Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
SOW Report
Contract 41224: 2008-907-00 EXP GENETIC ASSESSMENT OF COLUMBIA R. STOCKS
Project Number:
Title:
Genetic Assessment of Columbia River Stocks
BPA PM:
Stage:
Implementation
Area:
Province Subbasin %
Basinwide - 50.00%
Mainstem - 50.00%
Contract Number:
41224
Contract Title:
2008-907-00 EXP GENETIC ASSESSMENT OF COLUMBIA R. STOCKS
Contract Continuation:
Previous: Next:
n/a
Contract Status:
Closed
Contract Description:
This project combines four inter-related projects from the Accords that address Single Nucleotide Polymorphism (SNP) Discovery, Genetic Baseline Expansion, Genetic Stock Identification (GSI) to Evaluate Catch, and GSI of salmon and steelhead passing Bonneville Dam.  These four projects are highly related since SNP markers are needed to complete species specific baselines, and these baselines are requisite to complete GSI.  

The specific objectives are:

1) discover and evaluate SNP markers in salmon and steelhead

2) expand and create genetic baselines for multiple species (Chinook, steelhead, sockeye, and coho)

3) implement GSI programs for mainstem Chinook fisheries

4) GSI of fish passing Bonneville Dam (steelhead and Chinook).

These four objectives address needs for distinguishing specific stocks, determining genetic diversity, stock specific run timing, and estimating stock composition to provide information for fisheries management and harvest.  Newly discovered SNP markers may also be useful for other applications such as pedigree studies for estimating reproductive success, and evaluating adaptive divergence of populations to specific environments.
Account Type(s):
Expense
Contract Start Date:
03/01/2009
Contract End Date:
03/31/2010
Current Contract Value:
$716,579
Expenditures:
$716,579

* Expenditures data includes accruals and are based on data through 31-Jan-2021.

Env. Compliance Lead:
Work Order Task(s):
Contract Type:
Contract (IGC)
Pricing Method:
Cost Reimbursement (CNF)
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Full Name Organization Write Permission Contact Role Email Work Phone
Matthew Campbell Idaho Department of Fish and Game (IDFG) No Interested Party matthew.campbell@idfg.idaho.gov (208) 939-6713
Nate Campbell Columbia River Inter-Tribal Fish Commission (CRITFC) Yes Technical Contact camn@critfc.org (208) 837-9096x1128
Israel Duran Bonneville Power Administration No Env. Compliance Lead induran@bpa.gov (503) 230-3967
Christine Golightly Columbia River Inter-Tribal Fish Commission (CRITFC) Yes Interested Party golc@critfc.org (503) 731-1288
Douglas Hatch Columbia River Inter-Tribal Fish Commission (CRITFC) No Interested Party hatd@critfc.org (503) 731-1263
Jon Hess Columbia River Inter-Tribal Fish Commission (CRITFC) Yes Technical Contact hesj@critfc.org (208) 837-9096x1107
Paul Krueger Bonneville Power Administration Yes F&W Approver pqkrueger@bpa.gov (503) 230-5723
Andrew Matala Columbia River Inter-Tribal Fish Commission (CRITFC) Yes Technical Contact mata@critfc.org (208) 837-9096x1111
George Nandor Pacific States Marine Fisheries Commission No Interested Party gnandor@psmfc.org (503) 595-3144
Shawn Narum Columbia River Inter-Tribal Fish Commission (CRITFC) Yes Contract Manager nars@critfc.org (208) 837-9096x1120
Phillip Roger Columbia River Inter-Tribal Fish Commission (CRITFC) No Supervisor rogp@critfc.org (503) 731-1301
Barbara Shields Bonneville Power Administration Yes COTR bashields@bpa.gov (503) 230-4748
Kristi Van Leuven Bonneville Power Administration No Contracting Officer kjvleuven@bpa.gov (503) 230-3605
Nancy Weintraub Bonneville Power Administration No Interested Party nhweintraub@bpa.gov (503) 230-5373


