Data from: Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs

The development of high-throughput sequencing has prompted a transition in
wildlife genetics from using microsatellites toward sets of Single
Nucleotide Polymorphisms (SNPs). However, genotyping large numbers of
targeted SNPs using non-invasive samples remains challenging due to
relatively large DNA input requirements. Recently, target enrichment has
emerged as a promising approach requiring little template DNA. We assessed
the efficacy of Tecan Genomics’ Allegro Targeted Genotyping (ATG) for
generating genome-wide SNP data in feral horses using DNA isolated from
fecal swabs. Total and host-specific DNA were quantified for 989 samples
collected as part of a long-term individual-based study of feral horses on
Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a
host-specific qPCR assay, respectively. Forty-eight samples representing
44 individuals containing at least 10ng of host DNA (ATG’s recommended
minimum input) were genotyped using a custom multiplex panel targeting 279
SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG
genotypes with those obtained from the same individuals with SNP
microarrays, and from multiple samples from the same horse, respectively.
62% of swabs yielded the minimum recommended amount of host DNA for ATG.
Ignoring samples that failed to amplify, ATG recovered an average of 86.7%
targeted sites per sample, while genotype concordance between ATG and SNP
microarrays was 98.5%. The repeatability of genotypes from the same
individual approached unity with an average of 99.9%. This study
demonstrates the suitability of ATG for genome-wide, non-invasive targeted
SNP genotyping, and will facilitate further ecological and conservation
genetics research in equids and related species.