参考群筛选方法及规模对基因型填充准确性的影响

doi:10.11843/j.issn.0366-6964.2021.012.004

Abstract

Abstract: The study aimed to explore the influence of different reference population screening methods and size on accuracy of genotype imputation, such as maximizing the expected genetic relationship for matrix A (RELA), minimized the target population genetic variance for matrix A(MCA), the highest mean kinship coefficients (KIN), random selection (RAN), common ancestor (CA). In this study, the dwarf and yellow-feathered chicken population were used, and the chicken 600K SNP array(Affymetrix Axion HD genotyping array) was used for genotyping. The body weight of 435 offspring cocks at 45, 56, 70, 84 and 91 days of age were measured. The Beagle software was used to impute low-density SNP chips into high-density SNP chips, to compare the influence of reference population screening methods and reference population size on accuracy of imputed genotype and accuracy of imputed chips for genomic prediction. The results showed that the best imputation method was using Beagle 4.0 with pedigree information, followed by Beagle 4.0, and Beagle 5.1 was comparatively the worst. MCA method had the highest accuracy of genotype imputation, RAN method had the lowest accuracy of genotype imputation, the accuracy of MCA, RELA and CA methods for genotype imputation had small difference. Compared with other methods, MCA method has higher prediction accuracy to select key individuals as reference population and to impute from low-density SNP chips to high-density SNP chips for genome selection, which was slightly different from that of real high-density SNP chips. With the increase of reference population size, the accuracy of genotype imputation were also increased, but the growth rate were gradually decreased and finally tended towards stability. In conclusion, the accuracy of genotype imputation and genome prediction,as well as lower costs were guaranteed by selecting key individual screening methods and controlling the size of reference population. This study provides technical reference for the application of genotype imputation in livestock genetic breeding.

Key words: chicken, genotype imputation, selection method of reference population, size of reference population, accuracy of imputation

CLC Number:

S831.2

YANG Wenpan, YE Shaopan, YE Haoqiang, LIN Qing, WEI Chen, ZHANG Zhigang, ZHANG Xiquan, CHEN Zanmou, ZHANG Zhe. Effect of Reference Population Selection Method and Size on Genotype Imputation Accuracy[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(12): 3357-3365.

References 40

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Effect of Reference Population Selection Method and Size on Genotype Imputation Accuracy

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