FY07-09 proposal 200711000
Jump to Reviews and Recommendations
Section 1. Administrative
Proposal title | Differences in Functional Genes Between Hatchery and Wild Chinook Salmon |
Proposal ID | 200711000 |
Organization | University of Idaho - Aquaculture Research Institute |
Short description | This project will examine functional genetic differences between hatchery and wild Chinook salmon with the goal of identifying and reducing negative hatchery effects through modified hatchery practices. |
Information transfer | Information gathered and generated during this project will be disseminated via publication in peer-reviewed, scientific journals. |
Proposal contact person or principal investigator |
Contacts
Contact | Organization | |
---|---|---|
Form submitter | ||
Madison Powell | University of Idaho | mpowell@uidaho.edu |
All assigned contacts | ||
Tom Flagg | NOAA Fisheries, Manchester Research Station | tom.flagg@noaa.gov |
Ronald Hardy | University of Idaho | rhardy@uidaho.edu |
Madison Powell | University of Idaho | mpowell@uidaho.edu |
Section 2. Locations
Province / subbasin: Mainstem/Systemwide / Systemwide
Latitude | Longitude | Waterbody | Description |
---|---|---|---|
46.4346 | 117.0142 | [none] | Aquaculture Research Institute - University of Idaho |
42.4535 | -114.5122 | [none] | Hagerman Fish Culture Experiment Station |
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 |
---|---|---|---|
[Funding Source left blank] | [no entry] | [Relationship field left blank] |
Section 6. Biological objectives
Biological objectives | Full description | Associated subbasin plan | Strategy |
---|---|---|---|
Quantify differences between hatchery & wild salmo | A series of hypothesis-driven, comparative studies of Chinook salmon populations in Idaho, Washington and Oregon will be used to address this objective. These studies are observational and focus on functional genetic differences between hatchery and wild Chinook salmon as observed using DNA microarray data (RM&E Uncertainties Research). | None | [Strategy left blank] |
Reduce differences between hatchery & wild salmon | Two hypothesis-driven, manipulative studies will be used to address this objective. This study will examine changes in gene expression in Chinook salmon when subjected to different hatchery protocols. Specifically, the effectiveness of alternative “hatchery reform” practices on reducing differences in gene expression between hatchery and wild fish. | None | [Strategy left blank] |
Section 7. Work elements (coming back to this)
Work element name | Work element title | Description | Start date | End date | Est budget |
---|---|---|---|---|---|
Produce/Submit Scientific Findings Report | Produce Manuscript of Differential Gene Expression and Functional Testing | Produce a peer-reviewed manuscript of experimental findings | 7/1/2008 | 10/31/2009 | $0 |
Biological objectives Reduce differences between hatchery & wild salmon |
Metrics |
||||
Produce/Submit Scientific Findings Report | Produce Manuscript of Microarray Analyses | Produce a peer-reviewed manuscript of experimental findings. | 7/1/2008 | 7/1/2009 | $0 |
Biological objectives Quantify differences between hatchery & wild salmo |
Metrics |
||||
Analyze/Interpret Data | Analyze and Interpret Functional Testing | Analyze and correlate functional testing with bioinformatics data | 7/1/2008 | 10/31/2009 | $53,497 |
Biological objectives Reduce differences between hatchery & wild salmon |
Metrics Primary R, M, and E Type: Action Effectiveness Research |
||||
Analyze/Interpret Data | Analyze Microarray and Bioinformatics Data | Complete analysis and post-analysis interpretation of differential expression observed using microarrays | 7/1/2007 | 7/1/2009 | $250,516 |
Biological objectives Quantify differences between hatchery & wild salmo |
Metrics Primary R, M, and E Type: Uncertainties Research |
||||
Analyze/Interpret Data | Analyze Microarray and Bioinformatics Data | Analyze and interpret all microarray, RT-PCR and bioinformatics data. | 7/1/2007 | 10/31/2009 | $498,067 |
Biological objectives Reduce differences between hatchery & wild salmon |
Metrics Primary R, M, and E Type: Uncertainties research |
||||
Collect/Generate/Validate Field and Lab Data | Collect and analyze Chinook salmon smolts | Both hatchery and wild Chinook salmon smolts will be collected during outmigration at four locations. Tissues from samples will then be analyzed using DNA microarrays. | 5/1/2007 | 10/31/2009 | $306,187 |
Biological objectives Quantify differences between hatchery & wild salmo |
