Proposal for 2010 Fast Track review

1. Technical Justification, Program Significance and Consistency, and Project Relationships The need for the monitoring of hatchery salmon and steelhead performance once released is an essential feature of management obligations to evaluate the efficacy of the artificial production programs in terms of their yields to fisheries and impacts to natural population. The ISAB/ISRP, as well as the Pacific Salmon Commission technical team, recently concluded that Parental Based Tagging (PBT) has the potential to provide important data for cohort analysis of salmon and steelhead populations. The project proponents (IDFG) propose to genotype the entirety of Chinook salmon and steelhead broodstock from 14 Snake River hatcheries to empirically test and validate whether PBT can be used to replace coded-wire tags (CWT) for estimating stock contributions of Snake River steelhead and Chinook salmon to fisheries, run-timing, straying, etc., of adult salmon in the Snake/Columbia River basins. The technical justification of using PBT as a replacement for CWT-based assessment of hatchery production in harvest, straying, and returns to hatcheries (life-cycle survival) is adequately described. The ISRP notes, however, that successful implementation of PBT will not eliminate all problems associated with CWTs, mass marking, and selective fisheries. For example, there will still be a need to handle and mass mark juvenile hatchery fish with an adipose fin clip or some other highly-visible mark for selective fisheries. The technological development to bring PBT to pilot scale trial is consistent with the BiOp, Fish and Wildlife Program, and Lower Snake River Compensation Plan. Relationships with other projects in the Basin are sufficiently described, and evidence is provided that the proponents are familiar with other PBT trials in Puget Sound, Washington and the Sacramento River, California. The proposed project involves coordination with the Columbia River Intertribal Fish Commission (CRITFIC) and other Genetics Analysis of Pacific Salmon (GAPS) and Stevan Phelps Allele Nomenclature (SPAN) laboratories to develop a coastwide Single-Nucleotide Polymorphism (SNPS) baseline. One concern is that the ISRP could not determine whether this proposed project unnecessarily duplicates work already being performed or proposed by other BPA-funded projects. For example, the proposed work is contingent upon the success (efficiency, precision, and accuracy) of efforts associated with BPA Project #200890700, “Genetic Assessment of Columbia River Stocks.” Moreover, the project will "identify SNP loci" for Chinook salmon and steelhead. Presumably, BPA Project #200890700 should be far enough along to inform these choices now without significant new work. Finally, the proposed project will not analyze future harvested or escaped (from fishery) Snake River salmon and steelhead except as a test (objective 5). The ISRP does not understand why BPA Proposal No. 201002600: “Chinook and steelhead genotyping for genetic stock identification (GSI) at Lower Granite Dam,” which is contingent on the results of this proposed project, was submitted as a separate proposal. As a result, is there unnecessary overlap or duplication of some work elements between the two proposals? 2. Project History and Results The proposed project is new, but efforts to begin collecting tissue for genetic analysis are already underway, e.g., samples from broodstock at most Snake River hatcheries were obtained in 2008 and 2009. Since this project is closely linked with the CRITFC project developing SNP assays for Columbia River salmon ESUs (BPA Project #200890700), a more detailed description of the number of SNPs identified to date and how many of those have been polymorphic in the populations of interest would have been useful. 3. Objectives, Work Elements, and Methods The objectives are relatively straightforward. The overall work plan and strategy to collect tissue samples; develop SNPs; identify a SNP panel for both genetic stock identification (GSI) and PBT; and then test that panel using progeny from known populations; and finally cross check with harvested fish that carry CWTs is sound. One difficulty for ISRP reviewers not expert in the field of salmon genetics was that proponents used lots of technical jargon without defining their terminology. In addition, publications and computer software packages were frequently cited for methods without providing a concise summary or explanation of these methods in the proposal. The ISRP suggests that for objective 4, 157...SNP Genotyping (juveniles) - a number of non-hatchery wild juveniles originating from major population groups (MPGs) or reporting groups should be tested against the parents used to establish the PBT baseline. They should not assign to any of the hatcheries. It was not apparent from the objectives and methods that this testing was included. One final concern is that the high throughput requirements for analysis of 16.5K samples per year plus any future samples from fisheries, etc., may quickly overwhelm the system. Given the genetic laboratory's other demands, proponents need to verify in contracting that results can be provided in accordance with proposed schedules.