Sex identification of northern ungulates using low quality and quantity DNA

We evaluated PCR primer sets to determine the most effective technique for identifying sex of northern ungulates. We sought markers that required only a single pair of primers to amplify both X- and Y-linked alleles; that amplified X- and Y-linked products that were easily distinguishable using agarose gel electrophoresis; and that produced short amplicons amenable to amplification using DNA of poor quality and low quantity, as is often found in non-invasively collected samples such as feces. Primer pairs KY1/KY2 and SE47/SE48, which amplify X- and Y-specific alleles of the amelogenin gene, met our criteria and were tested for moose (Alces alces), mountain goat (Oreamnos americanus), Sitka black-tailed deer (Odocoileus hemionus sitkensis), and caribou (Rangifer tarandus). KY primers amplified shorter PCR products than did SE primers; moreover, SE primers inconsistently amplified certain Y-chromosome products, creating potential for misidentification of sex. DNA fragments amplified using KY primers were sequenced for each species, allowing us to characterize a 45-bp deletion for Y-linked alleles (136-bp product) relative to X-linked alleles (181-bp product) in all species and a 9-bp deletion in the X-linked allele of moose relative to other species. This is the first sex-determination technique using PCR reported for several ungulate species of Alaska. Although other protocols exist for cervids and bovids, this is the first report of markers meeting the aforementioned criteria for Odocoileus, the most abundant and intensively managed genus of large mammals in North America.