Development & Evaluation of Chinook Salmon Single Nucleotide Polymorphism (SNP) Markers for Genetic Stock Identification
Project Objectives:
- Discover 45 new single nucleotide polymorphisms (SNPs) in Chinook salmon for use in genetic stock identification (GSI).
- Evaluate statistical power of newly discovered and previously described SNPs across the species range to assess their utility in GSI.
Progress Update:
Washington State University Vancouver:
- Out of 20 rainbow trout primers, 11 have successfully amplified in Chinook salmon.
- Of the 11 successful amplifications, nine have been sequenced.
- Seven of the nine sequences have at least one SNP.
- Sequencing of ascertainment samples indicates that most SNPs are polymorphic in at least half of the populations.
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SNP Workshop 2, a cooperative multi-agency meeting. |
Northwest Fisheries Science Center
- Seventeen gene regions have been examined for SNPs.
- Nine SNP's have been discovered.
- Nine TaqMan assays are under development.
Southwest Fisheries Science Center:
- Tests for amplification of primer sets in Chinook salmon have begun.
SNP Evaluation:
SNP evaluation began in January 2006. There are currently 30 published SNP assays that will be included in the selection pool. Any new SNPs discovered by the GAPS group will be added to the selection pool for coastwide population evaluation. Selection criteria for SNPs will include markers that are widely screened, represent independent loci, have Taqman assays developed, have robust assays, and are genes of interest (e.g., MHC).
Thirty six to 45 SNPs will be screened on 3,787 samples representing 29 populations. The population list includes the following:
Auke Bay Laboratories (ABL)
Tahini River; King Salmon River; Situk River; Harding River; Unuk River
Alaska Department of Fish and Game (ADFG)
Klukshu River; Big Boulder Creek; Kowatua Creek; Chickamin River
Canadian Department of Fish and Oceans (CDFO)
Harrison; Big Qulicum; Kitimat; Lower Kalum; Blanchard River
Columbia River Inter-Tribal Fish Commission (CRITFC)
Secesh River - spring/summer; Hanford Reach - fall upriver bright; Cowlitz Hatchery - spring; Spring Creek Hatchery - fall tule
Idaho Department of Fish and Game (IDFG)
Grande Ronde River - spring/summer; Imnaha River - spring/summer; Clearwater River - spring/summer
Oregon State University (OSU)
Nehalem - fall; Siuslaw - fall; Umpqua - spring; Rogue Cole Rivers - spring
Washington Department of Fish and Wildlife (WDFW)
Quinalt River - fall; Puyallup River - fall; Mid-Hood Canal - fall; Wenatchee River - summer
Co-investigators and cooperating agencies:
Michael Banks, Oregon State University
Matt Campbell, Idaho Department of Fish and Game
Carlos Garza, Southwest Fisheries Science Center NOAA Fisheries
Chuck Guthrie, Alaska Fisheries Science Center NOAA Fisheries
Kristi Miller, Canadian Department of Fisheries and Oceans
Paul Moran, Northwest Fisheries Science Center NOAA Fisheries
Shawn Narum, Columbia River Inter-Tribal Fish Commission
Ruth Phillips, Washington State University Vancouver
Lisa Seeb, Alaska Department of Fish and Game
Christian Smith, Alaska Department of Fish and Game
Sewall Young, Washington Department of Fish and Wildlife
Funding:
Chinook Technical Committee, Pacific Salmon Commission
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