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Chinook and Steelhead Genotyping for Genetic Stock Identification at Lower Granite Dam: 2013 Annual Progress Report

Oct 14, 2020


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 (sp/sum) Chinook Salmon for the 01/01/2013 to 12/31/2013 reporting period. Three 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 GSI for both species in the basin; and 3) the implementation of GSI to estimate genetic stock composition and life-history diversity of steelhead and sp/sum Chinook Salmon passing Lower Granite Dam (LGR). For both species, panels of 192 SNPs have been identified and are being used 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. We describe SNP baselines for steelhead and Chinook Salmon; steelhead baseline version 2.0 (v2) consists of 63 collections and 4,116 individuals. Chinook Salmon baseline v2 consists of 39 collections and 3,327 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. Finally, we summarize GSI results for returning adults and emigrating juveniles during 2012 at LGR using v2 baselines as reference. 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 sp/sum Chinook Salmon ESU.


Michael Ackerman, Ninh Vu, Jesse McCane, Craig Steele, Matthew Campbell, Andrew Matala, Jon Hess, and Shawn Narum


Ackerman, M.W., N.V. Vu, J. McCane, C.A. Steele, M.R. Campbell, A.P. Matala, J.E. Hess, and S.R. Narum. 2014. Chinook and steelhead genotyping for genetics stock identification at Lower Granite Dam Project: 2013 annual progress report. Idaho Department of Fish and Game Report No. 14-01. Boise, Idaho. 68p.



Report No.


Media Type

Inter-Agency Report