FY 2007 Solicitation Homepage

Project Proposal Request for FY 2007 - FY 2009 Funding

Proposal 200722700: Rapid DNA Profiling of Hatchery and Wild Salmon Stocks with Single Nucleotide Polymorphism (SNP) Profiling

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Table of Contents
Part 1. Administration and Budgeting
Section 1: General Administrative
Section 2: Project Location
Section 3: Project Species
Section 4: Past Accomplishments
Section 5: Relationship to Other Projects
Section 6: Biological Objectives
Section 7: Work Elements
Section 8: Budget
Section 9: Project Future
Section 10: Documents
Part 2. Reviews
Part 1 of 2. Administration and Budgeting
Section 1: General Administrative Information
Process Information:
Date Proposal Submitted & Finalized Status Form Generator
January 9, 2006 Finalized Ann Miracle

Proposal Type: New
Proposal Number: 200722700
Proposal Name: Rapid DNA Profiling of Hatchery and Wild Salmon Stocks with Single Nucleotide Polymorphism (SNP) Profiling
Agency, Institution or Organization: Pacific Northwest National Laboratory
Short Description: The objective of this proposal is to provide genetic profiling by single nucleotide polymorphism (SNP) analysis to the genetic issues that underlie Chinook salmon protection and enhancement with the Columbia basin.
Information Transfer: The results of this study will be made available in reports, published manuscripts, and included in ongoing database efforts to provide genotype information.
 
Project Proposal Contacts
Contact Organization Address Phone/Email Roles Notes
Form Submitter
Ann Miracle Pacific Northwest National Laboratory PO Box 999; K3-61
Richland, WA 99352
Ph: (509) 372-4327
Fax: (509) 375-6936
Email: ann.miracle@pnl.gov
Form Submitter
All Assigned Contacts
Ann Miracle Pacific Northwest National Laboratory PO Box 999; K3-61
Richland, WA 99352
Ph: (509) 372-4327
Fax: (509) 375-6936
Email: ann.miracle@pnl.gov
Project Lead

Section 2: Project Location
Sponsor Province: Mainstem/Systemwide ARG Province: No Change
Sponsor Subbasin: Systemwide ARG Subbasin: No Change
Location(s) at which the action will be implemented
Latitude Longitude Waterbody Location Description County/State Subbasin Primary?
Willamette Hatchery , Oregon Willamette No
Lookingglass Hatchery , Oregon Grande Ronde No
Warm Springs Hatchery , Oregon Deschutes No
Cle Elum Hatchery , Washington Yakima No
Methow Hatchery , Washington Methow No
Priest Rapids Hatchery , Washington Columbia Lower Middle No
Big Creek Hatchery , Washington Columbia Estuary No
Lyons Ferry , Washington Snake Lower No
Wells Hatchery , Washington Columbia Upper Middle No
Prosser Hatchery , Washington Yakima No

Section 3: Focal Species
Focal Species:
Primary Secondary Additional Species
Chinook All Populations

Section 4: Past Accomplishments
Past Accomplishments for Each Fiscal Year of This Project This proposal is for funding a new project, and has no past accomplishments.

Section 5: Relationships to Other Projects
Other Current Projects Related to this Project (any funding source)
Funding Source Related ID Related Project Title Relationship
PCSRF - CRITFC 2002-5-04 Fall Chinook Stock Composition Aids in sub-basin assignment.
PCSRF - CRITFC 2003-5-01 Fall Chinook Stock Composition Aids in sub-basin assignment.
PCSRF - CRITFC 2004-5-02 Fall Chinook Salmon Stock Comp Aids in sub-basin assingment
PCSRF - CRITFC 2005-5-02 Fall Chinook Salmon Stock Comp Aids in sub-basin assignment.

