Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
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Project Summary

Project 2010-026-00 - Chinook and Steelhead Genotyping for Genetic Stock Identification (GSI) at Lower Granite Dam
Project Number:
2010-026-00
Title:
Chinook and Steelhead Genotyping for Genetic Stock Identification (GSI) at Lower Granite Dam
Summary:
This project will develop and implement GSI methodologies within the Snake River basin for wild Chinook salmon and steelhead passing Lower Granite Dam. Project leads will ensure that all SNP genotype data generated from this project will be standardized and available for Columbia River genetic baseline expansions (CRITFC 200890700-objective 2). In addition, side by side comparisons of Parentage Based Tagging datasets (BPA project #201003100) and GSI datasets, will allow the identification of a single set of SNPs that can be used for both technologies. This will allow the integration of sampling programs at Bonneville and Lower Granite Dam and in Columbia River and Snake River mainstem fisheries such that any sampled wild adult can be included in mixture analyses to determine stock composition and any sampled Snake River hatchery adult can be assigned to a stock and cohort. Once standardized SNP marker sets have been developed and tested, this project will genotype 2000 adults and 2000 juveniles (for each species) annually as they migrate past Lower Granite Dam on the Snake River. An additional 1000 samples (for each species) will be genotyped annually as part of generational genetic baseline development and maintenance. This sampling and genotyping will provide a robust baseline from which GSI mixture analyses can be performed, and will also provide temporal monitoring of genetic diversity/structure across the basin allowing estimation of gene flow and effective population size. Incorporating age and sex information collected simultaneously from migrating adults and juveniles will provide data on abundance and biodiversity of Snake River Chinook salmon and steelhead that have previously been unavailable for managing wild stocks in the basin.
Proposer:
Proponent Orgs:
Idaho Department of Fish and Game (IDFG) (Govt - State)
Starting FY:
2010
Ending FY:
2022
BPA PM:
Stage:
Implementation - Project Status Report
Area:
Province Subbasin %
Blue Mountain Grande Ronde 20.00%
Imnaha 20.00%
Columbia Plateau Snake Lower 20.00%
Mountain Snake Clearwater 20.00%
Salmon 20.00%
Purpose:
Programmatic
Emphasis:
RM and E
Focal Species:
Chinook - Snake River Fall ESU
Chinook - Snake River Spring/Summer
Chinook - Snake River Spring/Summer ESU
Steelhead - Snake River DPS
Species Benefit:
Anadromous: 100.0%   Resident: 0.0%   Wildlife: 0.0%
Special:
None

Description: Page: 49 Figure 1: Steelhead populations representing steelhead baseline v1.0 for the Snake River. Population numbers correspond to numbers in Table 1. The locations of Lower Granite Dam and Hells Canyon Dam is noted.

Project: 2010-026-00

Document: P121841

Dimensions: 975 x 853

Description: Page: 50 Figure 2: Chinook salmon populations representing Chinook baseline v1.0 for the Snake River. Population numbers correspond to numbers in Table 2. The locations of Lower Granite Dam and Hells Canyon Dam is noted.

Project: 2010-026-00

Document: P121841

Dimensions: 949 x 826


Summary of Budgets

To view all expenditures for all fiscal years, click "Project Exp. by FY"

To see more detailed project budget information, please visit the "Project Budget" page

Decided Budget Transfers  (FY2019 - FY2021)

Acct FY Acct Type Amount Fund Budget Decision Date
FY2019 Expense $665,448 From: Fish Accord - Idaho Accord Extensions (State of Idaho) 10/1/2018 10/01/2018
FY2019 Expense $28,681 To: BiOp FCRPS 2008 (non-Accord) Jan 2nd FY19 01/02/2019
FY2019 Expense $28,681 From: BiOp FCRPS 2008 (non-Accord) April 29th Transfers 04/30/2019
FY2020 Expense $665,448 From: Fish Accord - Idaho Accord Extensions (State of Idaho) 10/1/2018 10/01/2018
FY2020 Expense $76,131 To: Fish Accord - Idaho Idaho Accord Budget Cleanup 3/17/20 03/18/2020
FY2020 Expense $76,131 From: General Fish Accord Budget Cleanup Idaho 03/18/20 03/18/2020
FY2021 Expense $673,766 From: Fish Accord - Idaho Accord Extensions (State of Idaho) 10/1/2018 10/01/2018

