PARENTAGE VERIFICATION USING IMPUTED MICROSATELLITE AND SNP DATA IN SLOVENIAN BROWN SWISS POPULATION

Abstract

Parentage verification for cattle in Slovenia is routinely done using microsatellite markers (MS). With the incoming SNP data there is currently a discordance between genotypic data available for different animals, which is not suitable for parentage verification. To overcome this problem imputation of MS from SNP data was implemented for Slovenian Brown-Swiss animals. The imputation was performed adopting McClure et al. (2013) methodology and haplotype reference. MS imputation was performed utilising Beagle software. The overall microsatellite imputation accuracy was 91.7 %. Additionally, already confirmed parentages were re-tested using imputed MS. Out of 65 cases of two-parents testing 15.4 % and 44.6 % had 0 and 1 MS misconcordances, respectively, and the parentage was confirmed. For 40.0 % cases with ≥ 2 MS misconcordances parentage was rejected. Next, parentage verification using 800 SNPs was implemented. Out of 43 cases of one-parent testing 90.7 % and 9.3 % had 0 and 1 SNP misconcordances, respectively, therefore verifying all tested parentages. When replacing the real parent with a half-sibling or grandparent, the number of SNP misconcordances was >25 in all cases. The results suggest that MS imputation needs additional optimisation to reach required accuracies, possibly by using a haplotype reference consisting of animals that are genetically more similar to the studied Brown-Swiss population. On the other hand, verification using SNPs has proven as a reliable tool for routine use.