Section 6: Biological Objectives
Biological Objectives of this Proposed Project
Biological Objective Full Description Associated Subbasin Plan Strategy Page Nos
Identify new SNP loci Twenty to thirty new SNPs will be identified to increase the resolution of specific genotypes. Lower Columbia 10. Increased genetic research to identify genotypic variations in habitat use. A-262
Sub-basin genotype profiles This objective will provide the genetic basis for fish and hydropower managers to make near-real time, cost effective, decisions related to the protection and enhancement of wild fish and production of hatchery fish in the Columbia Basin, and form the genetic basis for subsequently measuring genetic interactions between hatchery and wild populations. Lower Columbia H.S2, H.S4 Operate hatcheries to promote region-wide recovery through the application of appropriate risk containment measures. Design hatchery programs to be consistent with region-wide recovery. A-252, A-253

Section 7: Work Elements
Work Elements and Associated Biological Objectives
Work Element Name Work Element Title Description Start Date End Date Estimated Budget
Collect/Generate/Validate Field and Lab Data Blind study We will conduct a limited “blind” study using the double-coded samples to determine if the SNP genoptypes can correctly identify or classify each fish to its sub-basin stock. 4/1/2008 3/31/2009 $54,896
Biological Objectives Metrics
Sub-basin genotype profiles
Primary R, M, and E Type: Status and Trend Monitoring

Collect/Generate/Validate Field and Lab Data Genoytpes of sub-basin samples The SNP profiles obtained from the 30-40 individual polymorphic loci will be used to construct haplotypes for each hatchery population. 7/1/2007 9/30/2008 $217,306
Biological Objectives Metrics
Sub-basin genotype profiles
Primary R, M, and E Type: Uncertainties Research

Collect/Generate/Validate Field and Lab Data Report A final report will be prepared describing the results of this research and the ability of rapid, SNP profiling to be applied to genetic stock identification. 10/1/2008 3/31/2009 $43,572
Biological Objectives Metrics
Sub-basin genotype profiles
Primary R, M, and E Type: Status and Trend Monitoring

Collect/Generate/Validate Field and Lab Data Sample Collection Fin clips from stock-specific groups of salmon will be collected in cooperation with ongoing hatchery operations. 10/1/2006 9/30/2008 $90,263
Biological Objectives Metrics
Sub-basin genotype profiles
Focal Area: Hatchery

Collect/Generate/Validate Field and Lab Data SNP generation 20 to 30 new single nucleotide polymorphisms will be identified to increase the resolution power of genotypes for hatchery and in-river Chinook within the Columbia basin. 10/1/2006 3/31/2008 $106,162
Biological Objectives Metrics
Identify new SNP loci
Primary R, M, and E Type: Uncertainties Research


Section 8: Budget

Itemized Estimated Budget
Item Note FY 2007 Cost FY 2008 Cost FY 2009 Cost
Personnel Research Scientist/Eng FY07 .48 FTE, FY08 .53 FTE, FY09 .19 FTE $39,771 $47,237 $20,407
Fringe Benefits [blank] $13,762 $15,966 $6,632
Supplies enzymes, DNA extraction kits, molecular reagents, labware, cloning kits, primers, probes, 96-well plate centrifuge $47,348 $52,700 $4,317
Travel trips to hatcheries within Washington and Oregon $4,252 $1,675 $ 0
Overhead G&A, PDM, Org Overhead $66,697 $74,650 $26,526
Other Grad Student $41,420 $39,966 $8,873
Totals $213,250 $232,194 $66,755

Total Estimated FY 2007-2009 Budgets
Total Itemized Budget$512,199
Total Work Element budget$512,199

Cost sharing
Funding Source or Organization Item or Service Provided FY 2007 Est Value ($) FY 2008 Est Value ($) FY 2009 Est Value ($) Cash or in-kind? Status

Section 9: Project Future
Project Future Costs and/or Termination
FY 2010 Est Budget FY 2011 Est Budget Comments
$232,194 $232,194 Continue monitoring genotypes in same and other sub-basins
Future Operations & Maintenance Costs
Continue compiling genotypes and integrating results of PIT-tag data.
 
Termination Date Comments
March 31, 2009 This termination date concludes the experimental, proff-of-concept phase for linking genotypes with sub-basins, and correlating genotypes with PIT-tag data. This project could conceivably continue with the addition of other sub-basins, and the continuous updating of PIT-tag tracking.
 
