Evaluation of the Effectiveness of Single-Nucleotide Polymorphisms Versus Microsatellites for Parentage Verification in Horse Breeds

This study aimed to generate information for parentage testing in horse breeds using microsatellites (STRs) and single-nucleotide polymorphisms (SNPs). Genotype data were obtained from 189 horse hair root samples, including 38 Thoroughbreds (TBs), 17 Jeju horses (JHs), 20 Quarter horses (QHs), 21 American Miniatures (AMs), and 93 Mongolian horses (MHs), using 15 STR markers and 71 SNP markers. Comparative analysis revealed that the mean expected heterozygosity ranged from 0.468 (AM) to 0.491 (JH) for SNPs and from 0.695 (TB) to 0.791 (MH) for STRs. The mean observed heterozygosity ranged from 0.415 (AM) to 0.487 (MH) for SNPs and from 0.706 (JH) to 0.776 (MH) for STRs. The mean polymorphic information content ranged from 0.349 (AM) to 0.364 (MH) for SNPs and from 0.635 (TB) to 0.761 (MH) for STRs. The inbreeding coefficient ranged from -0.009 (MH) to 0.113 (AM) for SNPs and from -0.058 (TB) to 0.043 (AM) for STRs. The cumulative exclusion probability (PE) for the 71-SNP panel exceeded 0.9999, indicating that SNP markers may be sufficient for parentage testing. In comparison, the STR markers yielded a combined PE of 0.9988 when one parent was known and 0.9999 when both parents were known. These findings highlight the potential of SNPs as alternatives to STRs for routine paternity verification in horses.