FY07-09 proposal 200717500
Jump to Reviews and Recommendations
Section 1. Administrative
Proposal title | DNA typing to identify native inland Oncorhynchus mykiss |
Proposal ID | 200717500 |
Organization | Washington State University |
Short description | New DNA-Based Tests, which distinquish the Inland and Coastal forms of Rainbow Trout will be developed. These tests should be widely useful for genetic characterization of Columbia Basin Populations. |
Information transfer | Publications in Journals and Presentations at Scientific Meetings |
Proposal contact person or principal investigator |
Contacts
Contact | Organization | |
---|---|---|
Form submitter | ||
Gary Thorgaard | Washington State University | thorglab@wsu.edu |
All assigned contacts | ||
Dan Nordquist | Washington State University | ogrd@wsu.edu |
Lori Selby | Washington State University | spfo@wsu.edu |
Gary Thorgaard | Washington State University | thorglab@wsu.edu |
Section 2. Locations
Province / subbasin: Mainstem/Systemwide / Systemwide
Latitude | Longitude | Waterbody | Description |
---|
Section 3. Focal species
primary: Interior Redband Troutsecondary: Steelhead All Populations
Section 4. Past accomplishments
Year | Accomplishments |
---|
Section 5. Relationships to other projects
Funding source | Related ID | Related title | Relationship |
---|---|---|---|
BPA | 200103200 | Coeur D'Alene Fisheries Enhanc | Involves assessment of genetic purity of native trout. |
BPA | 199404900 | Kootenai River Resident Fish A | Involves assessment of genetic purity of redband trout |
BPA | 198909600 | Genetic M&E Prog For Sal/Steel | Utilizes genetic markers on an ongoing basis and would benefit from improved marker technology |
BPA | 199800200 | Snake River Native Salmonid As | Would benefit from improved DNA marker technology |
BPA | 200007900 | Assess Res Fish Owyhee DVIR | Would benefit from DNA marker technologies for identifying purity of redband trout populations |
BPA | 199701900 | Stinking Water Salmonid Projec | Malheur River redband trout may have hybridized with introduced rainbow trout. |
Section 6. Biological objectives
Biological objectives | Full description | Associated subbasin plan | Strategy |
---|---|---|---|
Assess resident fish losses | Identify hybridized populations | Boise/Payette/Weiser | Determine extent of redband/ rainbow hybridization |
Assess resident fish losses | Identify hybridized populations | Clearwater | Redband populations will be identified and typed with DNA marker technology |
Assess resident fish losses | Identify hybridized populations | Bruneau | Develop genetic markers to distinguish between native redband trout and nonnative rainbow trout from hatchery origin |
Assess resident fish losses | Identify hybridized populations | Intermountain | Determine genetic distribution of resident redband trout (San Poil River) |
Assess resident fish losses | Identify hybridized populations | Intermountain | Determine genetic distribution of native focal species, including rainbow/ redband trout (Upper Columbia) |
Assess resident fish losses | Identify hybridized populations | Malheur | Genetic evaluation of redband trout to determine degree of integration and hybridization with introduced rainbow trout |
Assess resident fish losses | Identify hybridized populations | Snake Hells Canyon | No information is available regarding genetic integrity of redband trout |
Assess resident fish losses | Identify hybridized populations | Walla Walla | What is the rate of hybridization between endemic wild and out-of-basin hatchery reared stocks? |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Asotin | Coordinated assessment of genetic analyses |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Burnt | Expedite analysis of archived data and encourage additional genetic sampling of redband trout |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Fifteenmile | Conduct genetic sampling of steelhead returning to Fifteenmile Compare resident trout and steelhead genetics in Fifteenmile Creek Genetic sampling of Mill Creek steelhead |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Grande Ronde | Determine and compare genetic characteristics of hatchery and natural fish in the Grande Ronde subbasin |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Hood | Monitor population genetic structure of steelhead and resident rainbow trout |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Lower Snake | Genetic characterization of steelhead and resident rainbow trout |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Middle Snake | Continue genetic evaluation of redband trout |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Owyhee | Assess population structure, including genetic structure, of fish populations on the DVIR. |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Powder | Expedite analysis of archived data and encourage additional genetic sampling of redband trout. |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Salmon | Continue collection of life history characteristics and genetic diversity data on focal fish species |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Intermountain | Perform assessment of native salmonid stocks composition using DNA analysis or other appropriate techniques by 2010 (Spokane system) |
Conserve biodiversity in rainbow trout | Test patterns of genetic variation | Umatilla | Assess and monitor the genetic characteristics of natural and hatchery reared steelhead |
Section 7. Work elements (coming back to this)
Work element name | Work element title | Description | Start date | End date | Est budget |
---|---|---|---|---|---|
Develop RM&E Methods and Designs | Develop DNA-based tests for identifying hybrdization and monitoring biodiversity in rainbow trout | Tests wil be developed which could replace allozyme tests currently being used. This will facilitate sampling and testing. New DNA tests to differentiate redband and coastal rainbow trout will also be developed. | 2/1/2007 | 9/30/2009 | $333,946 |
Biological objectives |
Metrics |
Section 8. Budgets
Itemized estimated budget
Item | Note | FY07 | FY08 | FY09 |
---|---|---|---|---|
Personnel | 50% salaries are requested for Joseph Brunelli (assistant research professor) and a research associate to be identified. Funding for an hourly lab employee (10 hours/ week) is also requested. | $28,733 | $45,080 | $46,883 |
Fringe Benefits | [blank] | $8,696 | $13,570 | $14,112 |
Supplies | Costs of molecular biology supplies and DNA sequencing. Allozyme typing costs are included in year one. | $16,700 | $25,000 | $26,000 |
Travel | Travel for sample collection and to attend meetings | $670 | $1,000 | $1,040 |
Overhead | 46.8% TDC | $25,646 | $39,616 | $41,200 |
Totals | $80,445 | $124,266 | $129,235 |
Total estimated FY 2007-2009 budgets
Total itemized budget: | $333,946 |
Total work element budget: | $333,946 |
Cost sharing
Funding source/org | Item or service provided | FY 07 est value ($) | FY 08 est value ($) | FY 09 est value ($) | Cash or in-kind? | Status |
---|---|---|---|---|---|---|
Washington State University | 5% salary for PI | $8,651 | $8,997 | $9,357 | In-Kind | Under Review |
Totals | $8,651 | $8,997 | $9,357 |
Section 9. Project future
FY 2010 estimated budget: $0 FY 2011 estimated budget: $0 |
Comments: |
Future O&M costs:
Termination date: 9/30/09
Comments: We expect to publish several papers from this research and to present the results at meetings to share the technology we develop with interested researchers.
