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

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

• Research Article • Previous Articles Next Articles

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)

Abstract

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

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.

Figures/Tables 10

Table 1

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Fig. 4

Table 2

Table 3

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Table 4

Supplemental Table 1

References 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

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

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