不同芯片密度对华西牛重要经济性状基因组评估准确性的影响

doi:10.11843/j.issn.0366-6964.2025.02.011

摘要/Abstract

摘要：

旨在基于Illumina BovineHD 770K与Cattle 110K芯片在华西牛中的实际应用情况，系统比较在不同标记密度下基因组选择预测准确性的差异，探索两款芯片在华西牛遗传评估中结合使用方法。本试验以课题组前期构建的华西牛基因组选择参考群体为研究对象，利用重测序数据将3 948头华西牛770K芯片填充至790K后，分别取90K(两款芯片交集)、110K、770K、790K(两款芯片并集)4种标记密度，对华西牛遗传评估所涉及的5个性状(断奶重、育肥期平均日增重、产犊难易度、胴体重、屠宰率)进行遗传力估计，并通过GBLUP模型利用五折交叉验证对基因组评估准确性进行比较，筛选并确定华西牛遗传评估中最适标记密度。结果显示：1)4种标记密度下，估计的华西牛5个性状遗传力差异不显著，断奶重和平均日增重的遗传力为0.47~0.50，属于高遗传力；胴体重为0.37~0.39，属于中等遗传力；产犊难易度和屠宰率性状为0.14~0.21，属于中低遗传力。2)在GBLUP评估模型中，Cattle 110K在各个性状上的预测准确性均表现良好，并较Illumina BovineHD 770K芯片有显著提升(P < 0.05)，其中胴体重、产犊难易度和屠宰率3个性状提升较为明显，分别提升了14.9%、13.8%和8.4%；断奶重和育肥期平均日增重分别提升2.8%和4.5%。3)各性状预测准确性随着遗传力的升高而增加，不同标记密度的回归系数分别为0.439 2(90K)、0.374 1(110K)、0.413 6(770K)、0.459 3(790K)。因此，在华西牛实际遗传评估中，可直接使用Cattle 110K芯片进行评估，在获得较好评估准确性的同时降低成本。

关键词: 华西牛, 基因组选择, 标记密度, 育种芯片, 中国肉牛基因组选择指数

Abstract:

This study systematically compared the effects of different marker densities on the predictive accuracy and explored methods for combining these two chips of genetic evaluations in Huaxi cattle based on the practical application of the Illumina BovineHD 770K and Cattle 110K chips. In this study, a genomic selection reference population of 3 948 Huaxi cattle was used. The 770K chip data were imputed to 790K by using resequencing data. Then 4 marker densities were selected: 90K (intersection of the two chips), 110K, 770K, and 790K (union of the two chips). The heritability of 5 traits (weaning weight, daily weight gain during the fattening period, calving ease, carcass weight, and dressing percentage) were estimated, and the predictive accuracy of genomic evaluations was compared using the GBLUP model, identifying the optimal marker density for genetic evaluations in Huaxi cattle. The results showed that: 1) There were no significant differences in the estimated heritability of the 5 traits across the 4 marker densities. The heritability for weaning weight and daily weight gain during fattening period ranged from 0.47 to 0.50 (high heritability), carcass weight ranged from 0.37 to 0.39 (moderate heritability), and calving ease and dressing percentage ranged from 0.14 to 0.21 (low to moderate heritability). 2) The Cattle 110K chip demonstrated significantly better predictive accuracy for all traits compared to the Illumina BovineHD 770K chip (P < 0.05) in the GBLUP model. The improvements were particularly notable for carcass weight, calving ease and dressing percentage, with increases of 14.9%, 13.8%, and 8.4%, respectively. For weaning weight and daily weight gain during fattening period, the improvements were 2.8% and 4.5%, respectively. 3) The predictive accuracy of traits increased with higher heritability under the 4 marker densities. The regression coefficients for the different marker densities were 0.439 2 (90K), 0.374 1 (110K), 0.413 6 (770K), and 0.459 3 (790K). Therefore, the Cattle 110K chip can be used directly, achieving good predictive accuracy while reducing costs in practical genetic evaluations of Huaxi cattle.

Key words: Huaxi cattle, genomic selection, marker density, breeding chip, genomic China beef index

中图分类号:

S823.2

王元清, 王泽昭, 朱波, 陈燕, 徐凌洋, 张路培, 高会江, 李超, 李俊雅, 高雪. 不同芯片密度对华西牛重要经济性状基因组评估准确性的影响[J]. 畜牧兽医学报, 2025, 56(2): 591-602.

