利用SNP芯片信息评估新疆近交牛基因组纯合度

doi:10.16288/j.yczz.20-071

遗传 ›› 2020, Vol. 42 ›› Issue (5): 493-505.doi: 10.16288/j.yczz.20-071

利用SNP芯片信息评估新疆近交牛基因组纯合度

师睿¹, 张毅¹, 王雅春¹(), 黄涛²(), 卢国昌³, 岳涛⁴, 卢振西³, 黄锡霞⁵, 卫新璞⁶, 冯书堂⁷, 陈军⁸, 乌兰·卡格德尔⁸, 茹先古丽·阿不力孜⁸, 努尔胡马尔·木合塔尔⁸

^1. 中国农业大学动物科技学院,农业农村部动物遗传育种与繁殖(家畜)重点实验室,畜禽育种国家工程实验室,北京 100193
^2. 新疆石河子大学动物科学技术学院,石河子 832000
^3. 新疆锦盛旺农业科技有限公司,塔城 834700
^4. 新疆塔城地区畜牧科技研究推广中心,塔城 834700
^5. 新疆农业大学动物科学学院,乌鲁木齐 830052
^6. 新疆呼图壁种牛场有限公司,昌吉 831100
^7. 中国农业科学院北京畜牧兽医研究所,北京 100193
^8. 新疆维吾尔自治区畜牧总站,乌鲁木齐 830009

收稿日期:2020-03-15 修回日期:2020-04-09 出版日期:2020-05-20 发布日期:2020-05-09
通讯作者: 王雅春,黄涛 E-mail:wangyachun@cau.edu.cn;taohuagn100@sina.com
作者简介:师睿,在读硕士研究生,专业方向：动物遗传育种与繁殖。E-mail: srandeffy@163.com
基金资助:
现代农业(奶牛)产业技术体系建设专项资金编号(CARS-36);长江学者和创新团队发展计划项目资助编号(IRT_15R62)

The evaluation of genomic homozygosity for Xinjiang inbred population by SNP panels

Rui Shi¹, Yi Zhang¹, Yachun Wang¹(), Tao Huang²(), Guochang Lu³, Tao Yue⁴, Zhenxi Lu³, Xixia Huang⁵, Xinpu Wei⁶, Shutang Feng⁷, Jun Chen⁸, Wulan Kagedeer⁸, Ruxianguli Abulizi⁸, Nuerhumaer Muhetaer⁸

^1. Key Laboratory of Animal Genetics, Breeding and Reproduction(MARA), National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
^2. College of Animal Science and Technology, Xinjiang Shihezi University, Shihezi 832000, China
^3. Xinjiang Jinshengwang Agriculture and Science Technology Co., Ltd, Tacheng 834700, China
^4. Livestock Science and Technology Research and Extension Center of Tangcheng Area, Tacheng 834700, China
^5. College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
^6. Xinjiang Hutubi Cattle Farm Co., Ltd, Changji 831100, China
^7. Insititute of Animal Scienece, Chinese Academy of Agricultural Sciences, Beijing 100193, China
^8. Animal Husbandry Service of Xinjiang Uygur Autonomous Region, Urumqi 830009, China;

Received:2020-03-15 Revised:2020-04-09 Online:2020-05-20 Published:2020-05-09
Contact: Wang Yachun,Huang Tao E-mail:wangyachun@cau.edu.cn;taohuagn100@sina.com
Supported by:
Supported by China Agriculture Research System No(CARS-36);the Program for Changjiang Scholar and Innovation Research Team in University No(IRT_15R62)

摘要/Abstract

摘要：

新疆近交牛是经45年近亲繁育形成的近交群体,但由于繁育记录缺失,其原始亲本品种未知。为了明确新疆近交牛的遗传背景,并探索利用基因组信息评价牛群近交水平的可行性,本研究利用该群体及荷斯坦牛、新疆褐牛和哈萨克牛等16个国内外牛品种的SNP芯片数据,应用主成分分析和Admixture方法对塔城地区新疆近交牛的群体结构进行分析;通过进一步计算新疆近交牛、荷斯坦牛、新疆褐牛和哈萨克牛的群体遗传学参数以及基因组近交指标评估各群体近交程度;结合新疆近交牛的体型分类和基因组近交指标信息,探讨了个体近交程度与体型表现的关系;最后,基于对新疆近交牛和哈萨克牛高频长纯合片段区域的筛选,鉴定了新疆近交牛基因组特征区域。研究结果显示,新疆近交牛的遗传背景与哈萨克牛基本一致,近交牛基因组纯合程度明显高于其他群体,且基因纯合率越高的近交牛其体型越小,在一定程度上呈现了近交衰退对体型的影响。本研究还鉴定到与新疆近交牛基因组特征区域相关的6个基本生物学通路以及与重要经济性状相关的32个数量基因座(quantitative trait loci, QTL)。本研究结果为新疆近交牛这一特殊遗传资源的育种规划及未来该群体的开发利用提供了科学依据。

