奶牛乳房健康基因检测芯片在中国荷斯坦牛及巴基斯坦本地奶牛群中的应用研究

doi:10.11843/j.issn.0366-6964.2024.10.021

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (10): 4489-4499.doi: 10.11843/j.issn.0366-6964.2024.10.021

奶牛乳房健康基因检测芯片在中国荷斯坦牛及巴基斯坦本地奶牛群中的应用研究

赖婉仪¹(), 陶欣月¹, 杨庚新², 余文莉², 李树静², Tahir Usman³, 俞英¹^,*()

1. 中国农业大学动物科学技术学院, 北京 100193
2. 石家庄天泉良种奶牛有限公司, 石家庄 050200
3. 阿卜杜勒·瓦利汗大学兽医与畜牧学院, 马尔丹 23200

收稿日期:2024-04-07 出版日期:2024-10-23 发布日期:2024-11-04
通讯作者: 俞英 E-mail:laiwanyi@cau.edu.cn;yuying@cau.edu.cn
作者简介:赖婉仪(2003-), 女, 福建漳州人, 本科生, 主要从事奶牛抗病育种研究, E-mail: laiwanyi@cau.edu.cn
基金资助:
河北省科技计划“揭榜挂帅”项目(23227602Z);“十四五”国家重点研发计划(2021YFD1200903);“十四五”国家重点研发计划(2023YFF1000902);国家自然科学基金国际(地区)合作项目(31961143009);现代农业产业技术体系项目(CARS-36)

Application Study of Chinese Cow's SNPs Chip-Ⅰ in Chinese Holstein and Pakistani Indigenous Dairy Cattle Populations

Wanyi LAI¹(), Xinyue TAO¹, Gengxin YANG², Wenli YU², Shujing LI², Tahir USMAN³, Ying YU¹^,*()

1. College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
2. Shijiazhuang Tianquan Elite Dairy Cattle Co., LTD., Shijiazhuang 050200, China
3. College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan 23200, Pakistan

Received:2024-04-07 Online:2024-10-23 Published:2024-11-04
Contact: Ying YU E-mail:laiwanyi@cau.edu.cn;yuying@cau.edu.cn

摘要/Abstract

摘要：

旨在筛选与奶牛乳房健康相关的SNP位点或组合，提升奶牛乳房健康水平，同时促进“一带一路”国家的奶牛产业健康发展。本研究基于1 097头中国荷斯坦牛、161头巴基斯坦荷斯坦牛的尾静脉血及116头Achai牛、104头辛地红牛的尾根毛囊，提取基因组DNA，使用奶牛乳房健康分子检测芯片(Chinese Cow's SNPs Chip-Ⅰ, CCSC-Ⅰ)获得基因型，结合相应DHI数据报告中的乳房健康指标——体细胞数(somatic cell count, SCC)及体细胞评分(somatic cell score, SCS)，通过单个SNP和成对SNP关联分析，鉴定有意义的SNP位点或组合。单位点关联分析结果显示，SNP3、6、8、11、19、20在中国荷斯坦牛群体中为显著位点(P＜0.05)，针对巴基斯坦奶牛群同样鉴定出SNP3和SNP11为显著位点(P＜0.05)；在成对位点关联分析中，中国荷斯坦牛群体使用大样本(北京、浙江、河北地区牧场)和河北地区样本分别分析，保留稳定的SNP11-SNP15组合，SNP19和SNP20的AA基因型同占优势，针对巴基斯坦荷斯坦牛鉴定了SNP11-SNP2、4、8、9、12、16、19等极显著组合(P＜0.01)，而针对巴基斯坦本地奶牛Achai鉴定出了SNP3-SNP11、15等极显著组合(P＜0.01)。本研究结果显示，奶牛乳房健康分子检测芯片具有广泛适用性。SNP11、15、19、20等位点对奶牛乳房健康具有重要影响。在荷斯坦牛群体中，CD4、TRAPPC9和PTK2基因表现出潜在的乳房炎抗性；而在巴基斯坦本地奶牛中，CD4、DGAT1和TRAPPC9基因则表现出显著的抗性特征。这些发现为未来的精准选育提供了有力的科学依据。

关键词: 中国荷斯坦牛, 巴基斯坦荷斯坦牛, 巴基斯坦本地奶牛, 奶牛乳房炎, 单核苷酸多态性

Abstract:

