基于智能项圈系统荷斯坦牛发情相关指标的遗传参数估计及全基因组关联分析

doi:10.3864/j.issn.0578-1752.2023.05.014

中国农业科学 ›› 2023, Vol. 56 ›› Issue (5): 995-1006.doi: 10.3864/j.issn.0578-1752.2023.05.014

基于智能项圈系统荷斯坦牛发情相关指标的遗传参数估计及全基因组关联分析

杨明路¹^,²(), 张海亮¹, 罗汉鹏¹, 黄锡霞², 张翰林⁴, 章施施⁴, 王炎⁴, 刘林³, 郭刚⁴(), 王雅春¹()

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 新疆农业大学动物科学学院，乌鲁木齐 830052
³ 北京奶牛中心，北京 100192
⁴ 北京首农畜牧发展有限公司，北京 100029

收稿日期:2021-10-08 接受日期:2022-12-28 出版日期:2023-03-01 发布日期:2023-03-13
通信作者: 郭刚，E-mail：guogang2180@126.com。王雅春，E-mail：wangyachun@cau.edu.cn
联系方式: 杨明路，E-mail：2510660222@qq.com。
基金资助:
国家现代农业产业技术体系(CARS-36); 长江学者和创新团队发展计划(IRT_15R62); 北京三元种业科技股份有限公司自立科研课题(SYZYZ20190005)

Estimation of Genetic Parameters and Genome-Wide Association Study of Heat Indicators in Holstein Cattle Based on Collar-Mounted Device

YANG MingLu¹^,²(), ZHANG HaiLiang¹, LUO HanPeng¹, HUANG XiXia², ZHANG HanLin⁴, ZHANG ShiShi⁴, WANG Yan⁴, LIU Lin³, GUO Gang⁴(), WANG YaChun¹()

¹ College of Animal Science and Technology, China Agricultural University/Key Laboratory of Animal Genetics/Breeding and Reproduction of Ministry of Agriculture and Rural Affairs/National Engineering Laboratory for Animal Breeding, Beijing 100193
² College of Animal Science, Xinjiang Agricultural University, Urumqi 830052
³ Beijing Dairy Center, Beijing 100192
⁴ Beijing Sunlon Livestock Development Co., Ltd, Beijing 100029

Received:2021-10-08 Accepted:2022-12-28 Published:2023-03-01 Online:2023-03-13

摘要/Abstract

摘要：

【目的】探究基于奶牛智能项圈系统产生的发情指数和活动峰值指标的群体规律及其影响因素，对其进行遗传参数估计，并利用全基因组关联分析（genome-wide association study, GWAS）挖掘与奶牛发情相关指标的遗传标记，以期为从遗传育种角度制定选育策略提高奶牛繁殖力提供有用信息。【方法】试验以北京市某规模化牧场健康的泌乳期荷斯坦牛为研究对象，收集了该牧场2017年7月至2020年5月2 074 头泌乳牛的发情记录，包括发情指数和活动峰值，同时收集了试验牛的产犊记录；采用 SAS 9.4中MIXED过程，分析了非遗传因素对发情指数和活动峰值的影响；基于DMU软件DMUAI模块，使用双性状动物模型估计了发情指数与活动峰值的遗传力及遗传相关，并计算了发情指数与常规繁殖性状的近似遗传相关；以逆回归育种值为关联分析的表型，利用FarmCPU软件分别对发情指数和活动峰值进行了GWAS。【结果】荷斯坦牛发情指数为（71.77±19.13）au，活动峰值为（105.94±30.73）au/2h。发情指数遗传力为0.04±0.01，活动峰值遗传力为0.19±0.04，均为低遗传力性状；发情指数与活动峰值之间的遗传相关为0.45±0.03；发情指数与经产牛首末次配种间隔、首次产犊日龄和青年牛首末次配种间隔的近似遗传相关分别为0.37、-0.41、-0.55。两个性状的GWAS共找到7个在全基因组水平上显著的SNP位点，分别位于7条染色体上，显著位点附近（300 kb内）共发现基因31个。【结论】通过项圈系统获得的发情指数和活动峰值是可遗传的，两者之间存在中等遗传相关，活动峰值为中低遗传力，且能够一定程度上反映奶牛的发情指数，活动峰值和发情指数为研究奶牛的发情行为以及提高母牛的繁殖力提供了新的方向。GWAS鉴定到的候选基因PTGS1（Prostaglandin-Endoperoxide Synthase1）和NDUFA8（Ubiquinone Oxidoreductase Subunit A8）的功能与供体胚胎总数有关，VEGFA（Vascular Endothelial Growth Factor A）基因功能与奶牛繁殖有关，可作为奶牛发情相关指标的候选基因进行深入研究。

