2009 Annual Report: President's Message

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). These four projects are highly related since SNP markers are needed to complete species specific baselines, and these baselines are requisite to complete GSI. In the first year of this project, SNP discovery goals (Objective 1) were achieved with successful development of 10 new assays for steelhead, 30 new assays for coho salmon, and 21 new assays for sockeye salmon. These newly discovered SNP markers were 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 52 Chinook salmon and 54 steelhead populations 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 landscape genetic analyses (based on selective divergence). The first 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 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 and these Chinook salmon stocks were also the most strongly represented at Bonneville Dam. During the spring Chinook test and sport fisheries, a fourth stock, Williamette R. , was found because these fisheries include harvests spanning an earlier part of the season and locations closer to the mouth of the Columbia R. For fall Chinook fisheries, the sport fishery at Buoy10 had predominantly Lower Columbia fall stocks (>60% composition), and less than 20% composition of the following stocks (in descending order): Snake R. fall, upper Columbia R. summer/fall, and Deschutes R. fall. The entire Zone 6 tribal Chinook fishery was heavily comprised of Upper Columbia R. summer/fall stock (60-80% depending on region), but Region 1 (closest region to Bonneville Dam) of Zone 6 contained more Lower Columbia R. fall stock (~30%) than Region 2 (< 5%), whereas Snake R. fall stock was similar in both regions (12-15%). Weekly composition of Chinook salmon stocks were highly variable and differed among the two regions in Zone 6. Results of Objective 4 indicate that four “major” stocks of steelhead were sampled as they migrated past Bonneville Dam: upper Columbia R. (0.135 ± 0.013), middle Columbia R. /lower Snake R. (0.254 ± 0.050), upper Clearwater R (0.320 ± 0.069), and upper Salmon R. (0.154 ± 0.037). These four steelhead stocks varied considerably in peak run timing (weeks 24-25, 28-29, 38-39, and 32-33, respectively), and clear transitions occurred when each stock of steelhead was most abundant in the mainstem Columbia R.