Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes

Abstract

The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n=3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n=5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size of eight. In the data set with dairy-only animals, sufficient sires with paternal half-sib progeny groups up to 12 were available and the within-animal mean genotype concordance rates continued to increase up to this group size. The accuracy of imputation was worst for the low-density genotypes, especially with smaller half-sib progeny group sizes but the difference in imputation accuracy between density panels diminished as progeny group size increased; the difference between high and medium-density genotype panels was relatively small across all half-sib progeny group sizes. Where biological material or genotypes are not available on individual animals, at least five progeny can be genotyped (on either a medium or high-density genotyping platform) and the parental alleles imputed with, on average, 96% accuracy.