自主研发奶牛13K和40K液相SNP芯片的性能验证及在基因组选择中的应用

doi:10.11843/j.issn.0366-6964.2025.11.013

Abstract

Abstract:

This study aimed to evaluate the call rate, genotype concordance, imputation accuracy, and genomic prediction accuracy of the self-developed 13K and 40K liquid-phase SNP chips for dairy cattle. Genotyping was performed on 203 individuals in the validation population using the 13K, 40K, and existing commercial 126K and 150K SNP chips. Call rates and genotype concordances were then compared. Beagle software was used to impute the genotypic data of the 4 chips to a 50K density level based on the Chinese Holstein genomic selection reference population. The GBLUP method was employed to assess the genomic prediction accuracy for 9 traits in the validation population. Imputation accuracy and genomic prediction accuracy were then compared among the 4 chips. In the validation population, the call rates of the 13K and 40K chips were 97.70% and 97.20%, respectively, while those of the 126K and 150K chips were 99.30% and 98.27%. The 13K and 40K chips shared 11 331 and 11 125 SNPs and 42 504 and 40 881 SNPs with the 126K and 150K chips, respectively, with genotype concordance rates of 96.23%, 96.50%, 97.18%, and 97.43%. The 13K chip (MAF>0.01) achieved an accuracy of 95.90%, slightly lower than that of high-density commercial chips but higher than the international low-density Illumina 7K (94.30%) chips. Meanwhile, The imputation accuracy of the 40K chip (MAF>0.01) reached 99.07%, comparable to the 126K (99.23%) and 150K chips (99.05%).The genomic prediction accuracies for 9 traits—milk yield, fat percentage, protein percentage, fat yield, protein yield, udder system score, final score, somatic cell score, and feet and legs score—using the 13K, 40K, 126K, and 150K chips ranged from 0.619 0 to 0.735 2, 0.642 0 to 0.758 7, 0.620 8 to 0.742 8, and 0.633 4 to 0.751 4, respectively, with no significant differences observed. The findings indicate that the self-developed 13K and 40K liquid-phase SNP chips demonstrate robust performance and are suitable for early genetic evaluation and elite selection in Holstein dairy cattle.

Key words: liquid-phase SNP chip, dairy cattle, call rate, genotype imputation, genomic prediction accuracy

CLC Number:

S823.2

SONG Jian, HE Jinfeng, ZHENG Weijie, LIU Lin, MA Zhu, QIAN Changsong, ZHOU Jinghang, HAN Bo, ZHANG Qi, SUN Dongxiao. Performance Validation and Application of Self-developed 13K and 40K Liquid-phase SNP Chips in Genomic Selection of Dairy Cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(11): 5502-5511.

Figures/Tables 8

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芯片 Chip	共有位点数 Common SNPs	分型一致位点数 Genotyped concordant SNP count	基因型一致性/% Genotype concordance
13K-126K	11 331	10 903	96.23
13K-150K	11 125	10 811	97.18
40K-126K	42 504	41 018	96.50
40K-150K	40 881	39 832	97.43

芯片 Chip	填充前位点数 Number of SNPs before imputation	填充并质控后位点数 Number of SNPs after imputation and quality control	基因型一致性DR²/% Genotype concordance DR²
13K-50K	11 358	44 378	95.90
40K-50K	44 373	44 853	99.07
126K-50K	120 155	44 941	99.23
150K-50K	139 097	44 820	99.05

性状 Trait	产奶量 Milk yield	乳脂率 Fat percentage	乳蛋白率 Protein percentage	乳脂量 Fat yield	乳蛋白量 Protein yield	体型总分 Final score	泌乳系统评分 Udder system score	肢蹄评分 Feet and legs score	体细胞评分 Somatic cell score
遗传力 Heritability	0.33	0.43	0.52	0.29	0.29	0.27	0.26	0.45	0.26

性状 Trait	芯片Chip
性状 Trait	13K	40K	126K	150K
产奶量Milk yield	0.667 6	0.691 6	0.672 3	0.683 0
乳脂率Fat percentage	0.707 1	0.731 1	0.713 1	0.723 3
乳蛋白率Protein percentage	0.735 2	0.758 7	0.742 8	0.751 4
乳脂量Fat yield	0.650 3	0.674 1	0.654 5	0.665 2
乳蛋白量Protein yield	0.646 9	0.670 9	0.650 8	0.661 8
体型总分Final score	0.626 8	0.650 7	0.629 7	0.642 0
泌乳系统评分Udder system score	0.621 7	0.645 8	0.624 4	0.636 9
肢蹄评分Feet and legs score	0.701 5	0.726 1	0.707 7	0.719 1
体细胞评分Somatic cell score	0.619 0	0.642 0	0.620 8	0.633 4

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Performance Validation and Application of Self-developed 13K and 40K Liquid-phase SNP Chips in Genomic Selection of Dairy Cattle

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