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

  • Jana Obsteter Agricultural Institute of Slovenia
Keywords: parentage verification, cattle, microsatellite imputation, SNP haplotype, Slovenia

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.

Published
2017-03-06