Microsatellites Versus Genome-Wide SNPs Data for Pedigree Reconstruction in Twin Simmental Crossbred Cattle

Abstract

Simple Summary This study compared two DNA-based methods for determining mother-calf relationships in a herd of crossbred cattle with a high rate of twinning. One method used 12 standard microsatellite markers, and the other used thousands of genome-wide SNP markers. The SNP method correctly identified 92.3% of known mother-calf groups, while the microsatellite method identified only 84.6% and produced several incorrect groupings. One of the 12 microsatellite markers was completely uninformative in this population, contributing to the lower accuracy. Among the calves, nine pairs were dizygotic twins, one pair was monozygotic, and an additional pair of adult cows was identified as dizygotic twin sisters. These results indicate that genome-wide SNPs show a favourable trend in accuracy and are less prone to false-positive clustering for pedigree reconstruction in genetically diverse cattle populations, especially when pedigree records are incomplete.