Metrics Primary R, M, and E Type: Uncertainties research |
||||
Collect/Generate/Validate Field and Lab Data | Culture, Sample and Analyze Chinook salmon | Chinook salmon from two locations will be cultured under two separate hatchery protocols. Samples will be taken and analyzed for differential gene expression using QPCR and for physiological differences. | 9/1/2007 | 10/31/2009 | $163,257 |
Biological objectives Reduce differences between hatchery & wild salmon |
Metrics Primary R, M, and E Type: Action Effectiveness Research |
||||
Collect/Generate/Validate Field and Lab Data | Functional Testing | Functional testing of cultured, experimental and control fish. | 7/1/2007 | 10/31/2009 | $317,902 |
Biological objectives Reduce differences between hatchery & wild salmon |
Metrics Primary R, M, and E Type: Action Effectiveness Research |
Section 8. Budgets
Itemized estimated budget
Item | Note | FY07 | FY08 | FY09 |
---|---|---|---|---|
Personnel | Principal Investigator - Ron Hardy | $10,818 | $11,251 | $11,700 |
Personnel | Co-P.I. - Matt Powell | $7,265 | $7,557 | $7,858 |
Personnel | Co-P.I. - Barrie Robison | $5,275 | $5,485 | $5,703 |
Personnel | Co-P.I. - Rod Hill | $5,687 | $5,913 | $6,151 |
Personnel | Post-doctoral Fellow | $44,720 | $46,509 | $48,360 |
Personnel | Scientific Aide - Joyce Faler | $25,490 | $26,520 | $13,790 |
Personnel | Scientific Aide - Churchill | $10,768 | $14,560 | $7,571 |
Personnel | Graduate Student | $21,632 | $22,495 | $23,400 |
Personnel | Hourly Student Labor | $13,000 | $13,520 | $14,061 |
Fringe Benefits | Principal Investigator - Hardy | $3,570 | $3,713 | $3,861 |
Fringe Benefits | Co-P.I. - Powell | $2,398 | $2,494 | $2,593 |
Fringe Benefits | Co-P.I. - Robison | $1,846 | $1,920 | $1,996 |
Fringe Benefits | Co-P.I. - Hill | $1,933 | $2,011 | $2,091 |
Fringe Benefits | Post-doctoral Fellow | $15,652 | $16,278 | $16,926 |
Fringe Benefits | Scientific Aide - Faler | $8,922 | $9,282 | $4,827 |
Fringe Benefits | Sicentific Aide - Churchill | $4,953 | $6,698 | $3,483 |
Fringe Benefits | Graduate Student | $130 | $135 | $141 |
Fringe Benefits | Hourly Student Labor | $1,170 | $1,217 | $1,265 |
Supplies | Lab supplies for genetic analyses | $32,000 | $48,000 | $27,200 |
Supplies | Microarry chips @$120 ea. | $48,000 | $72,000 | $40,800 |
Supplies | Functional testing @ $100/fish | $11,000 | $19,000 | $6,000 |
Supplies | Tank and fish rearing supplies | $3,000 | $6,000 | $6,000 |
Supplies | RT-PCR supplies | $0 | $7,500 | $12,500 |
Travel | Regional travel for project | $6,000 | $6,000 | $4,000 |
Travel | National travel to scientific meetings | $4,000 | $4,000 | $3,000 |
Other | Subcontract - CRITFC | $2,500 | $20,000 | $20,000 |
Other | Subcontract - IDFG | $20,000 | $20,000 | $20,000 |
Other | Subcontract - ODFW | $2,500 | $20,000 | $20,000 |
Other | Subcontract - WDFW | $20,000 | $20,000 | $20,000 |
Other | Subcontract - NOAA Fisheries | $25,000 | $25,000 | $30,000 |
Overhead | Facilities and Administrative Rates @31.5% | $112,789 | $146,109 | $120,964 |
Personnel | Co-P.I. - Tom Flagg | $0 | $0 | $0 |
Personnel | Co-P.I. - Paul Kline | $0 | $0 | $0 |
Personnel | Co.-P.I. - Paul Seidel | $0 | $0 | $0 |
Totals | $472,018 | $611,167 | $506,241 |
Total estimated FY 2007-2009 budgets
Total itemized budget: | $1,589,426 |
Total work element budget: | $1,589,426 |
Cost sharing
Funding source/org | Item or service provided | FY 07 est value ($) | FY 08 est value ($) | FY 09 est value ($) | Cash or in-kind? | Status |
---|---|---|---|---|---|---|
CRITFC | sample collection/research | $1,250 | $8,571 | $8,182 | In-Kind | Confirmed |
IDFG | sample collection/research | $10,000 | $8,571 | $8,182 | In-Kind | Confirmed |
National Science Foundation | Capital Equipment | $25,000 | $0 | $0 | In-Kind | Confirmed |
NOAA-Fisheries | sample colleciton/research | $12,500 | $10,714 | $12,273 | In-Kind | Confirmed |
ODFW | sample collection/research | $1,250 | $8,571 | $8,182 | In-Kind | Confirmed |
University of idaho | Salaries | $24,052 | $25,013 | $26,012 | In-Kind | Confirmed |
WDFW | sample collection/research | $10,000 | $8,571 | $8,182 | Cash | Confirmed |
Totals | $84,052 | $70,011 | $71,013 |
Section 9. Project future
FY 2010 estimated budget: $0 FY 2011 estimated budget: $0 |
Comments: No outyear funds are requested. |
Future O&M costs:
Termination date: 10/31/09
Comments: All objectives will be complete by 10/31/09
Final deliverables: Final deliverables include manuscript(s) submitted for peer-review in scientific journals.
