FY07-09 proposal 200722700
Jump to Reviews and Recommendations
Section 1. Administrative
| Proposal title | Rapid DNA Profiling of Hatchery and Wild Salmon Stocks with Single Nucleotide Polymorphism (SNP) Profiling |
| Proposal ID | 200722700 |
| 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. |
| Proposal contact person or principal investigator | |
Contacts
| Contact | Organization | |
|---|---|---|
| Form submitter | ||
| Ann Miracle | Pacific Northwest National Laboratory | ann.miracle@pnl.gov |
| All assigned contacts | ||
| Ann Miracle | Pacific Northwest National Laboratory | ann.miracle@pnl.gov |
Section 2. Locations
Province / subbasin: Mainstem/Systemwide / Systemwide
| Latitude | Longitude | Waterbody | Description |
|---|---|---|---|
| Willamette Hatchery | |||
| Lookingglass Hatchery | |||
| Warm Springs Hatchery | |||
| Cle Elum Hatchery | |||
| Methow Hatchery | |||
| Priest Rapids Hatchery | |||
| Big Creek Hatchery | |||
| Lyons Ferry | |||
| Wells Hatchery | |||
| Prosser Hatchery |
Section 3. Focal species
primary: Chinook All PopulationsSection 4. Past accomplishments
| Year | Accomplishments |
|---|
Section 5. Relationships to other projects
| Funding source | Related ID | Related 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 | Full description | Associated subbasin plan | Strategy |
|---|---|---|---|
| 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. |
| 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. |
Section 7. Work elements (coming back to this)
| Work element name | Work element title | Description | Start date | End date | Est 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 Sub-basin genotype profiles |
Metrics 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 Sub-basin genotype profiles |
Metrics 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 Sub-basin genotype profiles |
Metrics 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 Sub-basin genotype profiles |
Metrics 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 Identify new SNP loci |
Metrics Primary R, M, and E Type: Uncertainties Research |
||||
Section 8. Budgets
Itemized estimated budget
| Item | Note | FY07 | FY08 | FY09 |
|---|---|---|---|---|
| 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: | $512,199 |
Cost sharing
| Funding source/org | Item or service provided | FY 07 est value ($) | FY 08 est value ($) | FY 09 est value ($) | Cash or in-kind? | Status |
|---|---|---|---|---|---|---|
| Totals | $0 | $0 | $0 | |||
Section 9. Project future
|
FY 2010 estimated budget: $232,194 FY 2011 estimated budget: $232,194 |
Comments: Continue monitoring genotypes in same and other sub-basins |
Future O&M costs: Continue compiling genotypes and integrating results of PIT-tag data.
Termination date: March 31, 2009
Comments: 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 and other documents
Reviews and recommendations
| FY07 budget | FY08 budget | FY09 budget | Total budget | Type | Category | Recommendation |
|---|---|---|---|---|---|---|
| NPCC FINAL FUNDING RECOMMENDATIONS (Oct 23, 2006) [full Council recs] | ||||||
| $0 | $0 | $0 | $0 | Expense | Basinwide | Do Not Fund |
| NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs] | ||||||
| $0 | $0 | $0 | $0 | Basinwide | ||
ISRP PRELIMINARY REVIEW (Jun 2, 2006)
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.
ISRP FINAL REVIEW (Aug 31, 2006)
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.