Western Alaska Salmon Stock Identification Program Technical Document 9: Chum salmon SNP discovery, first method

Alaska Department of Fish and Game, Department of Commercial Fisheries, Regional Information Report 5J12-14, Anchorage

Uncertainty about the magnitude, frequency, location, and timing of the nonlocal harvest of sockeye and chum salmon in Western Alaska fisheries was the impetus for the Western Alaska Salmon Stock Identification Project (WASSIP).  The project was designed to use genetic data in mixed stock analysis (MSA) to reduce this uncertainty.  A baseline of allele frequencies is required for use in MSA to estimate the stock of origin of harvested fish.  The single nucleotide polymorphism (SNP) baseline for chum salmon Oncorhynchus keta to be used in MSA for WASSIP is in a state of perpetual improvement. To meet the standards set by the Advisory Panel an emphasis was placed on selecting more markers to increase resolution among the four regional areas of coastal western Alaska. The Alaska Department of Fish and Game began the process of discovering additional SNP markers for chum salmon through a contract with International Program for Salmon Ecological Genetics (IPSEG; http://www.fish.washington.edu/research/ipseg/research.html) at the University of Washington. This process was published in an article in the journal Molecular Ecology Resources and this technical document highlights the importance of the article to WASSIP, gives a brief overview, and directs the Technical Committee and the Advisory Panel and any other interested readers to the published article.