Using SNP Genotyping Arrays for Kinship and Parentage Analysis in Threatened Equid Species

Single nucleotide polymorphisms (SNPs) are gaining increasing popularity as a genetic marker for many conservation genetics applications. However, their discovery in threatened species with limited access to genomic resources remains challenging. Large numbers of SNPs can now be interrogated simultaneously in numerous model and domestic organisms, including the domestic horse (Equus caballus), using whole-genome genotyping arrays. We explored the potential of using these commercially available platforms as a straightforward and cost-effective approach to SNP discovery in taxa sharing a recent evolutionary history with an array species. Collections of markers identified in equid species using the domestic horse genotyping array were evaluated for their power to predict kinship and parentage. Samples from the order Perissodactyla (n=106), including species with up to 55 million years divergence from the domestic horse, have been genotyped on the equine 50K and 70K beadchips. Genotyping rates in the more closely Equus species was high, averaging 93%. Pairwise coancestry was estimated using Przewalski’s horse (Equus przewalksii) and Persian onager (Equus hemionus onager) samples with known ancestry. A pruned set of informative SNPs revealed a strong correlation between molecular and genealogical coancestry for Persian onager (r=0.85-0.96). More variable correlations were reported for Przewalski’s horse (r=0.50-0.92). Simulations suggest as few as 50 highly polymorphic SNPs will provide sufficient power for paternity assignment with 95% confidence in both species. These results indicate a relatively small panel of SNP markers could be used to clarify pedigree relationships and parentage, with numerous applications for the genetic management of captive equid species.