Development of nuclear microsatellite markers for American badger subspecies (Taxidea taxus spp.) using next generation sequencing

Several American badger subspecies are of conservation concern and most notably Taxidea taxus jacksoni and T. t. jeffersonii are both considered endangered in Canada. Previous studies report extremely low genetic diversity in T. t. jacksoni making individual genetic identifications from non-invasive samples challenging with existing markers. We used 454 next generation sequencing to identify additional panels of polymorphic microsatellites for the American badger. We designed nineteen dinucleotide microsatellite primers of >17 uninterrupted repeat motifs. Of these markers, only eight showed polymorphism in T. t. jacksoni. We also amplified these loci in T. t. jeffersonii and T. t. taxus. Total allele number per locus ranged from 2 to 11 and expected heterozygosity from 0.3 to 0.87. T. t. taxus showed higher heterozygosity across loci, whereas T. t. jacksoni showed the lowest genetic diversity. These microsatellites will provide an enhanced capacity for identifying closely related individuals from non-invasive samples.