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: Response requested
NPCC comments: Although the technique proposed for use in this proposal is potentially a very valuable tool, the ISRP does not recommend funding the proposal as worded. The ISRP believes that the utility of the technique as it stands now is more uncertain than portrayed, and the proposal needs to provide further explanation. The proposal should acknowledge that baseline data are needed to determine how the results of the micro array assays should be interpreted. For example, it should be acknowledged that an individual fish raised in different environments would give different assay results -- but how different, and how would the authors interpret those different array assays? The technical aspects of gene chip arrays and the molecular methods are well developed. We question the actual experimental design in some cases, however, as being sound enough to test what is being proposed. For example, it is assumed that a result showing that gene expression differences have become similar (as measured by quantification of expression at a molecular level) means that "for the purposes of evolutionary fitness, the hatchery environment can then serve as a surrogate to the natural environment for rearing salmon and steelhead." We don’t believe that such a level of cause/effect has ever been shown. It is still a long way from similarity in micro array results to fitness equality. The underlying approach of this proposal may be inadequate and should be further justified in a response. The ISRP also feels that there is a need to identify how application to management will occur or at least to demonstrate how communication with the relevant management agencies would occur. Technical and scientific background: There is quite a bit of technical background given on the potential of this new technique, but we are not convinced that the authors are fairly stating what it will or will not be able to answer. There is substantial muddling of the concerns regarding the inherent genetic differences between stocked and wild spawned fish (including issues associated with inbreeding and out breeding depression) with those of how rearing a fish in a hatchery environment can change its phenotypic expression of genes, resulting in an organism that looks, behaves, performs differently than if it were raised in the wild. A clear explanation of how this technique can or cannot address those two quite different questions is needed. It is not evident from the authors' explanation that this difference is clearly appreciated and understood. Rationale and significance to subbasin plans and regional programs: In concept, the problem addressed (hatchery vs. wild differences) is an important issue. The relationship of the proposal to subbasin plans and regional programs is explained only superficially. In addition, as is pervasive throughout this proposal, there is substantial overstatement of the potential impacts of the results. As an example, "The proposed project offers to add a new dimension to our understanding of factors that affect differences in hatchery and wild fish by determining the functional role of differentially expressed genes." The ISRP is not convinced that it will be all that easy or clear - much less accomplishable within this timeframe. Relationships to other projects: Although the proposal states, "The proposed project will provide information to support most artificial propagation programs in the Columbia River Basin," few details are given and no other projects are identified on the cover proposal or narrative. Objectives: Objectives are concise and have nice sets of alternative hypotheses, but eventual applicability to management is unclear. Tasks (work elements) and methods: Innovative approaches to assessing the functional differences between hatchery and wild fish are proposed, which may at some time serve to assess reforms in hatchery rearing protocols. It is just not clear, however, that without substantial basic research on what the assays are telling us, that the technique will be able to answer those questions. Monitoring and evaluation: This is a proposal to develop assessment technology. If it works it could make a significant contribution to deciding whether hatchery practices can be modify sufficiently to make hatchery production compatible with the need to protect natural populations. It is not clear, however, how the results will be interpreted nor how they will be used to change management strategies. Facilities, equipment, and personnel: This laboratory seems to be an excellent venue for such studies, but until we see a response that uses better evolutionary bases for the experimental design, together with a more realistic set of expectations of the technique, we question the level of understanding by the personnel. Information transfer: The sponsors have a track record of publishing the findings of their work in the peer-reviewed literature and producing annual reports, and presenting at regional and national conferences. Benefits to focal and non-focal species: A successful project could affect the focal species positively. However, if the (simplistic?) approach of assuming that array assay similarity translates into fitness/genetic equivalence is transferred to field applications prematurely, there could be risk for harm to the focal species. Until an adequate response is provided, we remain concerned over this possibility. We are not certain there is much of an effect on non-focal species, unless a misinterpretation of results allows rampant stocking.
