-6964.2025.09.016

吐鲁番黑羊体重和体尺性状全基因组关联分析

白锋¹(), 玛尔孜娅·亚森¹, 阿米妮古丽·阿不来孜¹, 滕文³, 罗春彦¹, 纳扎开提·艾尼万尔², 张耘韬², 纪新民², 张艳花¹^,*()

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. 新疆农业大学动物科学学院, 乌鲁木齐 830052
3. 托克逊县风城国营牧业有限公司, 吐鲁番 838100

收稿日期:2025-02-12 出版日期:2025-09-23 发布日期:2025-09-30
通讯作者: 张艳花 E-mail:BF95114@outlook.com;181103221@qq.com
作者简介:白锋(1996-), 男，苗族，重庆酉阳人，硕士，主要从事动物遗传育种与繁殖研究，E-mail：BF95114@outlook.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)；新疆自治区产业技术体系(XJARS-09-05)；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)；新疆牧区地方肉羊选育改良计划(XJMQ-1)

Genome-Wide Association Study of Body Weight and Body Size Traits In Turpan Black Sheep

BAI Feng¹(), MAERZIYA·Yasen ¹, AMINIGULI·Abulaizi ¹, TENG Wen³, LUO Chunyan¹, NAZHAKAITI·Ainiwaner ², ZHANG Yuntao², JI Xinmin², ZHANG Yanhua¹^,*()

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

Received:2025-02-12 Online:2025-09-23 Published:2025-09-30
Contact: ZHANG Yanhua E-mail:BF95114@outlook.com;181103221@qq.com

摘要/Abstract

摘要：

旨在利用全基因组关联分析(genome-wide association study, GWAS)挖掘与鉴定吐鲁番黑羊体重和体尺性状的相关候选基因及分子标记，为吐鲁番黑羊的选育提高及资源开发利用提供科学依据。本研究选取129只年龄在1~3岁、饲养环境一致的健康吐鲁番黑羊公羊，测定体重、体高、体斜长、胸围、管围、胸宽、胸深、尾宽、尾长共9项体重体尺性状表型数据；随后使用的一次性采血管(添加EDTA-K2抗凝剂)采集5 mL颈静脉外周血提取DNA。对合格的DNA样本进行简化基因组测序(genotyping-by-sequencing, GBS)，运用samtools、bcftools等软件对原始测序数据进行检测、过滤及功能注释；然后利用GCTA、TreeBeST、GEMMA等软件分别完成群体遗传结构分析、群体分层评估及全基因组关联分析。本研究测序得到160.88 G的Raw data，质控后Clean data为157.87 G，获得460 766个SNPs位点。全基因关联分析在9个性状中共筛选到74个显著SNPs位点(P＜10^-5)，进一步注释得到到39个候选基因。单倍型分析发现候选基因的多个显著位点均位于单倍型block区域内。本研究鉴定了与吐鲁番黑羊体重体尺性状显著关联的SNP位点及候选基因，为深入解析这些性状的遗传机制提供了重要依据，同时也为吐鲁番黑羊分子标记辅助育种提供了基础数据。

关键词: 吐鲁番黑羊, 体尺性状, 全基因组关联分析, 单倍型分析

Abstract:

This study aimed to identify candidate genes and molecular markers associated with body weight and body size traits in Turpan black sheep using genome-wide association study (GWAS), thereby providing a scientific basis for genetic breeding and resource development of Turpan black sheep. In this study, 129 healthy male Turpan black sheep aged 1 to 3 years, raised under the uniform conditions, were selected. Phenotypic data for 9 traits were measured: body weight, body height, body length, chest circumference, tube circumference, chest width, chest depth, tail width, and tail length. Peripheral blood samples (5 mL) were collected from the jugular vein using EDTA-K₂ anticoagulant vacuum tubes for DNA extraction. Qualified DNA samples underwent genotyping-by-sequencing (GBS). Raw sequencing data were processed, filtered, and annotated using software such as samtools and bcftools.Subsequently, population genetic structure analysis, population stratification assessment, and GWAS were performed using GCTA, TreeBeST, and GEMMA softwares, respectively. Sequencing yielded 160.88 G of raw data. After quality control, 157.87 G of clean data were obtained, identifying 460 766 SNP loci. GWAS detected 74 significant SNPs (P < 10^-5) associated with the 9 traits. Annotation revealed 39 candidate genes. Haplotype analysis showed that multiple significant SNPs were located within haplotype blocks. This study identified important genetic loci and candidate genes associated with body weight and body size traits of Turpan black sheep.The findings provide crucial insights for elucidating the genetic mechanisms underlying these traits and lay the foundation for molecular marker-assisted breeding in Turpan black sheep.

Key words: Turpan black sheep, body size traits, genome-wide association study, haplotype analysis

中图分类号:

S826.2

白锋, 玛尔孜娅·亚森, 阿米妮古丽·阿不来孜, 滕文, 罗春彦, 纳扎开提·艾尼万尔, 张耘韬, 纪新民, 张艳花. 吐鲁番黑羊体重和体尺性状全基因组关联分析[J]. 畜牧兽医学报, 2025, 56(9): 4315-4327.

BAI Feng, MAERZIYA·Yasen , AMINIGULI·Abulaizi , TENG Wen, LUO Chunyan, NAZHAKAITI·Ainiwaner , ZHANG Yuntao, JI Xinmin, ZHANG Yanhua. Genome-Wide Association Study of Body Weight and Body Size Traits In Turpan Black Sheep[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(9): 4315-4327.

