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

Abstract 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.