Evaluation of a Set of 101 SNP Markers for DNA Typing in the Domestic Horse

Genetic markers are important resources for individual identification and parentage assessment. Short tandem repeats (STRs) have been the traditional DNA marker of choice in many species. However, technological advances have led to single nucleotide polymorphisms (SNPs) becoming an attractive alternative. SNPs can be highly multiplexed and automatically scored, which allows for easier standardization and sharing among different laboratories. We obtained a publicly available data set of 729 horses representing 32 diverse horse breeds genotyped on the Equine SNP50 in order to select SNP markers for DNA typing. A proposed set of 101 SNPs was analyzed for typing suitability. The overall MAF of the panel across all 32 breeds was 0.376 (range 0.304-0.419). A set of 395 horses representing 35 breeds was used to evaluate marker performance on known families. There were 112 parent-offspring pairs and 102 full trios. No horses shared identical genotypes across all markers, indicating the selected set is sufficient for individual identification. The number of opposing homozygous genotypes was calculated for all pairwise comparisons. Relationships were classified using ISAG rules, with 0-1 excluding markers considered an accepted parent-offspring pair, 2-3 excluding markers considered doubtful, and 4+ excluding markers rejecting parentage. False positives included 6 grandparent-grand-offspring and 9 sibling pairs. There were 11 parent-offspring pairs classified as doubtful and 2 were rejected. Our developed marker set is both present on current generation SNP chips and can be highly multiplexed in standalone panels, and thus is a promising resource for SNP based DNA typing.