WANG Yuanqing, WANG Zezhao, ZHU Bo, CHEN Yan, XU Lingyang, ZHANG Lupei, GAO Huijiang, LI Chao, LI Junya, GAO Xue. Comparison of Prediction Accuracy of Genomic Selection for Economically Important Traits in Huaxi Cattle Based on Different Chip Densities[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(2): 591-602.

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芯片密度 Chip density	质控前 Before quality control		质控后 After quality control
芯片密度 Chip density	个体数 Count	位点数量 Number of loci	个体数 Count	位点数量 Number of loci
90K	3 948	90 749	3 919	63 902
110K	3 948	112 180	3 919	80 939
770K	3 948	774 660	3 919	624 923
790K	3 948	796 091	3 919	641 959

性状 Trait	年份 Year	性别 Sex	场 Farm	季节 Season	产犊年龄 Calving age	后代性别 Calf sex
断奶重 Weaning weight	√	√	√	×	×	×
育肥期平均日增重 Daily weight gain during fattening period	√	√	√	√	×	×
产犊难易度 Calving ease	√	×	×	×	√	√
胴体重 Carcass weight	√	√	√	√	×	×
屠宰率 Dressing percentage	√	√	√	√	×	×

性状 Trait	个体数 Count	最小值 Minimum	最大值 Maximum	平均值 Mean	标准差 Standard deviation
断奶重/kg Weaning weight	1 294	40.00	395.00	203.75	53.13
育肥期平均日增重/kg Daily weight gain during fattening period	1 324	0.37	2.41	0.96	0.21
产犊难易度 Calving ease	944	1.00	4.00	1.11	0.39
胴体重/kg Carcass weight	1 694	162.60	482.00	297.56	64.03
屠宰率/% Dressing percentage	1 687	41.00	69.51	53.86	4.21

性状 Trait	芯片密度 Chip density	表型方差 Phenotype variance	残差方差 Residual variance	加性方差 Additive variance	遗传力 Heritability
断奶重 Weaning weight	90K	2 090.034 0	1 039.189 0	1 050.845 0	0.502 8
	110K	2 091.601 0	1 062.287 0	1 029.314 0	0.492 1
	770K	2 092.303 0	1 040.916 0	1 051.387 0	0.502 5
	790K	2 091.518 0	1 043.308 0	1 048.210 0	0.501 2
育肥期平均日增重 Daily weight gain during fattening period	90K	0.029 6	0.015 6	0.014 0	0.473 3
	110K	0.029 5	0.015 2	0.014 3	0.485 7
	770K	0.029 5	0.015 3	0.014 2	0.480 6
	790K	0.029 5	0.015 0	0.014 5	0.490 5
产犊难易度 Calving ease	90K	0.146 4	0.124 4	0.022 0	0.150 0
	110K	0.146 2	0.125 5	0.020 8	0.141 8
	770K	0.146 5	0.122 9	0.023 6	0.160 8
	790K	0.146 5	0.123 1	0.023 4	0.159 6
胴体重 Carcass weight	90K	1 018.409 2	636.122 2	382.287 0	0.375 4
	110K	1 012.938 2	622.160 6	390.777 6	0.385 8
	770K	1 016.092 7	644.958 8	371.133 9	0.365 3
	790K	1 014.752 5	632.317 4	382.435 1	0.376 9
屠宰率 Dressing percentage	90K	0.000 6	0.000 5	0.000 1	0.195 3
	110K	0.000 6	0.000 5	0.000 1	0.206 9
	770K	0.000 6	0.000 5	0.000 1	0.205 3
	790K	0.000 6	0.000 5	0.000 1	0.208 5

芯片密度 Chip density	无偏性 Unbiasedness
芯片密度 Chip density	断奶重 Weaning weight	平均日增重 Daily weight gain during fattening period	产犊难易度 Calving ease	屠宰率 Dressing percentage	胴体重 Carcass weight
90K	0.946 1 ±0.063 3	0.988 7 ±0.090 5	0.870 1 ±0.141 2	1.010 5 ±0.084 4	0.907 9 ±0.064 7
110K	0.851 0 ±0.041 3	0.994 2 ±0.029 2	0.974 5 ±0.091 3	0.951 0 ±0.089 8	0.934 6 ±0.075 2
770K	0.877 3 ±0.122 6	0.986 7 ±0.132 7	1.008 8 ±0.132 6	0.981 0 ±0.099 1	0.995 7 ±0.036 2
790K	0.899 5 ±0.087 4	1.038 6 ±0.118 6	0.871 8 ±0.126 9	1.012 4 ±0.085 3	0.915 7 ±0.055 6