Final deliverables: Publications, presentations, and new methods for DNA typing to distinguish inland from coastal rainbow trout, and to detect hybrids.
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: Fundable
NPCC comments: This project proposes to develop suites of molecular genetic markers for discriminating between coastal rainbow trout and inland rainbow trout. The problem of identification and historical mixing and introgression among these O. mykiss forms is identified and pervasive. Current methods based on allozyme polymorphism are inadequate for a number of reasons and beg for more modern approaches (to such age-old questions). The project is fundable as it will develop usable tools for conservation and restoration of native rainbow trout populations. The methods are largely demonstrated as tractable by sponsors, and the applicability throughout the basin is high. The ISRP recommends coordination of this work with studies proposed by IDFG (200721800) to avoid duplication and to enhance overall power of results. Several of the subbasin plans identify the mixing (and potential interbreeding) of these forms to be a current or historical issue needing methods to assess its extent and effects. While, the project will not specifically address any single problem or situation in a subbasin plan, it will provide the means to address these in the future. Ultimately, the project has direct relationship to numerous other genetics-based M&E or research projects. The project has two primary objectives regarding the development of usable and appropriate molecular genetic markers for identifying the level and extent of hybridization between introduced and native rainbow trout in the interior Columbia basin: 1) SNPs that are equivalent to presently available allozyme markers (LDH-B and SOD); and, 2) a suite of new AFLP marker variants associated with the inland and coastal forms. The objectives are part of several subbasin plans. The methods of developing the markers are adequately described and generally appropriate. The proposal will be stronger with the confirmation that populations selected are in fact monophyletic in terms of whether they are coastal or inland (as well as their allozyme genotype). The sponsors should indicate also that number of SNPs or AFLPs that will be targeted for development. Published information indicates that even with fixed differences among groups, at least 8 to 10 loci (or more) characters are needed to discriminate among various hybrid, backcross, and parental lineages in an admixture within a 95% confidence. For characters that are not fixed for alternative alleles or forms (such as with the allozymes) and even greater number is needed. Therefore, figuring the target of SNPs and AFLPs is important from a discriminatory power perspective. As a last minor improvement, the sponsors need to more clearly describe populations to be sampled, and sampling techniques.
ISRP FINAL REVIEW (Aug 31, 2006)
Recommendation: Fundable
NPCC comments: This project proposes to develop suites of molecular genetic markers for discriminating between coastal rainbow trout and inland rainbow trout. The problem of identification and historical mixing and introgression among these O. mykiss forms is identified and pervasive. Current methods based on allozyme polymorphism are inadequate for a number of reasons and beg for more modern approaches (to such age-old questions). The project is fundable as it will develop usable tools for conservation and restoration of native rainbow trout populations. The methods are largely demonstrated as tractable by the sponsors, and the applicability throughout the basin is high. The ISRP recommends coordination of this work with studies proposed by IDFG (200721800) to avoid duplication and to enhance overall power of results. Several of the subbasin plans identify the mixing (and potential interbreeding) of these forms to be a current or historical issue needing methods to assess its extent and effects. While, the project will not specifically address any single problem or situation in a subbasin plan, it will provide the means to address these in the future. Ultimately, the project has direct relationship to numerous other genetics-based M&E or research projects. The project has two primary objectives regarding the development of usable and appropriate molecular genetic markers for identifying the level and extent of hybridization between introduced and native rainbow trout in the interior Columbia basin: 1) SNPs that are equivalent to presently available allozyme markers (LDH-B and SOD); and, 2) a suite of new AFLP marker variants associated with the inland and coastal forms. The objectives are part of several subbasin plans. The methods of developing the markers are adequately described and generally appropriate. The proposal will be stronger with the confirmation that populations selected are in fact monophyletic in terms of whether they are coastal or inland (as well as their allozyme genotype). The sponsors should indicate also that number of SNPs or AFLPs that will be targeted for development. Published information indicates that even with fixed differences among groups, at least 8 to 10 loci (or more) characters are needed to discriminate among various hybrid, backcross, and parental lineages in an admixture within a 95% confidence. For characters that are not fixed for alternative alleles or forms (such as with the allozymes) and even greater number is needed. Therefore, figuring the target of SNPs and AFLPs is important from a discriminatory power perspective. As a last minor improvement, the sponsors need to more clearly describe populations to be sampled, and sampling techniques.