Use of the 5′-Nuclease Reaction for Single Nucleotide Polymorphism Genotyping in Chinook Salmon

Migratory and stock composition studies of Chinook salmon Oncorhynchus tshawytscha require genetic 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 corresponding data be transportable across laboratories. We developed 10 single nucleotide polymorphism (SNP) genotyping assays in Chinook salmon based on the 5′-nuclease reaction. Using these assays, a single technician with two thermal cyclers can generate thousands of genotypes per day. The genotyping assays described here are easy to standardize across laboratories, and the resulting genotype data are readily combined with those collected by means of any other sequence detection platform. The rapid rate at which genotyping may be done using these markers and the fact that SNP data are standardized across laboratories and platforms much more readily than are data from other genetic marker cl...