We propose expanding the initial SNP baseline (38 populations) generated by WDFW in the Southern Boundary region to include better representation of Canadian (CA) Chum salmon populations in the Fraser River and along Strait of Georgia, and Puget Sound populations in Hood Canal. The United States (US) developed a comprehensive panel of 500 SNPs for a Chum salmon baseline funded in part by the Southern Fund and NOAA Saltonstall Kennedy funding (Seeb et al. 2014, Rawson et al. 2014, Small et al. 2017a). In parallel, the DFO lab in Nanaimo has shifted their genotyping technology away from microsatellites to SNPs and are using the method for Coho salmon (Beacham et al. 2017) and Chinook salmon (Beacham et al. in press). The CA and US labs use different technologies for SNP genotyping, but the data are compatible allowing cooperative research and data sharing with minimal standardization. The new SNP technologies in both labs improve efficiency and processing speed, thus lowering costs. Because the DFO lab currently uses the new amplicon technology for Chinook and Coho salmon SNPs they seek to implement the US Chum SNP panel in order to shift all genetic stock identification (GSI) analysis for Chum salmon away from microsatellites.
Primary outcome of this proposal is a high-resolution, bilateral Chum salmon SNP baseline in the Southern Boundary Region. The baseline will have immediate application for mixed stock fishery analysis to understand the composition of fishery samples in the Southern Boundary Region, and provide a more efficient and effective option to the microsatellite baseline.