Proposal for 2010 Fast Track review

The proponent proposes to use single nucleotide polymorphism (SNPs) based genetic stock identification (GSI) for establishing the composition of various Snake River salmon and steelhead populations passing the Lower Granite Dam (LGD). Based on suites of genetic characters, GSI models the most likely composition of populations contributing to the fish passing. The modeling methods have a long history and this proposal builds on these to fit an advertised need to better estimate salmon populations in the Snake River basin. This methodology can be applied at Lower Granite Dam to evaluate populations that may not be amendable to analysis by PIT tagging. The proposed project has the potential to provide important data to understand the life-history and population dynamics of Snake River steelhead and Chinook salmon. 1. Technical Justification, Program Significance and Consistency, and Project Relationships This project will develop (and test) standardized SNP baselines for fine-scale GSI of Snake R. Basin stocks as adults migrate past Lower Granite Dam (LGD). The general explanation of life history variation in steelhead in the Snake River basin, and justification that a GSI approach can contribute to estimating abundance of MPGs and reporting groups (aggregates of spawning tributaries) is well summarized. Estimates of population components crossing LGD for one year are included in the problem statement. The project is greatly interdependent, in part, on project #201003100 which creates the reference baseline used to decompose the population mixture. The proposed project is consistent with BiOp RPAs, the regional monitoring strategy, and recommendations in the ISRP/AB tagging report. This and related projects provide an alternative tool for mark and recapture (referenced in our tagging report Section A.6 pp. 67-73). The project relationships are summarized and appear extensive. This project will use fish collected by other projects, and these are adequately summarized. At least a portion of the SNP development effort will involve collaboration with the Hagerman Laboratory operated by CRITFC, specifically project 200890700 Genetic Assessment of Columbia River Stocks, that will be using GSI to estimate stock proportions at Bonneville Dam. Section I. Key Personnel indicates that the CRITFC lab will be a subcontractor to develop SNPs and genotype fish. Geneticists throughout the Pacific Northwest have collaborated on development of microsatellite gene markers and standardized genes, alleles, and methods of analysis. The collaboration on SNP development and standardization of genotyping and analysis platforms is appropriate. The ISRP does believe a more thorough clarification of the roles of the different projects in the field, laboratory, and analysis is needed. 2. Objectives, Work Elements, and Methods The objectives are straight forward and build on previous or currently proposed work. The methods for developing SNP assays, evaluating the distribution of SNP alleles in Snake basin populations, and establishing the utility of a set of SNPs for both GSI of wild steelhead and Chinook at LGD and Parental Based Tagging of hatchery steelhead are consistent with practices and methods in the discipline. It is less clear that methodologies for using abundance estimates from LGD, partitioned into reporting groups in VSP analysis for BiOp monitoring and ESA delisting, etc are developed. The rationale for sampling and genotyping 2000 fish at LGD needs to be justified.