Single Nucleotide Polymorphisms (SNPs) Provide Standard DNA Data for

Migratory studies of Chinook Oncorhynchus tshawytscha, chum O. keta, and sockeye O. nerka salmon require markers for which a large number of individuals can be processed in a relatively short time. Genetic markers, especially allozymes, have provided substantial insight into key questions asked by BASIS investigators (see Kondzela et al. 2002; Urawa et al. 2004; Seeb et al. 2004). However, issues of sample collection and preservation as well as a desire for increased resolution have driven efforts to develop DNA markers to describe discrete aggregations of stocks. Given the multi-jurisdictional geographic range of these species, it is desirable that genetic markers and the corresponding data be transportable across laboratories. Allozymes meet these criteria while most DNA markers do not. To solve this DNA standardization dilemma, we are continuing to develop single nucleotide polymorphism (SNP) genotyping assays based upon the 5’-nuclease reaction. Various approaches to DNA analysis, each with advantages, were used to study Pacific salmon during the last decade. Initially the most common approach was the collection of SNP data that was obtained by restriction length polymorphism assays (RFLPs; e.g. Cronin et al. 1993; Park et al. 1993; Seeb and Crane 1999), amplification fragment length polymorphism assays (AFLPs; see Flannery et al. 2002), or DNA sequencing (e.g. Sato et al. 2004). SNP data were collected on mitochondrial DNA, nuclear DNA, neutral genes, and selected genes such as MH