关键词: 新疆近交牛, 群体结构, 基因组近交, 长纯合片段

Abstract:

Xinjiang inbred cattle is a population which has been highly inbred for 45 years. However, the breed origin of this population cannot be traced back due to the lack of original records. To demonstrate the genetic background of Xinjiang inbred cattle, we analysed the worldwide genomic information of 16 cattle breeds using principal components analysis, and Admixture method. Furthermore, the shared SNP markers of Xinjiang inbred cattle, local Kazakh cattle, Holstein cattle, and Xinjiang Brown cattle were extracted to calculate population genetic parameters and genomic inbreeding indicators in order to evaluate the magnitude of inbreeding in each population. We also evaluated the relationship between inbreeding indicators and body size in the Xinjiang inbred population. Finally, the high frequency runs of homozygosity (ROH) regions for Xinjiang inbred cattle and local Kazakh population were selected for genes and QTL annotations. These results demonstrate that the ancestry proportions of inbreeding breed are similar to those of Kazakh cattle. The genomic homozygosity of Xinjiang inbred cattle is significantly higher than other populations; the inbreeding depression is observed in body size to a certain extent because body size decreased when corresponding homozygosity increased. Totally, six basic bio-pathways and 32 QTL regions that related to bovine economical traits were annotated. Our results provide the insights into breeding strategies, future protection, and utilization plan design for this special genetic material-Xinjiang inbred cattle.

Key words: Xinjiang inbred cattle, population structure, genomic inbreeding, runs of homozygosity

师睿, 张毅, 王雅春, 黄涛, 卢国昌, 岳涛, 卢振西, 黄锡霞, 卫新璞, 冯书堂, 陈军, 乌兰·卡格德尔, 茹先古丽·阿不力孜, 努尔胡马尔·木合塔尔. 利用SNP芯片信息评估新疆近交牛基因组纯合度[J]. 遗传, 2020, 42(5): 493-505.

Rui Shi, Yi Zhang, Yachun Wang, Tao Huang, Guochang Lu, Tao Yue, Zhenxi Lu, Xixia Huang, Xinpu Wei, Shutang Feng, Jun Chen, Wulan Kagedeer, Ruxianguli Abulizi, Nuerhumaer Muhetaer. The evaluation of genomic homozygosity for Xinjiang inbred population by SNP panels[J]. Hereditas(Beijing), 2020, 42(5): 493-505.

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参考文献 34

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群体/品种	缩写	类别	样本来源	数据集1 (310头)	数据集2 (170头)	数据集3 (69头)	数据集4 (70头)	数据来源
新疆近交牛	XI	中国北方牛	新疆塔城	20	50	69(40)^*	50	本研究
哈萨克牛(塔城)	TL	中国北方牛	新疆塔城	20	20	-	20	本研究
新疆褐牛	XB	中国北方牛	新疆塔城	20	50	-	-	本研究
荷斯坦牛	HO	普通牛	北京大兴	20	50	-	-	本研究
瑞士褐牛	BS	普通牛	瑞士	20				[4]
西门塔尔牛	SI	普通牛	德国	20	-	-	-	[4]
加尔梅克牛	JA	普通牛	俄罗斯	20	-	-	-	[11]
延边牛	YB	中国北方牛	吉林延边	20	-	-	-	[4]
蒙古牛	MG	中国北方牛	内蒙古锡林郭勒	20	-	-	-	[4]
哈萨克牛(伊犁)	KA	中国北方牛	新疆伊犁	20	-	-	-	[4]
秦川牛	QC	中国中原牛	陕西宝鸡	20	-	-	-	[4]
晋南牛	JN	中国中原牛	山西运城	14	-	-	-	[4]
南阳牛	NY	中国中原牛	河南南阳	20	-	-	-	[4]
鲁西牛	LX	中国中原牛	山东梁山	16	-	-	-	[4]
温岭牛	WL	瘤牛	浙江温州	20	-	-	-	[4]
吉尔牛	GI	瘤牛	印度	20	-	-	-	[12]

