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

Abstract

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

CLC Number:

S823.2

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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References 55

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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

Comparison of Prediction Accuracy of Genomic Selection for Economically Important Traits in Huaxi Cattle Based on Different Chip Densities

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芯片密度 Chip density	截距 Intercept	斜率 Slope	R² R_squared
90K	0.277 5	0.439 2	0.545 6
110K	0.336 6	0.374 1	0.481 9
770K	0.286 9	0.413 6	0.549 5
790K	0.283 8	0.459 3	0.547 7

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