Salmon species identification via direct DNA sequencing of single amplicons

For Pacific salmonids, a key fisheries forensics and management goal is to identify individuals to specific species and potentially specific populations or geographic regions within species. Genetic variation can be used for both species and individual identification, and variation at single nucleotide polymorphisms (SNPs) within two specific DNA amplicons was used to distinguish among coho salmon ( Oncorhynchus kisutch ), Chinook salmon ( Oncorhynchus tshawytscha ), sockeye salmon ( Oncorhynchus nerka ), chum salmon ( Oncorhynchus keta ), pink salmon ( Oncorhynchus gorbuscha ), masu salmon ( Oncorhynchus masou ), steelhead/rainbow trout ( Oncorhynchus mykiss ), cutthroat trout ( Oncorhynchus clarkii ), and Atlantic salmon ( Salmo salar ). A total of 2510 individuals was evaluated from a Pacific rim distribution of populations for sockeye salmon, chum salmon, and pink salmon, whereas masu salmon samples were genotyped only from Japanese populations. Coho salmon, Chinook salmon, steehead trout, cutthroat trout, and Atlantic salmon samples were genotyped only from North American populations. All individual salmonids genotyped were assigned with 100% accuracy to their respective species via diagnostic homozygous SNP genotypes for each species except for cutthroat trout, where no diagnostic SNP genotypes were observed in the two amplicons evaluated.