Pending Budget Decision?  Yes


Actual Project Cost Share

Current Fiscal Year — 2020
Cost Share Partner Total Proposed Contribution Total Confirmed Contribution
There are no project cost share contributions to show.
Previous Fiscal Years
Fiscal Year Total Contributions % of Budget
2019
2017 (Draft)
2016
2015 $30,000 5%
2014 $30,000 5%
2013 $30,000 5%
2012 $94,876 13%
2011

Contracts

The table below contains contracts with the following statuses: Active, Complete, History, Issued.
* "Total Contracted Amount" column includes contracted amount from both capital and expense components of the contract.
Expense Contracts:
Number Contractor Name Title Status Total Contracted Amount Dates
82382 SOW Idaho Department of Fish and Game (IDFG) 2010-026-00 EXP CHINOOK AND STEELHEAD GENOTYPING Issued $665,448 7/1/2019 - 6/30/2020
85311 SOW Idaho Department of Fish and Game (IDFG) 2010-026-00 EXP CHINOOK AND STEELHEAD GENOTYPING Issued $665,448 7/1/2020 - 6/30/2021



Annual Progress Reports
Expected (since FY2004):10
Completed:10
On time:10
Status Reports
Completed:40
On time:37
Avg Days Early:5

Earliest Subsequent           Accepted Count of Contract Deliverables
Contract Contract(s) Title Contractor Start End Status Reports Complete Green Yellow Red Total % Green and Complete Canceled
48347 53239, 57343, 61826, 65455, 69548, 73153, 76531, 79581, 82382, 85311 2010-026-00 EXP IDF&G CHINOOK AND STEELHEAD GENOTYPING Idaho Department of Fish and Game (IDFG) 07/2010 07/2010 Issued 40 178 0 0 0 178 100.00% 1
Project Totals 40 178 0 0 0 178 100.00% 1


The table content is updated frequently and thus contains more recent information than what was in the original proposal reviewed by ISRP and Council.

Review: Fast Track ISRP Review 2010

Independent Scientific Review Panel Assessment

Assessment Number: 2010-026-00-ISRP-20100623
Project: 2010-026-00 - Chinook and Steelhead Genotyping for Genetic Stock Identification (GSI) at Lower Granite Dam
Review: Fast Track ISRP Review 2010
Completed Date: None
First Round ISRP Date: 2/24/2010
First Round ISRP Rating: Meets Scientific Review Criteria (Qualified)
First Round ISRP Comment:
The proponent proposes to use single nucleotide polymorphism (SNPs) based genetic stock identification (GSI) for establishing the composition of various Snake River salmon and steelhead populations passing the Lower Granite Dam (LGD). Based on suites of genetic characters, GSI models the most likely composition of populations contributing to the fish passing. The modeling methods have a long history and this proposal builds on these to fit an advertised need to better estimate salmon populations in the Snake River basin. This methodology can be applied at Lower Granite Dam to evaluate populations that may not be amendable to analysis by PIT tagging.

The proposed project has the potential to provide important data to understand the life-history and population dynamics of Snake River steelhead and Chinook salmon.

1. Technical Justification, Program Significance and Consistency, and Project Relationships
This project will develop (and test) standardized SNP baselines for fine-scale GSI of Snake R. Basin stocks as adults migrate past Lower Granite Dam (LGD).

The general explanation of life history variation in steelhead in the Snake River basin, and justification that a GSI approach can contribute to estimating abundance of MPGs and reporting groups (aggregates of spawning tributaries) is well summarized. Estimates of population components crossing LGD for one year are included in the problem statement.

The project is greatly interdependent, in part, on project #201003100 which creates the reference baseline used to decompose the population mixture.

The proposed project is consistent with BiOp RPAs, the regional monitoring strategy, and recommendations in the ISRP/AB tagging report. This and related projects provide an alternative tool for mark and recapture (referenced in our tagging report Section A.6 pp. 67-73).