Viewing of Work Statement Elements

Deliverable Title WSE Sort Letter, Number, Title Start End Complete
Funding Package - Submit draft to COTR A: 119. Obj. 1-4; Manage/Admin. Projects 01/04/2010 03/15/2010
Obtain Permit B: 165. Obj. 1-4; Environmental Compl. 03/01/2009 03/01/2009
Submit manuscript C: 183. Obj. 1-4; Journal articles 03/31/2010
Identify target genes D: 156. Obj. 1) SNP Ascertainment Strategy 04/01/2009 04/01/2009
Design Primers E: 157. Obj. 1) Sequencing and Assay Development 04/30/2009 04/30/2009
Estimate allele frequencies F: 162. Obj. 1) Analysis of SNP Frequencies 01/29/2010 03/15/2010
Report assays G: 161. Obj. 1) SNP Sites and Assays 01/29/2010 03/15/2010
List of SNPs and populations H: 156. Obj. 2) Determine SNP Markers and Baseline Samples 03/01/2009 04/30/2009
Multi-locus SNP genotypes I: 157. Obj. 2) SNP Genotyping 11/27/2009 11/29/2009
Submit to Database J: 159. Obj. 2) Baseline Genotypes to Database 01/29/2010 03/15/2010
Analyze Genetic Data K: 162. Obj. 2) Population Diversity and Differentiation 12/31/2009 12/30/2009
Report/Present Genetic Data L: 161. Obj. 2) Genotypes and Allele Frequencies 01/29/2010 03/15/2010
Hold Meeting M: 189. Obj. 3) Coordination Among Agencies 03/01/2009 06/30/2009
Written Sample Plan N: 156. Obj. 3) Develop Sampling Plan 03/01/2009 06/30/2009
Inventory of Samples O: 157. Obj. 3) Collect Tissue Samples from Fisheries 11/06/2009 12/31/2009
Spreadsheet of Genotypes P: 157. Obj. 3) Genotype Tissue Samples 12/31/2009 12/31/2009
Stock Composition Q: 162. Obj. 3) Estimate Stock Composition 01/29/2010 03/15/2010
Report Stock Composition R: 161. Obj. 3) Distribute GSI Estimates 01/29/2010 03/15/2010
Written sampling plan S: 156. Obj. 4) Sampling period, size, and logistics 04/01/2009 04/01/2009
Inventory of Samples T: 157. Obj. 4) Non-lethal sampling at Bonneville Dam 11/06/2009 12/11/2009
Spreadsheet of Genotypes U: 157. Obj. 4) Genotype tissue samples 12/31/2009 12/31/2009
Stock Composition V: 162. Obj. 4) GSI estimates 01/29/2010 03/23/2010
Post Results Online W: 161. Obj. 4) Post updates to CRITFC website 01/29/2010 03/23/2010

Viewing of Implementation Metrics
Viewing of Environmental Metrics Customize

Primary Focal Species Work Statement Elements
Chinook (Oncorhynchus tshawytscha) - All Populations
  • 1 instance of WE 183 Produce Journal Article
  • 5 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 3 instances of WE 161 Disseminate Raw/Summary Data and Results
  • 3 instances of WE 162 Analyze/Interpret Data
Coho (O. kisutch) - Unspecified Population
  • 1 instance of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 161 Disseminate Raw/Summary Data and Results
  • 1 instance of WE 162 Analyze/Interpret Data
Sockeye (Oncorhynchus nerka) - All Populations
  • 1 instance of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 161 Disseminate Raw/Summary Data and Results
  • 1 instance of WE 162 Analyze/Interpret Data
Steelhead (Oncorhynchus mykiss) - All Populations
  • 1 instance of WE 183 Produce Journal Article
  • 3 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 2 instances of WE 161 Disseminate Raw/Summary Data and Results
  • 2 instances of WE 162 Analyze/Interpret Data
Trout, Interior Redband (O. mykiss gairdnerii)
  • 1 instance of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 1 instance of WE 161 Disseminate Raw/Summary Data and Results
  • 1 instance of WE 162 Analyze/Interpret Data

Sort WE ID WE Title NEPA NOAA USFWS NHPA Has Provisions Inadvertent Discovery Completed
A 119 Obj. 1-4; Manage/Admin. Projects 02/09/2007
B 165 Obj. 1-4; Environmental Compl. 02/09/2007
C 183 Obj. 1-4; Journal articles 02/09/2007
D 156 Obj. 1) SNP Ascertainment Strategy 02/09/2007
E 157 Obj. 1) Sequencing and Assay Development 02/09/2007
F 162 Obj. 1) Analysis of SNP Frequencies 02/09/2007
G 161 Obj. 1) SNP Sites and Assays 02/09/2007
H 156 Obj. 2) Determine SNP Markers and Baseline Samples 02/09/2007
I 157 Obj. 2) SNP Genotyping 02/09/2007
J 159 Obj. 2) Baseline Genotypes to Database 02/09/2007
K 162 Obj. 2) Population Diversity and Differentiation 02/09/2007
L 161 Obj. 2) Genotypes and Allele Frequencies 02/09/2007
M 189 Obj. 3) Coordination Among Agencies 02/09/2007
N 156 Obj. 3) Develop Sampling Plan 02/09/2007
O 157 Obj. 3) Collect Tissue Samples from Fisheries 02/09/2007
P 157 Obj. 3) Genotype Tissue Samples 02/09/2007
Q 162 Obj. 3) Estimate Stock Composition 02/09/2007
R 161 Obj. 3) Distribute GSI Estimates 02/09/2007
S 156 Obj. 4) Sampling period, size, and logistics 02/09/2007
T 157 Obj. 4) Non-lethal sampling at Bonneville Dam 02/02/2009
U 157 Obj. 4) Genotype tissue samples 02/09/2007
V 162 Obj. 4) GSI estimates 02/09/2007
W 161 Obj. 4) Post updates to CRITFC website 02/09/2007
X 185 Obj. 1-4; Periodic Status Reports for BPA 02/09/2007
Y 132 Obj. 1-4; Submit Progress Report for the period (04/01/09) to (03/31/10) 02/09/2007