This project will evaluate a new, dynamic genetic technology that should be cheaper and more efficient than coded-wire tags for mass marking hatchery steelhead and Chinook salmon in the Snake River basin.  This technology, called Parentage Based Tagging (PBT), should provide a better tool to meet Fish & Wildlife Program objectives associated with marking hatchery stocks, conducting hatchery evaluations and reform, and enforcing salmonid fishery management measures.  This project will genotype approximately 16,500 samples annually to create the first PBT parental genetic baselines for hatchery steelhead and Chinook salmon in the Snake River basin. In doing so, it will effectively, permanently genetically mark ~12 million smolts, per species, per year.  This project will work closely with an existing BPA funded project (2008-907-00) to ensure that future genetic marker sets used in the Columbia River basin are standardized, providing unprecedented genetic tools for managing wild and hatchery stocks in the basin: with Genetic Stock Identification techniques segregating adult wild runs by stock of origin, and Parentage Based Tagging technologies identifying the stock and age of sampled hatchery fish.

In the ISRP review of Proposal 201003100: Snake River Chinook and Steelhead Parental Based Tagging, they suggested that two items be addressed during contracting:

1.)  They suggested 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.

While intuitively the screening of wild juveniles may seem necessary to test power of parentage assignments in terms of false-positive error rates (wild juveniles shouldn’t assign to the hatchery parental baseline), the highest likelihood for error will be within datasets that contain full siblings.  We will have ample opportunities to test for this type of error through the screening of both adult and juvenile hatchery samples, where it is likely that full siblings of their parents will be within the dataset.  In addition, since the SNP marker sets that will be run for PBT analyses will be the same marker sets used for wild GSI, there will be numerous wild samples whose genotypes could be tested against the hatchery parental baseline.

2.)They also expressed concern 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.

With the acquisition of new SNP genotyping instruments and an automated pipetting robot prior to the development of these proposals, along with the request of additional Personnel and laboratory equipment as part of these new proposals, we are confident that we will be able to provide results in accordance to proposed schedules.