High-Resolution Melting Analysis for the Discovery of Novel Single-Nucleotide Polymorphisms in Rainbow and Cutthroat Trout for Species Identification

We describe the use of high-resolution melting (HRM), a recent enhancement to traditional DNA melting analyses for the characterization of polymerase chain reaction products, in the identification of 11 novel single-nucleotide polymorphisms (SNPs) for distinguishing between rainbow trout Oncorhynchus mykiss and cutthroat trout O. clarkii. Single-nucleotide polymorphisms provide an important tool for species identification in studies of hybridization and introgression between these two species, but until now the time-consuming and costly nature of DNA sequencing has limited identification of new markers. The ability of HRM to accurately discern nucleotide changes in a DNA sequence make it a cost- and time-effective alternative to traditional sequencing for the detection of novel SNPs.