关键词: 繁殖性状, 发情指数, 活动峰值, 遗传参数, 全基因组关联分析

Abstract:

【Objective】 The study was to explore population characteristics and influencing factors of heat index and activity peak based on cattle collar data and system and to estimate its genetic parameters, and to identify the genetic markers related to the estrus indicators of cow, the genetic analysis and GWAS were performed for heat index and activity peak, so as to provide useful information for improving dairy cow fertility by formulating breeding strategies from the perspective of genetic breeding.【Method】The heat index and activity peak records of 2 074 milking cows from a large-scale dairy farm in Beijing area were collected from July 2017 to May 2020. The MIXED model in SAS 9.4 was used to analyze the impacts of various factors on heat index and activity peak in Holstein cattle, and the DMUAI module of DMU software was used to estimate the heritability and genetic correlations of heat index and activity peak. The GWAS for heat index and activity peak was performed based on De-regressed Proof (DRP) using FarmCPU software. 【Result】 In Chinese Holstein cattle, the average heat index was (71.77±19.13) au, and the activity peak was (105.94±30.73) au/2 h. The heritability of heat index and activity peak was 0.04±0.01 and 0.19±0.04, respectively. The genetic correlation between heat index and activity peak was 0.45±0.03. The approximate heat index between the age at first calving in heifer, interval from first to last insemination, and interval from first to last insemination was 0.37, -0.41, and -0.55, respectively. The GWAS for heat index and activity peak identified seven significant single nucleotide polymorphism loci (SNP) at the genome level, and 31 genes nearby the significant SNP (within 300 kb) were found. 【Conclusion】 The heat index and activity peak obtained by collar system were heritable, and there was a moderate genetic correlation between them. The activity peak was of low heritability and could reflect the heat index of cows to some extent. The activity peak and heat index provided a new direction for studying and breeding the estrus behavior of cows and improving the fecundity of cows. The function of PTGS1 (Prostaglandin-Endoperoxide Synthase1) and NDUFA8 (Ubiquinone Oxidoreductase Subunit A8) genes identified by GWAS was related to the total number of donor embryos, and the function of VEGFA (Vascular Endothelial Growth Factor A) gene was related to the reproduction of cows.

Key words: female fertility, heat index, activity peak, genetic parameter, genome-wide association study

杨明路, 张海亮, 罗汉鹏, 黄锡霞, 张翰林, 章施施, 王炎, 刘林, 郭刚, 王雅春. 基于智能项圈系统荷斯坦牛发情相关指标的遗传参数估计及全基因组关联分析[J]. 中国农业科学, 2023, 56(5): 995-1006.

YANG MingLu, ZHANG HaiLiang, LUO HanPeng, HUANG XiXia, ZHANG HanLin, ZHANG ShiShi, WANG Yan, LIU Lin, GUO Gang, WANG YaChun. Estimation of Genetic Parameters and Genome-Wide Association Study of Heat Indicators in Holstein Cattle Based on Collar-Mounted Device[J]. Scientia Agricultura Sinica, 2023, 56(5): 995-1006.

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性状 Trait	数据量 N	均值 Mean	标准差 SD	最大值 Mix	最小值 Min	变异系数 CV (%)
发情指数Heat index （au）	9 311	71.77	19.13	100	28	26.65%
活动峰值 Activity peak（au/2h）	2 637	105.94	30.73	253	39	29.01%

