Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (5): 995-1006.doi: 10.3864/j.issn.0578-1752.2023.05.014

• ANIMAL SCIENCE·VETERINARY SCIENCE • Previous Articles     Next Articles

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. 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 Online:2023-03-01 Published:2023-03-13

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

Table 1

Descriptive statistics on heat related traits of Chinese Holsteins"

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%

Table 2

Effects of various factors on heat index and peak activity in Chinese Holsteins (LSM±SE)"

效应
Effect
水平
Level
发情指数Heat index 活动峰值Activity peak
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
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
HR-LDn 3 095 73.84±0.49a 2 083 98.71±1.30b

Table 3

Estimates of genetic parameters for heat index and activity peak in Chinese Holsteins"

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

Table 4

Approximate genetic correlations between heat index and reproductive in Chinese Holsteins"

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

Fig. 1

Quantile-quantile (Q-Q) plots of genome-wide association study for heat index (left) and activity peak indicators (right)"

Fig. 2

Manhattan plots of genome-wide study for heat index and activity peak indicators in Chinese Holsteins Chromosome 30 is sex chromosome"

Table 5

The genome-wide significant SNP and candidate genes associated with heat index, activity peak in Chinese Holsteins"

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
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
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