image description
Method: O. mykiss and O. tshawytscha SNP marker sets for PBT and GSI use in the Columbia River basin v1.0
  • State: Finalized
  • Units of Measurement: English
  • Supplemental Information:
  • Recent Commenter: Jacque Schei
  • Subscribers: <none>
  • Version History: v1.0 Finalized (4/2/2012)
Basics

Over the last several years, the Columbia River Inter-Tribal Fish Commission's fish genetics lab in Hagerman, ID has tested hundreds of single nucleotide polymorphism (SNP) genetic markers developed by labs throughout the PNW (Smith et al 2005a, 2005b; Clemento et al 2011) for their possible conservation and management applications in the Columbia River basin. The CRITFC lab also developed and tested hundreds of additional SNP loci specifically for projects involving Genetic Stock Identification (GSI), Parentage Based Tagging, intraspecific hybridization/introgression, reproductive success, and selection studies (Campbell et al 2008). Currently, there are 192 SNP markers (two 96 panel sets) for both steelhead and Chinook salmon that have been selected for use by CRITFC and IDFG for BPA projects involving GSI and PBT in the Columbia River basin. For PBT broodstock tagging in the Snake River basin, one 96 SNP panel for each species has been optimized to provide sufficient power for parentage tagging (Steele et al 2011). For GSI, both the 96 PBT SNP panel and a second 96 SNP panel are run for GSI projects. Procedures for running SNPs on the Fluidigm EP1™ SNP Genotyping platform are described in method 1332. Primer/probe sequences and assay plate configurations are included in the attachment (Columbia River Basin OMY and OTS SNP sets 2apr12.pdf).

Details on the 192 SNP marker taqman assays for each species are described in attachment (Columbia River Basin OMY and OTS SNP sets 2apr12.pdf). 1.) Assay names 2.) Forward and Reverse primer names and sequences 3.) Probe names, VIC/FAM labeling, and sequences 4.) Assay Plate configurations 5.) Allele X and Allele Y nomenclature

Photos & Figures

Forms

The SNP taqman assays described in this method can be purchased from: http://www.lifetechnologies.com/us/en/home.html.

Advanced

Campbell, N.R., and S.R. Narum. 2008. Identification of Novel Single-Nucleotide Polymorphisms in Chinook Salmon and Variation among Life History Types. Transactions of the American Fisheries Society 137:96-106.

Narum, S., N. Campbell, A. Matala, and J. Hess. 2012. 2011 Annual Report: Genetic
Assessment of Columbia River Stocks. U.S. Department of Energy Bonneville Power
Administration Report Project #2008-907-00.

Smith CT, Elfstrom CM, Seeb JE, Seeb LW (2005a) Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Molecular Ecology, 14, 4193–4203.

Smith CT, Seeb JE, Schwenke P, Seeb LW (2005b) Use of the 5'- nuclease reaction for single nucleotide polymorphism genotyping in Chinook salmon. Transactions of the American Fisheries Society, 134, 207–217.

Steele, C., M. Ackerman, J. McCane, M. Campbell, M. Hess, N. Campbell, and S. Narum. 2011. Parentage based tagging of Snake River hatchery steelhead and Chinook salmon. Idaho Department of Fish and Game Report 11-111. Annual report 2010, BPA Project 2010-031-00.

Clemento AJ, A Abadia-Cardoso, HA Starks, JC Garza. 2011. Discovery and characterization of single-nucleotide polymorphisms in Chinook salmon. Molecular Ecology Resources 11(supp.1):50-66

Citation
Narum, S., N. Campbell, A. Matala, and J. Hess. 2012. Annual Report: Genetic Assessment of Columbia River Stocks. Columbia River Inter-Tribal Fish Commission 2011-2008-907-00.:123 http://www.critfc.org/tech/tech_rep.html
References & Customizations

Protocols that include this Method

Customizations of this Method

Metric Associations

Associations between a method and one or more metric subcategories are done by PNAMP and not by the Method Owner.

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