Natural Origin Steelhead And Chinook Salmon Life History And Genetic Diversity At Pit Tag Detection Locations Throughout The Snake River Basin PDF Download

This report summarizes the application of genetic techniques to the management and conservation of anadromous salmonids (steelhead Oncorhynchus mykiss and spring-summer Chinook Salmon O. tshawytscha) in the Snake River basin. 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 steelhead and spring-summer Chinook Salmon utilizing two genetic technologies that identify origins of hatchery and wild fish. The first technology, called parentage‐based tagging (PBT), involves annually sampling and genotyping all hatchery broodstock which are added to a genetic baseline of candidate parents. The genotyping of broodstock permanently genetically “tags” all of their offspring. A non‐lethal tissue sample from any offspring of these broodstock 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 non-lethally sampled, genotyped, and assigned to a stock of origin via assignment testing. 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 objectives established by the Bonneville Power Administration (BPA) Fish and Wildlife Program which involves 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 (2010-031-00), 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 Northwest Power and Conservation Council and state, tribal and federal fisheries managers. Combined there are eight objectives addressed in this report: 1) the maintenance and evaluation of single nucleotide polymorphism (SNP) panels for high-throughput genotyping of steelhead and Chinook Salmon in the Snake and Columbia river basins; 2) the updating, maintenance, and testing of SNP baselines to describe genetic variation and for use as a reference in conducting GSI for both species; 3) annual sampling of hatchery broodstock and creation of genetic parental databases; 4) utilization of PBT and GSI baselines to estimate genetic stock composition and life history diversity of steelhead and spring-summer Chinook Salmon passing Lower Granite Dam (LGR); 5) application of PBT baselines to estimate the stock composition of steelhead in the Columbia and Snake River tribal and sport fisheries; 6) the monitoring of integrated hatchery programs for Chinook Salmon; 7) the summarization of life history and genetic diversity information for steelhead and spring-summer Chinook Salmon detected at PIT tag detection systems; and 8) the development and application of grandparentage technology for use in the Snake River basin.