牛群	HOM%		ROH%
牛群	平均值	标准差	平均值	标准差
新疆近交牛(XI)	0.681^a	0.040	0.136^a	0.079
哈萨克牛(塔城,TL)	0.577^b	0.006	0.021^b	0.013
新疆褐牛(XB)	0.596^c	0.025	0.102^c	0.060
荷斯坦牛(HO)	0.541^d	0.011	0.102^c	0.028

体型分类	个体数	平均值±标准差
体型分类	个体数	体高(cm)	体斜长(cm)	胸围(cm)	管围(cm)	HOM%	ROH%
≥12月龄
小	10	86.30±9.99	96.60±10.72	111.70±11.97	12.40±1.41	0.612±0.053	0.188±0.143
中	28	102.56±4.15	122.41±8.21	141.24±7.09	14.59±1.08	0.611±0.032	0.186±0.088
大	31	111.96±4.66	140.56±8.12	155.84±9.30	16.00±0.98	0.593±0.032	0.130±0.084
≥24月龄
中	17	102.12±3.23	120.69±6.31	140.59±7.63	14.47±1.15	0.607±0.026	0.167±0.067
大	23	111.25±4.94	139.90±8.36	154.64±9.79	15.93±1.02	0.594±0.032	0.132±0.086

GO条目	通路名称	基因数	P值
GO生物学过程
GO:0051965	突触组装正调控	4	7.65E-04
GO:0007409	轴突生成	4	2.05E-03
GO:0006979	氧化应激反应	3	2.28E-02
GO:0032727	α干扰素生成正调控	2	3.03E-02
GO分子生物功能
GO:0030176	内质网膜组成	4	2.19E-03
GO:0005923	细胞紧密连接	3	3.11E-02

染色体	位置(Mb)	QTL类型	ID号*
5	20.22~48.75	肉质和胴体性状相关	22866
5	47.54~90.49	肉质和胴体性状相关	22864
5	48.08~48.99	肉质和胴体性状相关	24694
5	48.08~48.99	繁殖性状相关	24565
5	48.08~48.99	长寿性状相关	24524
5	48.08~48.99	肉质和胴体性状相关	24695
5	48.16~48.75	肉质和胴体性状相关	22878
12	52.26~60.51	产奶性状相关	56344
12	52.26~60.51	产奶性状相关	56385
22	31.48~34.13	产奶性状相关	126214
22	31.48~34.13	体型性状相关	126019
22	31.48~34.13	繁殖性状相关	126008
22	31.48~34.13	繁殖性状相关	126007
22	31.48~34.13	繁殖性状相关	126006
22	31.48~34.13	繁殖性状相关	126005
22	31.48~34.13	长寿性状相关	125994
22	31.48~34.13	长寿性状相关	125993
22	31.48~34.13	体型性状相关	125379
22	31.48~34.13	产奶性状相关	126225
22	31.48~34.13	体型性状相关	125955
22	31.48~34.13	体型性状相关	125925
22	31.48~34.13	体型性状相关	125877
22	31.48~34.13	体型性状相关	125876
22	31.48~34.13	产奶性状相关	126357
22	31.48~34.13	产奶性状相关	126236
22	31.48~34.13	长寿性状相关	125992
22	33.98~33.98	产奶性状相关	51582
22	33.98~33.98	产奶性状相关	51581
22	33.98~33.98	体型性状相关	51583
22	33.98~33.98	产奶性状相关	51580
22	8.96~41.99	产奶性状相关	56580
22	8.96~41.99	产奶性状相关	56581

利用SNP芯片信息评估新疆近交牛基因组纯合度

The evaluation of genomic homozygosity for Xinjiang inbred population by SNP panels

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[1]	刘刚,孙飞舟,朱芳贤,冯海永,韩旭. 连续性纯合片段在畜禽基因组研究中的应用[J]. 遗传, 2019, 41(4): 304-317.
[2]	潘登，符云新，张亚平. 基于线粒体控制区的滇金丝猴群体遗传学研究[J]. 遗传, 2006, 28(4): 432-436.