Final Deliverables
A final report will be prepared and we anticipate at least two peer-reviewed publications arising from this work. Results from this work will also be presented at regional and national meetings as the opportunities arise. We anticipate database and statistical tools forming the basis of an integrated fisheries management system that is tailor-made for BPA and hydropower managers.

Section 10: Narrative
Document Type Size Date

Part 2 of 2. Reviews of Proposal
Administrative Review Group (ARG) Results
Account Type:
Expense
No changes were made to this proposal


BPA's in lieu Funding Review of new project proposals (August 3, 2006) [Download letter and table]

BPA's in lieu Rating: 3.0
Approx. BPA share of total costs: BPA 100%
Status of Cost Share:
Notes: DNA profiling, fishery managers authorized/required


NPCC Final Funding Recommendations (October 23, 2006) [Full NPCC Council Recs]

FY 2007 Budget
$ 0
FY 2008 Budget
$ 0
FY 2009 Budget
$ 0
Total NPCC Rec
$ 0
Budget Type:Expense
Budget Category:Basinwide
Recommendation:Do Not Fund
Comments:


NPCC Draft Funding Recommendations (September 15, 2006) [Full NPCC Council Recs]

FY 2007 Budget
$ 0
FY 2008 Budget
$ 0
FY 2009 Budget
$ 0
Total NPCC Rec
$ 0
FY 2007 MSRT Rec
$ 0
FY 2008 MSRT Rec
$ 0
FY 2009 MSRT Rec
$ 0
Total MSRT Rec
$ 0
Budget Category:Basinwide
Comments:


Independent Scientific Review Panel Final Review (August 31, 2006) [Download full document]

Recommendation: Not fundable
NPCC Comments: There may be benefits from adding SNPs to the suite of gene markers to evaluate salmon. However, this proposal does not provide compelling evidence that more research effort is needed, and that this is the best lab and set of personnel to perform the task. The technical and scientific background section provides only a historical review of the various molecular/biochemical techniques as they have evolved. There is very little introduction to salmon conservation issues and how this proposal would participate in the larger salmon restoration program.

Specific subbasin and regional plans and programs that would use, or have called for this data are not identified. A weakness in this proposal is that although the genetics work may be of value somewhere down the road, the proposal is not well linked to other ongoing agency/co-manager activities in the basin. Specifically, the other projects developing and using genetic markers are not identified, and it is not apparent that other projects need this one to develop SNP markers for them. As a result, the application of this work is not clear.

The objectives as stated are more a simple list of tasks, not a set of strategic objectives. Although some details on the methodology are given (which are standard protocols), not enough experimental design details are given to evaluate this proposal adequately.

How monitoring and evaluation will occur is very sketchy and must be interpreted between the lines.

Facilities seem adequate, but experience of the personnel seems quite limited. For example, there is no track record to evaluate the sponsor’s performance in information dissemination.


Independent Scientific Review Panel Preliminary Review (June 2, 2006) [Download full document]

Recommendation: Not fundable
NPCC Comments: There may be benefits from adding SNPs to the suite of gene markers to evaluate salmon. However, this proposal does not provide compelling evidence that more research effort is needed, and that this is the best lab and set of personnel to perform the task. The technical and scientific background section provides only a historical review of the various molecular/biochemical techniques as they have evolved. There is very little introduction to salmon conservation issues and how this proposal would participate in the larger salmon restoration program.

Specific subbasin and regional plans and programs that would use, or have called for this data are not identified. A weakness in this proposal is that although the genetics work may be of value somewhere down the road, the proposal is not well linked to other ongoing agency/co-manager activities in the basin. Specifically, the other projects developing and using genetic markers are not identified, and it is not apparent that other projects need this one to develop SNP markers for them. As a result, the application of this work is not clear.

The objectives as stated are more a simple list of tasks, not a set of strategic objectives. Although some details on the methodology are given (which are standard protocols), not enough experimental design details are given to evaluate this proposal adequately.

How monitoring and evaluation will occur is very sketchy and must be interpreted between the lines.

Facilities seem adequate, but experience of the personnel seems quite limited. For example, there is no track record to evaluate the sponsor’s performance in information dissemination.

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