The project relationships are summarized and appear extensive. This project will use fish collected by other projects, and these are adequately summarized. At least a portion of the SNP development effort will involve collaboration with the Hagerman Laboratory operated by CRITFC, specifically project 200890700 Genetic Assessment of Columbia River Stocks, that will be using GSI to estimate stock proportions at Bonneville Dam. Section I. Key Personnel indicates that the CRITFC lab will be a subcontractor to develop SNPs and genotype fish. Geneticists throughout the Pacific Northwest have collaborated on development of microsatellite gene markers and standardized genes, alleles, and methods of analysis. The collaboration on SNP development and standardization of genotyping and analysis platforms is appropriate. The ISRP does believe a more thorough clarification of the roles of the different projects in the field, laboratory, and analysis is needed.

2. Objectives, Work Elements, and Methods
The objectives are straight forward and build on previous or currently proposed work. The methods for developing SNP assays, evaluating the distribution of SNP alleles in Snake basin populations, and establishing the utility of a set of SNPs for both GSI of wild steelhead and Chinook at LGD and Parental Based Tagging of hatchery steelhead are consistent with practices and methods in the discipline.

It is less clear that methodologies for using abundance estimates from LGD, partitioned into reporting groups in VSP analysis for BiOp monitoring and ESA delisting, etc are developed. The rationale for sampling and genotyping 2000 fish at LGD needs to be justified.
Documentation Links:
Review: RME / AP Category Review

Council Recommendation

Assessment Number: 2010-026-00-NPCC-20110624
Project: 2010-026-00 - Chinook and Steelhead Genotyping for Genetic Stock Identification (GSI) at Lower Granite Dam
Review: RME / AP Category Review
Proposal: RMECAT-2010-026-00
Proposal State: Pending BPA Response
Approved Date: 6/10/2011
Recommendation: Fund (Qualified)
Comments: Fund through 2016 per April-May 2010 decision for Fast Track projects. Implementation subject to regional hatchery effects evaluation process described in programmatic recommendation #4.
Conditions:
Council Condition #1 April-May 2010 Council decision for Fast Track project - Prior to contracting, BPA and sponsors to address ISRP qualification on analytical framework. In addition, BPA and Council will consider integration and coordination of similar genetic projects through the larger RM&E/Artificial production Categorical Review.
Council Condition #2 Programmatic Issue: RMECAT #4 Hatchery Effectiveness—.

2008 FCRPS BiOp Workgroup Assessment

Assessment Number: 2010-026-00-BIOP-20101105
Project Number: 2010-026-00
Review: RME / AP Category Review
Proposal Number: RMECAT-2010-026-00
Completed Date: None
2008 FCRPS BiOp Workgroup Rating: Supports 2008 FCRPS BiOp
Comments: BiOp Workgroup Comments: No BiOp Workgroup Comments

The BiOp RM&E Workgroups made the following determinations regarding the proposal's ability or need to support BiOp Research, Monitoring and Evaluation (RME) RPAs. If you have questions regarding these RPA association conclusions, please contact your BPA COTR and they will help clarify, or they will arrange further discussion with the appropriate RM&E Workgroup Leads. BiOp RPA associations for the proposed work are: ( 50.5 51.2 53.2 62.5)
All Questionable RPA Associations ( ) and
All Deleted RPA Associations (50.2 50.3 50.8 )
Proponent Response:

Project Relationships: None

Name Role Organization
Israel Duran Env. Compliance Lead Bonneville Power Administration
Matthew Campbell Project Lead Idaho Department of Fish and Game (IDFG)
Mike (PSMFC) Ackerman (Inactive) Technical Contact Pacific States Marine Fisheries Commission
Jeff Dillon Supervisor Idaho Department of Fish and Game (IDFG)
Conan Chiu (Inactive) Technical Contact Idaho Department of Fish and Game (IDFG)
Jesse McCane (Inactive) Technical Contact Idaho Department of Fish and Game (IDFG)
Jon Hess Interested Party Columbia River Inter-Tribal Fish Commission (CRITFC)
Maureen Hess Interested Party Columbia River Inter-Tribal Fish Commission (CRITFC)
Shawn Narum Interested Party Columbia River Inter-Tribal Fish Commission (CRITFC)
Craig Steele Technical Contact Pacific States Marine Fisheries Commission
Paul Kline Interested Party Idaho Department of Fish and Game (IDFG)
Martin Allen Project Manager Bonneville Power Administration
Russell Scranton Project SME Bonneville Power Administration