猪SNP液相芯片10K~50K基因型填充效果研究

doi:10.11843/j.issn.0366-6964.2022.10.010

畜牧兽医学报 ›› 2022, Vol. 53 ›› Issue (10): 3368-3376.doi: 10.11843/j.issn.0366-6964.2022.10.010

猪SNP液相芯片10K~50K基因型填充效果研究

陈宇^1,2, 邱奥², 张梓鹏², 都鹤鹤², 白俊艳¹, 王贵江³, 罗文学³, 倪俊卿³, 李凯⁴, 丁向东^2*

1. 河南科技大学动物科技学院, 洛阳 471000;
2. 中国农业大学动物科学技术学院畜禽育种国家工程实验室农业农村部动物遗传育种与繁殖重点实验室, 北京 100193;
3. 河北省畜牧良种工作总站, 石家庄 050061;
4. 河南省畜牧总站, 郑州 450008

收稿日期:2022-03-28 出版日期:2022-10-23 发布日期:2022-10-26
通讯作者: 丁向东,主要从事猪遗传育种与统计遗传学研究,E-mail:xding@cau.edu.cn
作者简介:陈宇(1998-),男,安徽马鞍山人,硕士生,主要从事动物遗传育种与繁殖研究,E-mail:1970374577@qq.com
基金资助:
河北省重点研发计划项目（19226376D）；财政部和农业农村部：国家现代农业产业技术体系（CARS-35）；国家重点研发计划项目（2019YFE0106800）

Study on the Genotype Imputation Effect of 10K-50K Genotype of Pig SNP Liquid Chip

CHEN Yu^1,2, QIU Ao², ZHANG Zipeng², DU Hehe², BAI Junyan¹, WANG Guijiang³, LUO Wenxue³, NI Junqing³, LI Kai⁴, DING Xiangdong^2*

1. College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China;
2. Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
3. Hebei Province Animal Husbandry and Improved Breeds Work Station, Shijiazhuang 050061, China;
4. Henan Province Animal Husbandry Station, Zhengzhou 450008, China

Received:2022-03-28 Online:2022-10-23 Published:2022-10-26

摘要/Abstract

摘要： 旨在探究低密度液相芯片在生产实践中的实用性，降低育种成本。本试验选用了3 761头约160日龄，110 kg左右健康大白猪，随机抽取100头大白猪，根据10K芯片标记信息，从50K芯片中抽取标记生成10K芯片，作为填充群体。再从剩余群体中，分别随机抽取800、2 000、3 600个个体作为参考群体，使用Beagle 4.1软件对100头填充群体进行基因型填充至50K芯片，重复10次，以基因型一致性和基因型相关系数来评价基因型填充的准确性。结果表明，10K和50K芯片平均连锁不平衡（r²）程度为0.227和0.258，相差不大。最小等位基因频率（MAF）为0.05是基因型填充准确性的拐点，剔除掉MAF<0.05标记后，填充准确性明显升高。填充准确性随参考群体规模增大而上升，参考群由800头扩大到3 600头，填充准确性从0.90提高到0.95，10次重复的标准差也从0.006下降到0.002。对于较小的参考群体规模，染色体基因型填充准确性波动较大，随着参考群体规模增大，每条染色体填充准确性相差不大。本研究结果表明，猪液相芯片从10K填充到50K是可行的，可以大规模用于基因组选择，降低基因组选择育种成本。

关键词: 猪, 液相芯片, 基因型填充, 分子育种

Abstract: The study aimed to explore the efficiency of low-density liquid-based chips in practical animal breeding and reduce breeding costs. A total of 3 761 healthy Large White pigs with about 160 days of age and 110 kg of body weight were used in this study, 100 out of these Large White pigs were randomly selected to serve as a validation population for imputation, in which a 10K SNP panel was generated by sampling markers from the 50 K panel, according to the marker information in 10K SNP panel. Meanwhile, 800, 2 000, 3 600 individuals were randomly selected from the remaining pigs as the reference populations, respectively. Beagle 4.1 was used to impute the 100 validation pigs to 50K SNP panel, and 10 replications were carried out. Genotype consistency and genotype correlation coefficients were used to evaluate the accuracy of genotype imputation. The results showed that the average linkage disequilibrium (r²) of the 10K and 50K SNP panel were 0.227 and 0.258, respectively, with little difference. Minor allele frequency (MAF) of 0.05 was the inflection point for the accuracy of genotype imputation, the accuracy significantly increased after removing markers with MAF less than 0.05. With the reference population size increased from 800 to 3 600, the imputation accuracy was improved from 0.90 to 0.95, and the standard deviation of imputation accuracy among 10 replicates was also decreased from 0.006 to 0.002. For small reference population with 800 individuals, the genotype imputation accuracy of each chromosome fluctuated obviously, while with enlarging the reference population, the imputation accuracy of each chromosome became very close. The study result demonstrates that the imputing from 10K to 50K liquid-based SNP panel is feasible and could be helpful for the application in genomic selection on a large scale, dramatically reducing the breeding cost of genomic selection.

Key words: pig, liquid chip, genotype imputation, molecular breeding

中图分类号:

S828.2

陈宇, 邱奥, 张梓鹏, 都鹤鹤, 白俊艳, 王贵江, 罗文学, 倪俊卿, 李凯, 丁向东. 猪SNP液相芯片10K~50K基因型填充效果研究[J]. 畜牧兽医学报, 2022, 53(10): 3368-3376.

CHEN Yu, QIU Ao, ZHANG Zipeng, DU Hehe, BAI Junyan, WANG Guijiang, LUO Wenxue, NI Junqing, LI Kai, DING Xiangdong. Study on the Genotype Imputation Effect of 10K-50K Genotype of Pig SNP Liquid Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(10): 3368-3376.

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猪SNP液相芯片10K~50K基因型填充效果研究

Study on the Genotype Imputation Effect of 10K-50K Genotype of Pig SNP Liquid Chip

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