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

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (11): 5502-5511.doi: 10.11843/j.issn.0366-6964.2025.11.013

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

宋建¹^,⁴(), 贺巾锋¹, 郑伟杰¹, 刘林², 麻柱², 钱长嵩³, 周靖航³, 韩博¹^,⁴, 张琪¹, 孙东晓¹^,⁴^,*()

1. 中国农业大学动物科学技术学院, 农业农村部动物遗传育种与繁殖重点实验室, 动物育种国家工程实验室, 畜禽生物育种全国重点实验室, 北京 100193
2. 北京奶牛中心, 北京 100192
3. 石家庄博瑞迪生物技术有限公司, 石家庄 050035
4. 中国农业大学三亚研究院, 三亚 572025

收稿日期:2025-02-14 出版日期:2025-11-23 发布日期:2025-11-27
通讯作者: 孙东晓 E-mail:sj1657033944@163.com;sundx@cau.edu.cn
作者简介:宋建(2002-)，男，山东临沂人，博士生，主要从事奶牛遗传育种的研究，E-mail: sj1657033944@163.com
基金资助:
国家重点研发计划项目(2021YFF1000700)；教育部创新团队发展计划(IRT_15R62)

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

SONG Jian¹^,⁴(), HE Jinfeng¹, ZHENG Weijie¹, LIU Lin², MA Zhu², QIAN Changsong³, ZHOU Jinghang³, HAN Bo¹^,⁴, ZHANG Qi¹, SUN Dongxiao¹^,⁴^,*()

1. Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
2. Beijing Dairy Cattle Center, Beijing 100192, China
3. Shijiazhuang Molbreeding Biotech Co., Ltd., Shijiazhuang 050035, China
4. Sanya Institute of China Agricultural University, Sanya 572025, China

Received:2025-02-14 Online:2025-11-23 Published:2025-11-27
Contact: SUN Dongxiao E-mail:sj1657033944@163.com;sundx@cau.edu.cn

摘要/Abstract

摘要：

旨在对自主研发奶牛13K和40K液相基因组SNP芯片的检出率、基因型检测一致性、填充准确性及基因组遗传评估准确性进行验证。本研究对203头验证群体进行13K、40K及已有商业化126K、150K芯片基因型检测并比较分析检出率与基因型一致性。基于中国荷斯坦牛基因组选择参考群体，采用Beagle软件将4款芯片的基因型数据分别填充至50K密度水平并采用GBLUP方法对验证群体的9个性状进行基因组遗传评估，比较其填充准确性及9个性状的基因组遗传评估准确性。结果表明，验证群体的13K和40K芯片检出率分别为97.70%和97.20%，126K和150K芯片检出率分别为99.30%和98.27%，13K和40K芯片与126K和150K芯片的共有位点数分别为11 331、11 125与42 504、40 881，共有位点基因型一致性分别为96.23%、96.50%与97.18%、97.43%；13K芯片填充准确性(MAF>0.01)为95.90%，略低于高密度商业化芯片，但高于国际通用Illumina 7K低密度芯片(填充准确性为94.30%)，40K芯片填充准确性(MAF>0.01)为99.07%，与126K(填充准确性为99.23%)和150K芯片(填充准确性为99.05%)基本一致；13K、40K、126K和150K芯片对验证群体产奶量、乳脂率、乳蛋白率、乳脂量、乳蛋白量、泌乳系统评分、体型总分、体细胞评分、肢蹄评分等9个性状基因组遗传评估准确性分别为0.619 0~0.735 2、0.642 0~0.758 7、0.620 8~0.742 8和0.633 4~0.751 4，无显著差异。研究结果表明，自主研发13K和40K液相芯片性能较好，可以用于荷斯坦奶牛早期遗传评估和优秀牛只选择。

关键词: 液相SNP芯片, 奶牛, 检出率, 基因型填充, 遗传评估准确性

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

中图分类号:

S823.2

宋建, 贺巾锋, 郑伟杰, 刘林, 麻柱, 钱长嵩, 周靖航, 韩博, 张琪, 孙东晓. 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[J]. 畜牧兽医学报, 2025, 56(11): 5502-5511.

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.

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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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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

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

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