Use of the 59-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 59nuclease 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 classes suggest that SNPs will become an increasingly important tool for mixture studies of Chinook salmon and other salmonids. Chinook salmon Oncorhynchus tshawytscha spawn in rivers around the North Pacific basin southward to approximately 408N. As is typical for many salmonids, Chinook salmon from throughout the range may form large aggregates during their oceanic and coastal migrations (Myers et al. 1987). The ability of fishery managers to identify the natal origins of fish comprising these aggregates is desirable both for fishery management and for the protection of individual stocks or populations. In recent years, mixed-stock analysis * Corresponding author: [email protected]. ak.us Received February 4, 2004; accepted June 24, 2004 techniques based on genetic markers have been successfully applied to estimate the origins of mixtures taken in nearshore fisheries and to delineate the oceanic migratory route of individual stocks or aggregates (e.g., Seeb et al. 2004). The allele frequency baselines required for such applications must often be composed of samples representing broad geographic sections of the species’ range. Given the interjurisdictional nature of these analyses, the genetic markers chosen for such studies should ideally be accessible through relatively rapid and transportable laboratory assays. Both allozymes and microsatellite DNA have been successfully used in stock composition analyses of Chinook salmon (Nelson et al. 2001; Beacham et al. 2003; Guthrie and Wilmot 2004). A challenge in using genetic markers for which the underlying DNA sequence is not ascertained during genotyping has been a lack of standardization of alleles and thus the inability of managers to combine data across laboratories. The geographic range of Chinook salmon encompasses multiple political and management jurisdictions, making collaboration among the respective management agencies and transparent analyses crucial to effective management. Given the lack of platform-independent reference standards for most allozyme and microsatellite alleles, merging of data generated in different laboratories entails time and monetary costs. In the case of allozymes, laboratories from throughout the North Pacific basin collaborated to standardized a database consisting of 33 loci in 254 Chinook salmon populations (Teel et al. 2000). In the case of microsatellites, no database for Chinook salmon has been successfully