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Scientific Report

2010 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; 2) expand and create genetic baselines for multiple species (Chinook, steelhead, sockeye, and coho); 3) implement Genetic Stock Identification (GSI) programs for mainstem Chinook fisheries and 4) GSI of fish passing Bonneville Dam (steelhead and Chinook). In the second year of this project, SNP discovery goals (Objective 1) were achieved with successful development of 22 new assays for Chinook salmon and 24 new assays for steelhead. These newly discovered SNP markers will be combined with existing SNP markers to generate genetic baselines and for two applications of genetic stock identification (GSI). For genetic baseline expansion (Objective 2), we successfully genotyped 96 SNP markers in 32 new Chinook salmon collections and 192 SNP markers in 61 steelhead 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 indicated that some loci may be candidate markers and valuable for analyses based on selective divergence. The second year of the project included two broad applications of GSI, stock composition of Chinook salmon fisheries (Objective 3), and stock composition of Chinook salmon and steelhead passing Bonneville Dam (Objective 4). Results of Objective 3 indicate that spring-run Chinook salmon harvested in the 2010 commercial, sport, and test fisheries were primarily composed of three adipose-clipped stocks (in descending order of stock composition): Rapid River Hatchery/Clearwater R., Upper Columbia R. (i.e., Carson stock), and Mid-Columbia R. These three Chinook salmon stocks were also the most strongly represented at Bonneville Dam. A fourth spring-run stock, Williamette R., was found primarily in harvests spanning an earlier part of the season and locations closer to the mouth of the Columbia R. For fall Chinook fisheries, the sport and commercial fisheries below Bonneville Dam contained large proportions of Lower Columbia fall stocks (20-55% composition), as well as the following stocks (in descending order): upper Columbia R. summer/fall, Snake R. fall, and Deschutes R. fall. The entire Zone 6 tribal Chinook fishery was heavily comprised of Upper Columbia R. summer/fall stock (30-70% depending on region), but Region 1 (closest region to Bonneville Dam) of Zone 6 contained far greater proportion of Lower Columbia R. fall stock (~54%) than Region 2 (< 6%), whereas Snake R. and Deschutes R. fall stocks were similar in both regions (9-20% and ~3%, respectively). Validation of the GSI results using coded wire tag information indicated that the percentage of individuals correctly assigned to a particular reporting group was on average 80% and ranged from greater than 90% (Willamette R. spring-run, Upper Columbia R. summer/fall, and lower Columbia R. fall stocks) to a low of 57% (Snake R. fall-run stock). For Objective 4, we calculated estimates of the run-timing distributions and abundance (units in 1000's of fish) of the "major" stocks of Chinook salmon sampled as they migrated past Bonneville Dam in 2010, and these estimates are listed in order of median day of peak run-timing as follows: Upper Columbia R. (May 1st, 102k), Rapid R./Clearwater R. (May 1st, 127k), middle Columbia R. spring-run (May 6th, 29k), Upper Salmon R. (June 6th, 23k), and South Fork Salmon R. (June 13th,16k), Snake R. fall (Sep 5th, 113k), lower Columbia R. fall (Sep. 7th, 59k), Upper Columbia R. summer/fall (Sep. 8th, 376k), and Deschutes R. fall (Sep. 11th, 28k). Future work will include the newly developed SNP baseline of steelhead populations to analyze recent years 2009-2010 of steelhead samples in a similar way.



Hess, J.E., N.R. Campbell, A.P. Matala, S.R. Narum. 2011. 2010 Annual Report: Genetic Assessment of Columbia River Stocks. Columbia River Inter-Tribal Fish Commission Technical Report #11-02, Portland, Oregon.


Mar 31st, 2011

Report No.


Media Type

CRITFC Technical Report

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