In 2010, Idaho Department of Fish and Game in collaboration with the Columbia River Inter-Tribal Fish Commission, initiated two BPA-funded projects (2010-026-00 and 2010-031-00) to test and implement genetic monitoring programs for Snake River basin Chinook Salmon and steelhead utilizing two genetic technologies. The first technology is called Parentage-based tagging (PBT) and involves the annual sampling and genotyping of all hatchery broodstock, creating a genetic baseline of candidate parents.  The genotyping of broodstock permanently genetically “tags” all of their offspring. A non-lethal tissue sample from any of these offspring can be genotyped and analyses can be completed to assign parentage, thereby identifying hatchery of origin and age. The second technology is called Genetic Stock Identification (GSI), and involves creating a reference genetic baseline from all contributing wild stocks.  Wild fish of unknown origin can then be sampled and genotyped, with a genetic assignment test used to identify their stock of origin.  Over the last decade, these projects have demonstrated the accuracy, efficiency, and utility of these technologies for monitoring both wild and hatchery stocks throughout the Snake River and Columbia River basins.  For hatchery stocks, PBT addresses Fish and Wildlife Program objectives that involve marking hatchery stocks, conducting hatchery evaluations and reform, and enforcing salmonid fishery management measures.  For wild stocks, GSI provides unprecedented tools for monitoring wild stock abundance, productivity and genetic diversity, which are required for NOAA ESA status assessments. These two projects were combined by BPA in 2021, with ongoing goals of keeping PBT and GSI baselines up-to-date in the Snake River basin, to maintain and enhance SNP genetic marker panels, and to continue projects that use these PBT and GSI baselines to address conservation and management issues of importance to the Council and state, tribal and federal fisheries managers.

In 2018, an additional objective was incorporated into Project 2010-031-00 to support integrated broodstock effectiveness monitoring using Parentage-Based Tagging (PBT). This objective, referred to as the Integrated Broodstock Evaluation, was developed to quantify the demographic and genetic performance of integrated Chinook Salmon broodstocks operating at the Sawtooth, Pahsimeroi, and McCall fish hatcheries.
This evaluation directly supports the project’s original goals by using PBT data to:
•    Assess the influence of natural-origin adults incorporated into integrated broodstocks (IB) on hatchery survival, productivity, and replacement rates;
•    Evaluate the contribution of IB spawners to naturally reproducing populations and resulting replacement rates; and
•    Examine how management actions such as smolt release locations and density affect natural spawning distribution and performance.
Current work elements expand upon existing PBT-based monitoring to include life-stage-specific data (juvenile PIT-tagging, screw-trap sampling, and statistical design for a management-strategy evaluation). These activities respond directly to ISRP recommendations for:
1.    Quantifying density dependence and early life-stage survival,
2.    Improving program-wide management-strategy evaluation (MSE) capacity, and
3.    Integrating demographic data across hatchery and natural environments.