Allele Characterization of Ten Short Tandem Repeat Loci of North American Bears (Ursids) Using Next-Generation Sequencing

Abstract

An identification method that provides higher genetic resolution than capillary electrophoresis (CE) is needed for isolated bear populations that possess low genetic diversity. Amplification conditions were optimized for ten bear STR loci. Amplicons were used to develop a library for next-generation sequencing (NGS) on the Ion Torrent™ PGM™ Sequencer. Through ligation of DNA barcode adaptors, seven black bear (Ursus americanus) samples were sequenced together. Sequencing reads were aligned to a virtual ladder and analyzed in NextGENe® software. Allele concordance was shown between CE and NGS. Variants within alleles (SNPs and INDELs) showed that NGS provided higher genetic resolution. These results have implications for improving individual identification and population assignment in wildlife forensics and conservation for populations with low genetic diversity.