Genetic Baseline for Upper Cook Inlet Sockeye Salmon: 96 SNPs and 10,000 Fish

Alaska Department of Fish and Game, Fishery Manuscript Series No. 12-06, Anchorage

This report updates the previously reported genetic baseline used in mixed stock analysis (MSA) of sockeye salmon Oncorhynchus nerka originating from all major spawning systems in Upper Cook Inlet, Alaska.  The baseline was augmented with new samples that provide better representation of existing populations and add 10 new populations.  All individuals in the baseline and test mixtures were genotyped for 39 previously reported single nucleotide polymorphic (SNP) markers and 57 new SNP markers representing 92 loci.  These markers reveal population structure similar to that observed in previous analyses.  Eight reporting groups important to fisheries management were tested and met the criteria to be used in MSA.  This baseline can be used for MSA of sockeye salmon harvested in Upper Cook Inlet fisheries and for inriver mixtures.  Finally, this baseline can be combined with other baselines throughout the Pacific Northwest for MSA of mixtures that might contain sockeye salmon from Cook Inlet.