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Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
SOW Report
Contract 73354 REL 39: 2008-907-00 EXP GENETIC ASSESSMENT OF COLUMBIA RIVER STOCKS

Basics

Project Number:
2008-907-00
Title:
Genetic Assessment of Columbia River Stocks
BPA PM:
Martin Allen
Stage:
Implementation
Area:
Province Subbasin %
Basinwide - 50.00%
Mainstem - 50.00%
Contract Number:
73354 REL 39
Contract Title:
2008-907-00 EXP GENETIC ASSESSMENT OF COLUMBIA RIVER STOCKS
Contract Continuation:
Previous: Next:
73354 REL 21: 2008-907-00 EXP GENETIC ASSESSMENT OF COLUMBIA RIVER STOCKS
  • 73354 REL 56: 2008-907-00 EXP GENETIC ASSESSMENT OF COLUMBIA RIVER STOCKS
Contract Status:
Closed
Contract Description:
This project combines multiple inter-related projects from the Accords focused on genetic monitoring in salmonids, genetic adaptation to local environments in salmonids, and genetic variation in white sturgeon.  These were initially three separate projects but have been combined into this single project due to overlapping objectives and efficiency for contracting and reporting.

The specific objectives are:

1) discover and evaluate SNP markers throughout the genome 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 stock ID of mainstem fisheries

4) GSI/PBT  for stock ID of fish passing Bonneville Dam

5) evaluate effects of environment and landscape on genetic variation in salmonids

6) determine the genetic basis for phenotypic expression of traits in salmonids

7) evaluate genetic variation in white sturgeon in the mainstem Columbia River

These 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.  They also address needs for monitoring genetic variation related to local adaptation and variation of life history traits important for long-term persistence.  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:
04/01/2020
Contract End Date:
03/31/2021
Current Contract Value:
$1,177,657
Expenditures:
$1,177,657

* Expenditures data includes accruals and are based on data through 31-Mar-2024.

BPA CO:
Elham Zolmajd-Haghighi
BPA COR:
Martin Allen
Env. Compliance Lead:
Israel Duran
Contract Contractor:
Columbia River Inter-Tribal Fish Commission (CRITFC) - COLURIVE00
Work Order Task(s):
WO: 00219436, Task: 1
Contract Type:
Release
Pricing Method:
Cost Reimbursement (CNF)
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Contract Contacts

Full Name Organization Write Permission Contact Role Email Work Phone
Martin Allen Bonneville Power Administration Yes COR mballen@bpa.gov (503) 230-5115
Israel Duran Bonneville Power Administration Yes Env. Compliance Lead induran@bpa.gov (503) 230-3967
Desmond Gelman Bonneville Power Administration No CO Assistant dxgelman@bpa.gov (503) 230-4960
Christine Golightly Columbia River Inter-Tribal Fish Commission (CRITFC) Yes Administrative Contact 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 Interested Party hesj@critfc.org (208) 837-9096x1107
Kristen Jule Bonneville Power Administration Yes F&W Approver krjule@bpa.gov (503) 230-3588
Shawn Narum Columbia River Inter-Tribal Fish Commission (CRITFC) Yes Contract Manager nars@critfc.org (208) 837-9096x1120
Zachary Penney Columbia River Inter-Tribal Fish Commission (CRITFC) No Supervisor zpenney@critfc.org (503) 731-1301
Elham Zolmajd-Haghighi Bonneville Power Administration Yes Contracting Officer ezolmajd-haghighi@bpa.gov (503) 230-7414


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Statement Of Work (SOW)