效应 Effect	水平 Level	发情指数Heat index		活动峰值Activity peak
效应 Effect	水平 Level	数据量 N	LSM±SE	数据量 N	LSM±SE
胎次 Parity	1	2 378	70.79±0.53b	773	108.82±1.66a
	2	2 707	72.05±0.50a	978	108.74±1.58a
	≥3	4 226	71.14±0.46a	886	105.23±1.66c
泌乳阶段 Lactation	（0 -21 d）	327	67.65±1.12c	92	104.14±3.30b
	（22-100 d）	4 798	74.66±0.40a	1 389	112.63±1.33a
	（101 -200 d）	2 979	73.11±0.41b	829	109.47±1.36a
	（201-305d）	1 207	69.91±0.61c	327	104.13±1.93b
情期数 Number of Estrous cycles	1	3 086	70.15±0.45c	850	108.77±1.42a
	2	2 275	70.46±0.53c	669	108.82±1.61a
	3	1 578	72.22±0.60b	456	105.32±1.78b
	≥4	2 372	72.49±0.58a	662	107.46±1.82a
测定季节 Test season	春季（3—5月） Spring（Mar-May）	2 054	71.23±0.55b	632	108.15±1.66a
	夏季（6—8月） Summer（Jun-Aug）	1 753	69.34±0.59c	503	101.67±1.85b
	秋季（9—11月） Autumn（Sep-Nov）	3 062	72.38±0.50a	784	108.50±1.60a
	冬季（12—2月） Winter（Dec-Feb）	2 442	72.38±0.50a	718	112.05±1.59a
测定年份 Test year	2017	2 054	70.94±0.84b	142	112.82±2.83a
	2018	1 753	67.22±0.41c	858	107.36±1.44b
	2019	3 062	72.80±0.43a	1 229	107.17±1.40b
	2020	2 442	74.36±0.67a	408	103.02±2.06c
昼夜 Day-and-night	夜间Day	4 918	72.63±0.63a	1 450	104.95±1.40b
昼夜 Day-and-night	白天Night	4 393	69.83±0.64b	1 187	110.23±1.44a
项圈类型 Heatime type	HR-LD	6 216	68.83±0.42b	554	116.47±1.85a
项圈类型 Heatime type	HR-LDn	3 095	73.84±0.49a	2 083	98.71±1.30b

性状 Trait	加性遗传方差 Additive variance	残差方差 Residual variance	遗传力 Heritability	表型相关 Phenotypic correlation	遗传相关 Genetic correlation
发情指数Heat index	13.80	362.86	0.04±0.01	0.31±0.02	0.45±0.03
活动峰值Activity peak	164.32	697.26	0.19±0.04

性状 Trait	个体数 N	近似遗传相关 Approximate genetic correlation
首次产犊日龄 Age at first calving in heifer	412	-0.41±0.05
首次配种日龄 Age at first service in heifer	419	0.06±0.05
产犊至首次配种间隔 Interval from calving to first service in cow	408	0.06±0.05
经产牛首末次配种间隔 Interval from first to last insemination in cow	404	0.37±0.05
青年牛首末次配种间隔 Interval from first to last insemination in heifer	107	-0.55±0.08

性状 Trait	SNP	染色体 Chromosome	位置 Position (bp)	最小等位基因频率 MAF	候选基因 Harbor genes	P值 P value
发情指数 Heat index	BTB-01605503	10	12659662	0.12	RAB11A、MIR2290、DENND4A、SLC24A1、HACD3、INTS14、DPP8	1.69E-07
	Hapmap51151-BTA-114546	11	93285949	0.14	PTGS1、MRRF、RBM18、LHX6、MORN5、NDUFA8	9.57E-09
	BovineHD1900003595	19	13596512	0.43	ACACA、C19H17orf78、TADA2A、DUSP14、SYNRG、LHX1	2.77E-07
	BovineHD3000015447	30	52853475	0.36	—	2.61E-07
活动峰值 Activity peak	BovineHD2100020097	21	68740864	0.33	ASPG、ATP5MPL	2.39E-09
	BovineHD2200007296	22	24876308	0.30	CNTN6	2.83E-07
	BovineHD2300004473	23	17552613	0.32	AARS2、TMEM151B、SLC35B2、HSP90AB1、SLC29A1、TMEM63B、MRPL14、NFKBIE、VEGFA	3.70E-08

基于智能项圈系统荷斯坦牛发情相关指标的遗传参数估计及全基因组关联分析

Estimation of Genetic Parameters and Genome-Wide Association Study of Heat Indicators in Holstein Cattle Based on Collar-Mounted Device

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