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Chinook and Steelhead Genotyping for Genetic Stock Identification at Lower Granite Dam: 2010 Annual Progress Report

Jun 17, 2011


This report summarizes the progress in development and implementation of genetic stock identification (GSI) technologies within the Snake River basin for natural origin steelhead and spring/summer Chinook Salmon passing Lower Granite Dam for the reporting period of 07/01/2010 to 06/30/2011. Three objectives for the project are addressed in this report: 1) the selection and evaluation of single nucleotide polymorphism (SNPs) panels for high-throughput genotyping of both steelhead and Chinook Salmon in the Snake/Columbia River basins, 2) the development of initial SNP baselines to describe genetic variation and for use as a reference in GSI methods for both species in the Snake River basin, and 3) the implementation of GSI to estimate the stock composition of steelhead and spring/summer Chinook Salmon passing Lower Granite Dam. For objective 1, the goal was to identify standardized sets of SNPs that could be used for both GSI and parentage-based tagging (PBT) for studies throughout the Snake/Columbia River basins. Standardized SNP panels will allow data to be exchanged between laboratories to facilitate collaboration and to avoid duplication of efforts and will allow the integration of sampling programs at Bonneville Dam and Lower Granite Dam and in Columbia River and Snake River mainstem fisheries. All sampled wild adult can be included in mixture analyses to determine stock composition and sampled Snake River hatchery adult can be assigned to a stock and cohort. For objective 2, using the identified standardized sets of SNPs, we genotyped collections of steelhead and Chinook Salmon populations from throughout the Snake River to describe genetic variation for both species and to provide a baseline that could be used for GSI estimations. Section 2 of this report briefly describes the genetic variation observed among populations for both species across the Snake River basin and also describes genetic variation for each SNP marker. Finally, in objective 3, we implemented GSI at Lower Granite Dam using the baselines developed in objective 2 to estimate stock compositions of steelhead and Chinook Salmon passing Lower Granite Dam. In section 3, we report initial results for adult steelhead for spawn year (SY) 2009 (07/01/2008 – 06/30/2009) and SY2010 (07/01/2009 – 06/30/2010) and for adult Chinook Salmon for SY2009 (03/01/2009 – 08/17/2009).


Mike Ackerman, Jesse McCane, Craig Steele, Matt Campbell, Andrew Matala, Jon Hess, and Shawn Narum


Ackerman, M., J. McCane, C. Steele, M. Campbell, A. Matala, J. Hess, and S. Narum. 2011. Chinook and steelhead genotyping for genetics stock identification at Lower Granite Dam: 2010 annual report. Idaho Department of Fish and Game Report No. 11-113. Boise, Idaho. 77p.



Report No.


Media Type

Inter-Agency Report