Use of SNPs from Illumina BovineSNP50K BeadChip v3 for imputation of microsatellite alleles for parentage verification and QTL reporting

The present study aimed to test the possibility of avoiding expensive retesting of the whole parental generation for single nucleotide polymorphisms (SNPs), to provide additional analysis of microsatellites in offspring in the transitional period and to analyse the likelihood of imputation of the International Society for Animal Genetics-recommended microsatellite markers from selected SNPs. The imputation and pedigree verification of 9 520 animals (representing 84 dairy bulls, 285 dairy cows, 3 202 beef bulls and 5 949 beef cows) were analysed by the method using 9 410 SNP haplotypes (incorporating an average of 73 SNPs per haplotype). The imputation method was confirmed to allow the parentage verification of up to 87% of the analysed animals without the need for retesting. The most problematic locus was TGLA53, with only 78% successful imputation. Seven loci (BM2113, ETH225, TGLA227, BM1824, SPS115, TGLA122 and TGLA126) had more than 90% imputing accuracy and success of imputation. The success of imputation also depends on the breed and the call rate of the test results. The highest imputation accuracy was found for the Holstein breed; the other six breeds had over 90% successful imputation rates, four breeds had imputation rates between 85.0 and 89.9%, and ten breeds (rarely bred in the Czech Republic) had imputation rates below 85.0%. A call rate of SNP tests lower than 90% indicates problems with haplotype construction and thus deterioration in the success of imputation. The analysis of a possibility of using all possible information from Illumina BovineSNP50K BeadChip v3 showed 109 SNPs encoding 51 quantitative trait loci markers. Haplotypes were designed for interpretation of the most important markers for diseases, exterior and performance. The most important markers for Holstein breeders were chosen as kappa- (variants A, B and E) and beta-casein (variants A1, A2), Holstein haplotypes affecting fertility (HH1, HH3, and HH4) and loci causing genetic defects, bovine leukocyte adhesion deficiency and deficiency of uridine monophosphate synthetase. The results estimated from bovine bead chips corresponded to the expected distribution of the incidence of these traits in the population and were verified by PCR-RFLP tests.