Detailed characterization of repeat motifs of nine canid microsatellite loci in African painted dogs (Lycaon pictus)

Microsatellite loci identified in domestic species are frequently amplified and genotyped in wildlife species for which limited genomic information is available. However, even when the loci amplify successfully, genotyping them accurately in novel species can be complicated when the repeat motif is unknown or when the expected product size in the new target species differs from that reported for the domestic species from which the locus was identified. In this study, we amplified nine microsatellite loci that were identified previously in the domestic dog and genotyped them in 114 endangered African painted dog (Lycaon pictus) individuals. Although primer sequences for these loci were published, minimal details about the repeat motifs were available in the literature, and some of our product sizes differed substantially from those reported for the domestic dog, which complicated initial multiplexing and genotyping efforts. We therefore cloned and sequenced these loci to characterize the repeat structures and amplicon size for each locus, specific to L. pictus. Seven of the nine loci contained imperfect, compound repeats that often were a combination of di- and tetranucleotide repeats or which contained strings of single nucleotides. The resulting amplicons were also considerably smaller or larger than expected based on the homologous domestic dog loci. This information may assist other researchers who are conducting molecular studies on this endangered species or on other closely related canids.