The purpose of this study was to identify significant SNP loci or combinations relevant to cow udder health, so as to improve udder health in dairy cattle and promote the healthy development of the dairy industry in "the Belt and Road" countries. In this study, genomic DNA was collected from the tail vein blood of 1 097 Chinese Holstein and 161 Pakistani Holstein, and the tail root hair follicles of 116 Achai cattle and 104 Red Sindhi. Chinese Cow's SNPs Chip-I (CCSC-I) was used to obtain the genotype. In conjunction with udder health indicators from corresponding DHI reports—somatic cell count (SCC) and somatic cell score (SCS), significant SNPs or combinations were identified through single SNP and pairwise SNP association analysis. The unit point association analysis showed that SNP3, 6, 8, 11, 19, and 20 were significant loci in the Chinese Holstein(P < 0.05), with SNP3 and 11 identified as significant loci in the Pakistani dairy cattle population(P < 0.05). In pairwise SNP association analysis, stable combinations of SNP11-SNP15 were retained for the Chinese Holstein using large samples (farms in Beijing, Zhejiang, and Hebei provinces) and samples from Hebei province specifically, with the AA genotype predominating for SNP19 and SNP20. Significant combinations of SNP11-SNP2, 4, 8, 9, 12, 16, 19 were identified for Pakistani Holstein(P < 0.01), and significant combinations like SNP3-SNP11, 15 were identified for the Pakistani indigenous Achai(P < 0.01). The results of this study show that Chinese Cow's SNPs Chip-I exhibits wide applicability. SNP11, 15, 19, 20 and other loci have important effects on cow udder health. In Holstein populations, CD4, TRAPPC9, and PTK2 showed potential resistance to mastitis. In the Pakistani indigenous dairy cattle populations, CD4, DGAT1, and TRAPPC9 showed significant resistance characteristics. These findings provide a strong scientific basis for future accurate breeding.

Key words: Chinese Holstein, Pakistani Holstein, Pakistani indigenous dairy cattle, mastitis, SNP

中图分类号:

S823.91

赖婉仪, 陶欣月, 杨庚新, 余文莉, 李树静, Tahir Usman, 俞英. 奶牛乳房健康基因检测芯片在中国荷斯坦牛及巴基斯坦本地奶牛群中的应用研究[J]. 畜牧兽医学报, 2024, 55(10): 4489-4499.

Wanyi LAI, Xinyue TAO, Gengxin YANG, Wenli YU, Shujing LI, Tahir USMAN, Ying YU. Application Study of Chinese Cow's SNPs Chip-Ⅰ in Chinese Holstein and Pakistani Indigenous Dairy Cattle Populations[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(10): 4489-4499.

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成对位点Pairwise SNP		基因1 Gene1	基因2 Gene2	模式 Model	P值 P-value	优势基因型 Advantage genotype
位点1 SNP1	位点2 SNP2	基因1 Gene1	基因2 Gene2	模式 Model	P值 P-value	优势基因型 Advantage genotype
SNP4	SNP9	JAK2	STAT5A	DD_int_rr_1vs0	0.002 8	TC+CC/CA+AA
SNP6	SNP8	JAK2	JAK2	RD_int_ro_1vs0	0.000 1	CC/CC
SNP8	SNP11	JAK2	CD4	DD_int_oo_1vs0	0.002 0	CT+TT/CT+TT
SNP8	SNP15	JAK2	DGAT1	DD_int_or_1vs0	0.005 4	CT+TT/AA
SNP11	SNP15	CD4	DGAT1	RD_int_or_1vs0	0.004 7	CC+CT/AG+GG
SNP11	SNP17	CD4	DGAT1	DD_int_ro_1vs0	0.002 1	CT+TT/TT
SNP15	SNP19	DGAT1	TRAPPC9	DD_int_rr_1vs0	0.000 6	AG+GG/GA+AA
SNP15	SNP20	DGAT1	PTK2	DD_int_rr_1vs0	0.000 7	AG+GG/GA+AA

