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Chinook and Steelhead Genotyping for Genetic Stock Identification at Lower Granite Dam: 2011 Annual Progress Report

Jul 7, 2020


This report summarizes progress in development and implementation of genetic stock identification (GSI) within the Snake River basin for natural origin steelhead and spring/summer Chinook Salmon for the 07/01/2011 to 06/30/2012 reporting periood. Three objectives for the project are addressed in this report: 1) the evaluation and maintenance 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 methods for both species in the basin; and 3) the implementation of GSI to estimate the stock composition and biological parameters of steelhead and spring/summer Chinook Salmon passing Lower Granite Dam. For both species, panels of 192 SNPs have been identified and are being used for GSI 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 updates to and testing of SNP baselines for steelhead and Chinook Salmon; steelhead baseline v2.0 consists of 63 populations represented by a total of 83 collections and 4,145 individuals. Chinook Salmon baseline v2.0 consists of 39 populations represented by a total of 111 collections and 3,392 individuals. Baselines were used to describe genetic variation and population structure throughout the Snake River baseline. Using that information, we define 10 reporting groups for steelhead and 7 reporting groups for Chinook Salmon for GSI analysis at Lower Granite Dam. Finally, we summarize three years of GSI results at Lower Granite Dam using the new v2.0 baselines as reference; SY2009, SY2010, and SY2011 adults and MY2010 and MY2011 juveniles. The information presented within should greatly assist managers in achieving sustainable harvest of larger populations, while protecting weaker stocks and the biodiversity present within them. Further, GSI monitoring at Lower Granite Dam provides crucial data for VSP monitoring of the Snake River steelhead DPS and the Snake River spring/summer Chinook Salmon ESU.


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


Ackerman, M.W., J. McCane, C.A. Steele, M.R. Campbell, A.P. Matala, J.E. Hess, and S.R. Narum. 2012. Chinook and steelhead genotyping for genetics stock identification at Lower Granite Dam Project: 2011 annual progress report. Idaho Department of Fish and Game Report No. 12-15. Boise, Idaho. 157p.



Report No.


Media Type

Inter-Agency Report