2012 Annual Report: Genetic Assessment of Columbia River Stocks
This project combines four inter-related studies from the Fish & Wildlife Program Accords that address these current and future objectives: 1) discover and evaluate SNP markers in salmon and steelhead and other anadromous fishes; 2) expand and create genetic baselines for multiple species including Chinook salmon, steelhead (O. mykiss), sockeye salmon and kokanee (O. nerka), and coho salmon; 3) implement Genetic Stock Identification (GSI) programs for mainstem Chinook salmon and steelhead fisheries and 4) GSI of fish passing Bonneville Dam (steelhead, sockeye, and Chinook salmon). In the third year of this project, SNP discovery and evaluation goals (Objective 1) were achieved with two completed projects on O. mykiss and one project on Pacific lamprey which identified SNP markers using restriction associated DNA sequence (RAD-seq) technology. For genetic baseline expansion (Objective 2), the Chinook salmon and steelhead GSI baselines continue to expand using a total of 192 SNP markers for each species which includes a 96-SNP panel optimized for parentage based tagging (PBT) and a 96-SNP panel optimized for GSI. In addition, a 96-SNP baseline for O. nerka has become available for assigning individuals to the three major Columbia River sockeye stocks. We have now compiled genotypes from 192 SNP markers in 79 Chinook salmon collections, 192 SNP markers in 145 steelhead collections, and 96 SNP markers in 22 O. nerka collections from the Columbia River Basin. Results from population genetics analyses suggest SNPs are a class of markers that perform well for distinguishing populations, and these baselines will be useful for estimating stock composition in GSI applications. Results also identified loci in all three species that may be candidate markers and showed selective divergence across the study collections. The third year of the project included two broad applications of GSI; namely, stock composition of Chinook salmon and steelhead fisheries (Objective 3), and stock composition of Chinook and sockeye salmon and steelhead passing Bonneville Dam (Objective 4).
Hess, J.E., N.R. Campbell, A.P. Matala, and S.R. Narum. 2014. 2012 Annual report: genetic assessment of Columbia River stocks. Columbia River Inter-Tribal Fish Commission Technical Report 13-08 for U.S. Dept. of Energy Bonneville Power Administration Report Project #2008-907-00. 148p.