图/表 7

表 1

图 1

图 2

图 3

表 2

与体重体尺性状显著相关的SNPs及候选基因"

性状 Trait	染色体 Chromosome	SNP位置 SNP location	基因型 Genotype	次等位基因频率 MAF	P值 P-value	功能注释 Functional annotation	候选基因 Candidate gene
体高 Body height	16	16:40065579	G/A	0.129 9	1.26×10^-6	intronic	ADAMTS12
体高 Body height	21	21:31871278	C/T	0.204 2	9.82×10^-7	intronic	OPCML
体长 Body length	14	14:60269030	G/T	0.068 0	2.86×10^-6	intronic	LOC101108416
	14	14:60269030	G/T	0.068 0	2.86×10^-6	intronic	LOC101112635
	18	18:63037938	G/A	0.264 0	3.49×10^-6	intronic	WDR25
	21	21:31871278	C/T	0.204 2	7.03×10^-6	intronic	OPCML
	24	24:24281700	G/A	0.472 9	3.48×10^-6	intronic	HS3ST4
体重 Body weight	1	1:162309133	A/G	0.238 3	3.55×10^-6	intronic	EPHA6
	3	3:6305883	C/T	0.267 7	2.67×10^-6	intronic	HMCN2
	3	3:209166910	T/C	0.101 6	7.67×10^-6	intergenic	C1RL
	7	7:60036524	C/G	0.075 6	6.42×10^-6	intronic	FBN1
	7	7:88861927	A/C	0.124 0	3.69×10^-6	intronic	NRXN3
	12	12:64948358	C/T	0.067 2	3.65×10^-6	intronic	C12H1orf21
	16	16:40065579	G/A	0.129 9	2.57×10^-6	intronic	ADAMTS12
	22	22:7206258	G/C	0.307 1	7.11×10^-6	intronic	PRKG1
	25	25:4258888	G/A	0.183 6	4.28×10^-6	intergenic	DISC1
	NW_024599828	NW_024599828: 1113906	A/C	0.359 5	1.88×10^-6	intronic	LOC101102275
	NW_024599828	NW_024599828: 1113906	A/C	0.359 5	1.88×10^-6	intronic	PAG3
胸围 Chest circumference	1	1:271185186	C/T	0.191 4	5.63×10^-6	intronic	KCNJ15
	3	3:203630569	C/T	0.230 5	7.19×10^-8	intronic	ETV6
	3	3:203630569	C/T	0.230 5	7.19×10^-8	intronic	LOC121819203
	6	6:86670534	T/A	0.475 8	7.88×10^-6	intergenic	LOC105612199
	16	16:40065579	G/A	0.129 9	1.15×10^-7	intronic	ADAMTS12
胸深 Chest depth	5	5:22169507	T/C	0.089 0	4.64×10^-7	intronic	MINAR2
	8	8:48325347	T/C	0.065 0	7.93×10^-6	UTR3	LOC101114365
	8	8:48325347	T/C	0.065 0	7.93×10^-6	UTR3	PM20D2
	10	10:82538718	T/C	0.119 8	3.26×10^-6	intronic	NALF1
胸宽 Chest width	19	19:19015339	A/G	0.101 6	8.97×10^-6	intronic	GRM7
	20	20:23813922	A/T	0.058 8	9.76×10^-6	intronic	PKHD1
	22	22:7206258	G/C	0.307 1	3.50×10^-6	intronic	PRKG1
尾长 Tail lenth	9	9:21983713	A/G	0.232 6	7.99×10^-6	intronic	KCNQ3
尾长 Tail lenth	20	20:22934892	G/A	0.346 2	3.20×10^-6	intergenic	TFAP2D
尾宽 Tail width	2	2:49086885	C/A	0.127 1	9.69×10^-6	intronic	ANKS6
	9	9:21983713	A/G	0.232 6	1.69×10^-6	intronic	KCNQ3
	14	14:6903044	T/C	0.259 7	3.28×10^-6	intronic	CDYL2
管围 Tube circumference	1	1:226721935	G/A	0.160 2	4.81×10^-6	intronic	LOC121818542
	1	1:226721935	G/A	0.160 2	4.81×10^-6	intronic	SPTSSB
	3	3:194022073	C/T	0.058 1	5.75×10^-6	intergenic	KCNJ8
	10	10:49503999	T/C	0.315 6	8.59×10^-6	intronic	KLF12

表 2

图 4

图 5

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性状 Trait	平均值 Mean value	标准差 Standard deviation	标准误 Standard error	最大值 Maximum value	最小值 Minimum value
体重/kg Body weight	56.70	15.28	1.35	87	37
体高/cm Body height	68.60	3.79	0.33	79	60
体斜长/cm Body lenth	70.81	3.90	0.34	84	62
胸宽/cm Chest width	21.19	9.09	0.80	79	15
胸深/cm Chest depth	29.27	3.14	0.28	36	21
胸围/cm Chest circumference	98.53	12.35	1.09	129	75
管围/cm Tube circumference	9.43	0.70	0.06	11.5	8
尾宽/cm Tail width	17.70	3.13	0.28	26	11
尾长/cm Tail lenth	13.88	3.04	0.27	20	5

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吐鲁番黑羊体重和体尺性状全基因组关联分析

Genome-Wide Association Study of Body Weight and Body Size Traits In Turpan Black Sheep

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