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Deliverable Status

Deliverable Title WSE Sort Letter, Number, Title Start End Concluded
Effective implementation management and timely contract administration B: 119. Obj. 1-7; Manage/Admin. Projects 03/31/2021 03/29/2021
Obtain Permit C: 165. Obj. 1-7; Environmental Compl. 03/31/2021 03/29/2021
Submit manuscript D: 183. Obj. 1-7; Journal articles 03/31/2021 03/29/2021
Sequencing and Assay development E: 157. Obj. 1) Sequencing and Assay Development 03/31/2021 03/29/2021
Estimate allele frequencies F: 162. Obj. 1) Analysis of SNP Frequencies 03/31/2021 03/29/2021
Report SNP sites G: 161. Obj. 1) SNP Sites and Assays 03/31/2021 03/29/2021
List of SNPs and populations H: 156. Obj. 2) Determine SNP Markers and Baseline Samples 03/31/2021 03/29/2021
Multi-locus SNP genotypes I: 157. Obj. 2) SNP Genotyping 03/31/2021 03/29/2021
Produce accessible, error-checked datasets J: 157. Obj. 2) SNP Genotyping for Fall Chinook PBT 03/31/2021 03/29/2021
Submit to Database K: 159. Obj. 2) Baseline Genotypes to Database 03/31/2021 03/29/2021
Analyze Genetic Data L: 162. Obj. 2) Population Diversity and Differentiation 03/31/2021 03/29/2021
Report/Present Genetic Data M: 161. Obj. 2) Genotypes and Allele Frequencies 03/31/2021 03/29/2021
Sample Plan N: 156. Obj. 3) Develop Sampling Plan 03/31/2021 03/29/2021
Inventory of Samples O: 157. Obj. 3) Collect Tissue Samples from Fisheries 03/31/2021 03/29/2021
Summary of Genotypes P: 157. Obj. 3) Genotype Tissue Samples 03/31/2021 03/29/2021
Stock Composition Q: 162. Obj. 3) Estimate Stock Composition 03/31/2021 03/29/2021
Report Stock Composition R: 161. Obj. 3) Distribute PBT/GSI Estimates 03/31/2021 03/29/2021
Sampling plan S: 156. Obj. 4) Sampling period, size, and logistics 03/31/2021 03/29/2021
Inventory of Samples T: 157. Obj. 4) Non-lethal sampling at Bonneville Dam 03/31/2021 03/29/2021
Summary of Genotypes U: 157. Obj. 4) Genotype tissue samples 03/31/2021 03/29/2021
Stock Composition V: 162. Obj. 4) PBT/GSI estimates 03/31/2021 03/29/2021
Landscape variables W: 156. Obj 5) Determine Landscape and Genetic Variables 03/31/2021 03/29/2021
Produce accessible, error-checked datasets X: 157. Obj. 5) Gather Landscape and Genetic Data 03/31/2021 03/29/2021
Data analyses Y: 162. Obj. 5) Landscape Genetics Analyses/Correlation 03/31/2021 03/29/2021
Sampling plan Z: 156. Obj. 6) Sampling Plan and SNP Analysis 03/31/2021 03/29/2021
Produce accessible, error-checked datasets AA: 157. Obj. 6) Tissue Sampling & Quantify SNP Frequencies 03/31/2021 03/29/2021
Statistical analyses AB: 162. Obj. 6) Genes Associated with Traits 03/31/2021 03/29/2021
SNP development AC: 156. Obj. 7) White sturgeon marker development 03/31/2021 03/29/2021
Produce accessible, error-checked datasets AD: 157. Obj. 7) White sturgeon - Collection, transformation and management of (polyploid) genetic data 03/31/2021 03/29/2021
Data analyses AE: 162. Obj. 7) White sturgeon - Analysis of SNP Frequencies 03/31/2021 03/29/2021
Completed Annual Report AF: 132. Submit Progress Report for the period (1/1/2020) to (12/31/2020) 03/31/2021 03/29/2021
Submit BiOp RPA Report in Taurus AG: 202. BiOp RPA Report for CY 2020 03/15/2021 03/15/2021

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Metrics

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Viewing of Environmental Metrics Customize

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Focal Species

Primary Focal Species Work Statement Elements
Chinook (Oncorhynchus tshawytscha) - All Populations
  • 1 instance of WE 183 Produce Journal Article
  • 9 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
  • 6 instances of WE 162 Analyze/Interpret 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
  • 3 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
  • 3 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
  • 8 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
  • 6 instances of WE 162 Analyze/Interpret Data
Sturgeon, White (A. transmontanus) - Lower Columbia River
  • 1 instance of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 162 Analyze/Interpret Data
Sturgeon, White (Acipenser transmontanus) - All Populations except Kootenai R. DPS
  • 1 instance of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 162 Analyze/Interpret Data
Trout, Interior Redband (O. mykiss gairdnerii)
  • 1 instance of WE 157 Collect/Generate/Validate Field and Lab Data
  • 2 instances of WE 162 Analyze/Interpret Data

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Environmental Compliance

Sort WE ID WE Title NEPA NOAA USFWS NHPA Has Provisions Inadvertent Discovery Completed
A 185 Periodic Status Reports for BPA
B 119 Obj. 1-7; Manage/Admin. Projects
C 165 Obj. 1-7; Environmental Compl.
D 183 Obj. 1-7; Journal articles
E 157 Obj. 1) Sequencing and Assay Development 07/01/2020
F 162 Obj. 1) Analysis of SNP Frequencies
G 161 Obj. 1) SNP Sites and Assays
H 156 Obj. 2) Determine SNP Markers and Baseline Samples 07/01/2020
I 157 Obj. 2) SNP Genotyping 07/01/2020
J 157 Obj. 2) SNP Genotyping for Fall Chinook PBT 07/01/2020
K 159 Obj. 2) Baseline Genotypes to Database
L 162 Obj. 2) Population Diversity and Differentiation
M 161 Obj. 2) Genotypes and Allele Frequencies
N 156 Obj. 3) Develop Sampling Plan 06/30/2020
O 157 Obj. 3) Collect Tissue Samples from Fisheries 07/01/2020
P 157 Obj. 3) Genotype Tissue Samples 07/01/2020
Q 162 Obj. 3) Estimate Stock Composition
R 161 Obj. 3) Distribute PBT/GSI Estimates
S 156 Obj. 4) Sampling period, size, and logistics 07/01/2020
T 157 Obj. 4) Non-lethal sampling at Bonneville Dam 07/01/2020
U 157 Obj. 4) Genotype tissue samples 07/01/2020
V 162 Obj. 4) PBT/GSI estimates
W 156 Obj 5) Determine Landscape and Genetic Variables 07/01/2020
X 157 Obj. 5) Gather Landscape and Genetic Data 07/01/2020
Y 162 Obj. 5) Landscape Genetics Analyses/Correlation
Z 156 Obj. 6) Sampling Plan and SNP Analysis 07/01/2020
AA 157 Obj. 6) Tissue Sampling & Quantify SNP Frequencies 07/01/2020
AB 162 Obj. 6) Genes Associated with Traits
AC 156 Obj. 7) White sturgeon marker development 07/01/2020
AD 157 Obj. 7) White sturgeon - Collection, transformation and management of (polyploid) genetic data 07/01/2020
AE 162 Obj. 7) White sturgeon - Analysis of SNP Frequencies
AF 132 Submit Progress Report for the period (1/1/2020) to (12/31/2020)
AG 202 BiOp RPA Report for CY 2020

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Reports


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