Abstract:

In the major livestock species, parentage verification is done using Single Nucleotide Polymorphism (SNP) markers. ISAG is working to produce a SNP panel for parental verification in horses. There will be a transition period between microsatellites (MS) and SNPs. Without any tool for the transition, breeders will have to double genotype foals or re-genotype mares and stallions with SNPs. We wanted to produce a tool to predict MS genotypes using SNP markers that could be included on a chip with the new ISAG panel. To achieve this we built a correspondence table between MS alleles and SNP haplotypes. We validated it using kfold cross-validation. With the highest SNP density, we obtained 3.4% of incompatibilities over 2 or more MS or 96.6% of parental verification achieved over the major breeds in our study, Selle-Français (SF, 54%), French Trotters (TF, 22%), Arabs (AR, 17%), Anglo-Arabs (AA, 3%) and other saddlebreds (SE, 4%).