Use of the 59-Nuclease Reaction for Single Nucleotide Polymorphism Genotyping in Chinook Salmon

Abstract.—Migratory and stock composition studies of Chinook salmon Oncorhynchus tshawytscha require ge-netic markers by which a large number of individuals can be processed in a relatively short time. Given the multijurisdictional geographic range of this species, it is further desirable that genetic markers and the corre-sponding data be transportable across laboratories. We developed 10 single nucleotide polymorphism (SNP) ge-notyping assays in Chinook salmon based on the 59-nuclease reaction. Using these assays, a single technician with two thermal cyclers can generate thousands of ge-notypes per day. The genotyping assays described here are easy to standardize across laboratories, and the re-sulting genotype data are readily combined with those collected by means of any other sequence detection plat