Forensic identification of endangered Chinook Salmon (Oncorhynchus tshawytscha) using a multilocus SNP assay

Upper Columbia River spring-run Chinook salmon are listed as endangered under the Endangered Species Act (ESA). Forensic genetic analyses are needed to assist the National Oceanic and Atmospheric Administration Fisheries Office of Law Enforcement (NOAA Fisheries OLE) during criminal investigations of ESA take violations. Previous genetic studies using allozyme markers have demonstrated that the spring-run and summer-run of Chinook salmon in the Upper Columbia River are genetically differentiated. Because many of the carcasses collected as forensic evidence are of compromised quality, we have developed a PCR based assay to distinguish between the spring-run and the summer-run Chinook salmon in the upper Columbia River Basin. A total of 347 Chinook salmon samples from the upper Columbia River in Washington State were surveyed for single nucleotide polymorphisms (SNPs) using PCR-RFLP at two nuclear genetic loci (Somatolactin and Cytochrome p450A), and a mitochondrial locus (Cytochrome Oxidase III/ND3). We found near fixed differences in our SNP baseline between the summer-run and the spring-run Chinook salmon in the upper Columbia River at these loci enabling us to assign individuals to the most likely population of origin with a high degree of accuracy.