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Chinook Salmon and Steelhead Genotyping for Genetic Stock Identification at Lower Granite Dam: 2018 Annual Progress Report

Feb 8, 2021


This report summarizes progress in the development and implementation of genetic stock identification (GSI) in the Snake River basin for natural-origin steelhead and spring/summer Chinook Salmon for the 01/01/2018 to 12/31/2018 reporting period. Four objectives for the GSI project are 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) the implementation of GSI to estimate genetic stock composition and life history diversity of steelhead and spring/summer Chinook Salmon passing Lower Granite Dam (LGR); and 4) the summarization of life history and genetic diversity information for steelhead and spring/summer Chinook Salmon detected at PIT tag detection systems. For both species, panels of up to 379 SNPs have been in use for GSI and parentage-based tagging (PBT) at both Idaho Department of Fish and Game’s Eagle Fish Genetics Lab, and its collaborating laboratory, the Columbia River Inter-Tribal Fish Commission’s Hagerman Genetics Lab. Steelhead SNP baseline version v3.1 consists of 45 collections and 5,967 individuals. Chinook Salmon SNP baseline v3.1 consists of 30 collections and 4,356 individuals. SNP baselines are used to describe genetic diversity and structure of natural-origin populations throughout the Snake River. Based on population structure we have defined 10 genetic stocks for steelhead and 7 genetic stocks for Chinook Salmon for GSI analysis at LGR. We summarize GSI results for returning adults and emigrating juveniles during 2017-2018 at LGR using v3.1 baselines as reference. Finally, we describe the life history variation and genetic diversity of steelhead and Chinook Salmon detected at IPTDS. The information presented in this report provides critical data for viable salmonid population (VSP) monitoring of the Snake River steelhead DPS and the Snake River spring/summer Chinook Salmon ESU.


John Hargrove, Thomas Delomas, Jesse McCane, Micah Davison, Matthew Campbell, Rebekah Horn, and Shawn Narum


Hargrove, J.S., T.A. Delomas, J. McCane, M. Davison, M.R. Campbell, R.L. Horn, and S.R. Narum. 2019. Chinook Salmon and steelhead genotyping for genetics stock identification at Lower Granite Dam Project: 2018 annual progress report. Idaho Department of Fish and Game Report No. 19-08. Boise, Idaho. 29p.



Report No.


Media Type

Inter-Agency Report