Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
SOW Report
Contract 64699: 2008-907-00 GENETIC ASSESSMENT OF COLUMBIA RIVER 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:
64699
Contract Title:
2008-907-00 GENETIC ASSESSMENT OF COLUMBIA RIVER STOCKS
Contract Continuation:
Previous: Next:
61126: 2008-907-00 EXP GENETIC ASSESSMENT OF COLUMBIA RIVER STOCKS
  • 68665: 2008-907-00 EXP GENETIC ASSESSMENT OF COLUMBIA RIVER STOCKS
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 fishes 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 salmonids and other fishes

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

3) implement GSI/PBT programs for mainstem fisheries

4) GSI/PBT of fish passing Bonneville Dam

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:
04/01/2014
Contract End Date:
03/31/2015
Current Contract Value:
$692,084
Expenditures:
$692,084

* 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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Viewing of Work Statement Elements

Deliverable Title WSE Sort Letter, Number, Title Start End Complete
All administrative tasks fulfilled with timely quality products B: 119. Obj. 1-4; Manage/Admin. Projects 03/31/2015 03/05/2015
Obtain Permit C: 165. Obj. 1-4; Environmental Compl. 04/01/2014 04/01/2014
Submit manuscript D: 183. Obj. 1-4; Journal articles 03/31/2015 03/05/2015
Description of approach E: 156. Obj. 1) SNP Ascertainment Strategy 01/30/2015 01/30/2015
Sequencing and Assay development F: 157. Obj. 1) Sequencing and Assay Development 01/30/2015 01/30/2015
Estimate allele frequencies G: 162. Obj. 1) Analysis of SNP Frequencies 03/31/2015 03/05/2015
Report SNP sites H: 161. Obj. 1) SNP Sites and Assays 03/31/2015 03/05/2015
List of SNPs and populations I: 156. Obj. 2) Determine SNP Markers and Baseline Samples 01/15/2015 01/15/2015
Multi-locus SNP genotypes J: 157. Obj. 2) SNP Genotyping 03/31/2015 03/05/2015
Submit to Database K: 159. Obj. 2) Baseline Genotypes to Database 03/31/2015 03/05/2015
Analyze Genetic Data L: 162. Obj. 2) Population Diversity and Differentiation 03/31/2015 03/05/2015
Report/Present Genetic Data M: 161. Obj. 2) Genotypes and Allele Frequencies 03/31/2015 03/05/2015
Hold Meetings N: 189. Obj. 3) Coordination Among Agencies 03/31/2015 03/05/2015
Sample Plan O: 156. Obj. 3) Develop Sampling Plan 12/12/2014 12/12/2014
Inventory of Samples P: 157. Obj. 3) Collect Tissue Samples from Fisheries 03/31/2015 03/05/2015
Summary of Genotypes Q: 157. Obj. 3) Genotype Tissue Samples 03/31/2015 03/05/2015
Stock Composition R: 162. Obj. 3) Estimate Stock Composition 03/31/2015 03/05/2015
Report Stock Composition S: 161. Obj. 3) Distribute GSI Estimates 03/31/2015 03/05/2015
Sampling plan T: 156. Obj. 4) Sampling period, size, and logistics 10/31/2014 10/31/2014
Inventory of Samples U: 157. Obj. 4) Non-lethal sampling at Bonneville Dam 01/15/2015 01/15/2015
Summary of Genotypes V: 157. Obj. 4) Genotype tissue samples 03/31/2015 03/05/2015
Stock Composition W: 162. Obj. 4) GSI estimates 03/31/2015 03/05/2015
Post Results Online X: 161. Obj. 4) Post updates to CRITFC website 03/31/2015 03/05/2015
Submit annual report for period 4/1/2013 - 3/31/2014 Y: 132. Obj. 1-4) Submit Draft Annual Technical Report for CY 2013 03/31/2015 03/05/2015
BiOp RM&E report for CY 2013 Z: 141. Other Reports for BPA 03/31/2015 03/05/2015
Attach Progress Report in Pisces AA: 132. Submit Progress Report for the period (4/1/2012) to (12/31/2012) 11/30/2014 11/30/2014
Multilocus SNP genotypes for each individual Fall Chinook compiled in a spreadsheet. AB: 157. Obj. 5) PBT baselines for Fall Chinook 03/31/2015 03/05/2015

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
  • 6 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 4 instances of WE 161 Disseminate Raw/Summary Data and Results
  • 4 instances of WE 162 Analyze/Interpret Data
Chinook (O. tshawytscha) - Snake River Fall ESU (Threatened)
  • 1 instance of WE 157 Collect/Generate/Validate Field and Lab Data
Coho (O. kisutch) - Unspecified Population
  • 6 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 4 instances of WE 161 Disseminate Raw/Summary Data and Results
  • 4 instances of WE 162 Analyze/Interpret Data
Sockeye (Oncorhynchus nerka) - All Populations
  • 1 instance of WE 183 Produce Journal Article
  • 6 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 4 instances of WE 161 Disseminate Raw/Summary Data and Results
  • 4 instances of WE 162 Analyze/Interpret Data
Steelhead (Oncorhynchus mykiss) - All Populations
  • 1 instance of WE 183 Produce Journal Article
  • 6 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 4 instances of WE 161 Disseminate Raw/Summary Data and Results
  • 4 instances of WE 162 Analyze/Interpret Data

Sort WE ID WE Title NEPA NOAA USFWS NHPA Has Provisions Inadvertent Discovery Completed
A 185 Periodic Status Reports for BPA 04/01/2014
B 119 Obj. 1-4; Manage/Admin. Projects 04/01/2014
C 165 Obj. 1-4; Environmental Compl. 04/01/2014
D 183 Obj. 1-4; Journal articles 04/01/2014
E 156 Obj. 1) SNP Ascertainment Strategy 04/01/2014
F 157 Obj. 1) Sequencing and Assay Development 04/01/2014
G 162 Obj. 1) Analysis of SNP Frequencies 04/01/2014
H 161 Obj. 1) SNP Sites and Assays 04/01/2014
I 156 Obj. 2) Determine SNP Markers and Baseline Samples 04/01/2014
J 157 Obj. 2) SNP Genotyping 04/01/2014
K 159 Obj. 2) Baseline Genotypes to Database 04/01/2014
L 162 Obj. 2) Population Diversity and Differentiation 04/01/2014
M 161 Obj. 2) Genotypes and Allele Frequencies 04/01/2014
N 189 Obj. 3) Coordination Among Agencies 04/01/2014
O 156 Obj. 3) Develop Sampling Plan 04/01/2014
P 157 Obj. 3) Collect Tissue Samples from Fisheries 04/01/2014
Q 157 Obj. 3) Genotype Tissue Samples 04/01/2014
R 162 Obj. 3) Estimate Stock Composition 04/01/2014
S 161 Obj. 3) Distribute GSI Estimates 04/01/2014
T 156 Obj. 4) Sampling period, size, and logistics 04/01/2014
U 157 Obj. 4) Non-lethal sampling at Bonneville Dam 04/01/2014
V 157 Obj. 4) Genotype tissue samples 04/01/2014
W 162 Obj. 4) GSI estimates 04/01/2014
X 161 Obj. 4) Post updates to CRITFC website 04/01/2014
Y 132 Obj. 1-4) Submit Draft Annual Technical Report for CY 2013 04/01/2014
Z 141 Other Reports for BPA 04/01/2014
AA 132 Submit Progress Report for the period (4/1/2012) to (12/31/2012) 04/01/2014
AB 157 Obj. 5) PBT baselines for Fall Chinook 04/01/2014