ISRP FINAL REVIEW (Aug 31, 2006)
Recommendation: Response requested
NPCC comments: Although the technique proposed for use in this proposal is potentially a very valuable tool, the ISRP does not recommend funding the proposal as worded. The ISRP believes that the utility of the technique as it stands now is more uncertain than portrayed, and the proposal needs to provide further explanation. The proposal should acknowledge that baseline data are needed to determine how the results of the micro array assays should be interpreted. For example, it should be acknowledged that an individual fish raised in different environments would give different assay results -- but how different, and how would the authors interpret those different array assays? The technical aspects of gene chip arrays and the molecular methods are well developed. We question the actual experimental design in some cases, however, as being sound enough to test what is being proposed. For example, it is assumed that a result showing that gene expression differences have become similar (as measured by quantification of expression at a molecular level) means that "for the purposes of evolutionary fitness, the hatchery environment can then serve as a surrogate to the natural environment for rearing salmon and steelhead." We don’t believe that such a level of cause/effect has ever been shown. It is still a long way from similarity in micro array results to fitness equality. The underlying approach of this proposal may be inadequate and should be further justified in a response. The ISRP also feels that there is a need to identify how application to management will occur or at least to demonstrate how communication with the relevant management agencies would occur. Technical and scientific background: There is quite a bit of technical background given on the potential of this new technique, but we are not convinced that the authors are fairly stating what it will or will not be able to answer. There is substantial muddling of the concerns regarding the inherent genetic differences between stocked and wild spawned fish (including issues associated with inbreeding and out breeding depression) with those of how rearing a fish in a hatchery environment can change its phenotypic expression of genes, resulting in an organism that looks, behaves, performs differently than if it were raised in the wild. A clear explanation of how this technique can or cannot address those two quite different questions is needed. It is not evident from the authors' explanation that this difference is clearly appreciated and understood. Rationale and significance to subbasin plans and regional programs: In concept, the problem addressed (hatchery vs. wild differences) is an important issue. The relationship of the proposal to subbasin plans and regional programs is explained only superficially. In addition, as is pervasive throughout this proposal, there is substantial overstatement of the potential impacts of the results. As an example, "The proposed project offers to add a new dimension to our understanding of factors that affect differences in hatchery and wild fish by determining the functional role of differentially expressed genes." The ISRP is not convinced that it will be all that easy or clear - much less accomplishable within this timeframe. Relationships to other projects: Although the proposal states, "The proposed project will provide information to support most artificial propagation programs in the Columbia River Basin," few details are given and no other projects are identified on the cover proposal or narrative. Objectives: Objectives are concise and have nice sets of alternative hypotheses, but eventual applicability to management is unclear. Tasks (work elements) and methods: Innovative approaches to assessing the functional differences between hatchery and wild fish are proposed, which may at some time serve to assess reforms in hatchery rearing protocols. It is just not clear, however, that without substantial basic research on what the assays are telling us, that the technique will be able to answer those questions. Monitoring and evaluation: This is a proposal to develop assessment technology. If it works it could make a significant contribution to deciding whether hatchery practices can be modify sufficiently to make hatchery production compatible with the need to protect natural populations. It is not clear, however, how the results will be interpreted nor how they will be used to change management strategies. Facilities, equipment, and personnel: This laboratory seems to be an excellent venue for such studies, but until we see a response that uses better evolutionary bases for the experimental design, together with a more realistic set of expectations of the technique, we question the level of understanding by the personnel. Information transfer: The sponsors have a track record of publishing the findings of their work in the peer-reviewed literature and producing annual reports, and presenting at regional and national conferences. Benefits to focal and non-focal species: A successful project could affect the focal species positively. However, if the (simplistic?) approach of assuming that array assay similarity translates into fitness/genetic equivalence is transferred to field applications prematurely, there could be risk for harm to the focal species. Until an adequate response is provided, we remain concerned over this possibility. We are not certain there is much of an effect on non-focal species, unless a misinterpretation of results allows rampant stocking.