Accuracy Analysis of Genotype Imputation from 10K to 50K SNP Loci in Layers
The aim of this study was to analyze the accuracy of using low-density chip genotyping data to obtain high-density genotype data through genotype imputation.In this study,the geno-typic consistency between the imputed genotypes based on 10K and the 50K real genotypes was analyzed.The 4 435 healthy brown laying hens from pure-line were selected,and 50K SNP array of laying hens was used for genotype determination.Some individuals were randomly selected as test and reference populations,respectively.The 10K genotype data was evenly selected from 50K typing data as known genotypes,and Beagle 4.0 software was used to impute genotypes of the rest 40K to obtain 50K data.The consistency of the imputed genotype and the real genotype was compared.The accuracy of genotype filling was evaluated by genotype filling consistency.We also analyzed the influence of following 3 aspects on the accuracy of genotype filling:1)usage of pedigree or not(100 individuals in test population vs.1 000 individuals in reference popula-tion);2)kinship between reference and test population(100 individuals in test population vs.1 000 individuals in reference population);3)reference population size(100 individuals in test population vs.500,1 000,2 000,3 000 individuals in reference population).The results showed that the consistency of genotypic imputation was not affected by the use of genealogical informa-tion or not(0.973 vs.0.973).The consistency of genotypic imputation was changed as the change of inter-population kinship.Using the individuals from 18th generation(1 000 individu-als)as reference population to impute the genotypes of 19th generation population(100 individu-als),the consistency of genotypic imputation was to 0.972.When using individuals from the 16th,17th and 18th generations as reference population to impute the genotypes of 19th genera-tion population,and the consistency of genotypic imputation was decreased to 0.968.The impu-tation consistency of genotype was increased with the increase of reference population size.The con-sistency of genotype imputation was 0.959,0.973,0.980,and 0.984 when the reference population size was 500,1 000,2 000,and 3 000,respectively.Collectively,this study shows that the im-putation of layer SNP array from 10K to 50K is feasible,and it can be applied in genome selection breeding to reduce genotyping costs.
万方数据
维普