成对位点Pairwise SNP		基因1 Gene1	基因2 Gene2	模式 Model	P值 P-value	优势基因型 Advantage genotype
位点1 SNP1	位点2 SNP2	基因1 Gene1	基因2 Gene2	模式 Model	P值 P-value	优势基因型 Advantage genotype
SNP6	SNP18	JAK2	TRAPPC9	RD_int_rr_1vs0	0.006 7	TT+TC/GG
SNP6	SNP19	JAK2	TRAPPC9	AA_int_ro_12	0.003 9	TT/AA
SNP6	SNP20	JAK2	PTK2	AA_int_ro_12	0.003 3	TT/AA
SNP9	SNP19	STAT5A	TRAPPC9	AA_int_rr_12	0.001 5	AA/AA
SNP9	SNP20	STAT5A	PTK2	AA_int_rr_12	0.001 5	AA/AA
SNP11	SNP15	CD4	DGAT1	AA_int_ro_12	0.008 9	CC/GG
SNP11	SNP18	CD4	TRAPPC9	DD_int_rr_1vs0	0.004 8	CT+TT/AG+GG
SNP12	SNP15	LAG3	DGAT1	AA_int_rr_12	0.002 2	AA/GG
SNP12	SNP17	LAG3	DGAT1	AA_int_rr_12	0.002 8	AA/CC

品种 Breed	成对位点Pairwise SNP		基因1 Gene1	基因2 Gene2	模式 Model	P值 P-value	优势基因型 Advantage genotype
品种 Breed	位点1 SNP1	位点2 SNP2	基因1 Gene1	基因2 Gene2	模式 Model	P值 P-value	优势基因型 Advantage genotype
阿卡牛Achai	SNP3	SNP11	TRAPPC9	CD4	DD_int_rr_1vs0	0.043 7	TT/TT
	SNP3	SNP15	TRAPPC9	DGAT1	AA_int_rr_12	0.032 5	TT/GG
	SNP16	SNP17	DGAT1	DGAT1	DD_int_rr_1vs0	0.010 0	GG/CC
	SNP17	SNP18	DGAT1	TRAPPC9	DR_int_or_1vs0	0.015 4	CC/GG
	SNP17	SNP19	DGAT1	TRAPPC9	DR_int_rr_1vs0	0.015 4	CC/GG+GA
巴基斯坦荷斯坦牛	SNP2	SNP11	TRAPPC9	CD4	AA_int_ro_12	0.015 0	CC/TT
Pakistani Holstein	SNP4	SNP11	JAK2	CD4	AA_int_ro_12	0.003 9	TT/TT
	SNP8	SNP11	JAK2	CD4	AA_int_ro_12	0.004 4	CC/TT
	SNP8	SNP15	JAK2	DGAT1	DD_int_ro_1vs0	0.019 6	CC/AG+GG
	SNP8	SNP19	JAK2	TRAPPC9	AA_int_ro_12	0.026 2	CC/AA
	SNP8	SNP20	JAK2	PTK2	DD_int_rr_1vs0	0.034 5	CC/GG
	SNP9	SNP11	STAT5A	CD4	AA_int_oo_12	0.008 9	AA/TT
	SNP9	SNP19	STAT5A	TRAPPC9	AA_int_oo_12	0.009 2	AA/AA
	SNP11	SNP12	CD4	LAG3	AA_int_rr_12	0.012 5	TT/AA
	SNP11	SNP16	CD4	DGAT1	RD_int_oo_1vs0	0.008 8	TT/AG+GG
	SNP11	SNP19	CD4	TRAPPC9	AA_int_rr_12	0.003 4	TT/AA
	SNP12	SNP16	LAG3	DGAT1	DD_int_or_1vs0	0.032 6	GA+AA/AA
	SNP15	SNP16	DGAT1	DGAT1	DD_int_or_1vs0	0.028 1	AG+GG/AA
	SNP17	SNP19	DGAT1	TRAPPC9	AA_int_ro_12	0.016 1	TT/AA
	SNP18	SNP19	TRAPPC9	TRAPPC9	DD_int_ro_1vs0	0.028 1	AA/GA+AA
	SNP19	SNP20	TRAPPC9	PTK2	DD_int_or_1vs0	0.000 3	GA+AA/GG

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奶牛乳房健康基因检测芯片在中国荷斯坦牛及巴基斯坦本地奶牛群中的应用研究

Application Study of Chinese Cow's SNPs Chip-Ⅰ in Chinese Holstein and Pakistani Indigenous Dairy Cattle Populations

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