FY07-09 proposal 200721800
Jump to Reviews and Recommendations
Section 1. Administrative
| Proposal title | Development of single nucleotide polymorphism (SNPs) genetic markers diagnostic between coastal rainbow trout and interior redband trout |
| Proposal ID | 200721800 |
| Organization | Idaho Department of Fish & Game |
| Short description | This project will attempt to identify unique nuclear DNA markers to allow differentiation of interior redband trout and coastal rainbow trout, allowing biologists to assess intraspecific hybridization and introgression |
| Information transfer | Such knowledge would be useful to 1) identify pure redband trout populations, 2) identify hybridized redband trout populations that are no longer pure, and 3) identify the level of hybridization and introgression within redband trout populations. 4) identify the origin of O. mykiss introgression observed in westslope cutthroat trout populations. Such identifications would be useful for the future management of both redband trout and westslope cutthroat trout, and for assessing the status of these subspecies throughout their native range. |
| Proposal contact person or principal investigator | |
Contacts
| Contact | Organization | |
|---|---|---|
| Form submitter | ||
| Matthew Campbell | IDFG | mcampbell@idfg.idaho.gov |
| All assigned contacts | ||
| Matthew Campbell | IDFG | mcampbell@idfg.idaho.gov |
Section 2. Locations
Province / subbasin: Mountain Columbia / Kootenai
| Latitude | Longitude | Waterbody | Description |
|---|---|---|---|
| 48°59'53 | 116°33'53 | Kootenai River and tributaries | lower most tributary of Kootenai in Idaho. |
| 48°37'17" | 116°03'20" | Kootenai River and tributaries | upper most tributary of Kootenai in Idaho. |
Section 3. Focal species
primary: Interior Redband Troutsecondary: Westslope Cutthroat
Section 4. Past accomplishments
| Year | Accomplishments |
|---|
Section 5. Relationships to other projects
| Funding source | Related ID | Related title | Relationship |
|---|---|---|---|
| BPA | 199800200 | Snake River Native Salmonid As | The Snake River Native Salmonid Assessment (NSA) project works to restore native salmonids in the Upper Snake River Basin (above Hell's Canyon Dam) to self-sustaining harvestable levels by implementing a 3-phased approach: 1) assess current status of native salmonids, 2) identify limiting factors, and 3) develop and implement recovery plans and strategies for populations at risk and in need of protection. Knowledge gained from this proposed genetic project would be beneficial for assessing current genetic purity of redband trout in the Upper Snake River Basin tributaries. |
| BPA | 198806500 | Kootenai R White Sturgeon Inve | The Kootenai River Investigations is comprised of four projects, one of which involves redband trout. Redband trout research is being conducted on life history, distribution, and abundance to enhance effective management. Recent trout research from 2001-2003 concentrated on determining redband trout recruitment sources to the Kootenai River upstream of Bonners Ferry. Radio tracking fish has identified spawning tributaries, and juvenile redband trout out-migration from tributaries has been monitored. The purity of these populations is unknown and the work proposed by our genetic project would help identify the purity of the redband trout populations in the Kootenai River drainage. |
Section 6. Biological objectives
| Biological objectives | Full description | Associated subbasin plan | Strategy |
|---|---|---|---|
| RBT1a | Maintain or increase the total number of genetically pure local populations. | Kootenai | -Evaluate potential effects of introduced fishes on redband trout. -Characterize, conserve, and monitor genetic diversity in isolate populations. - Incorporate conservation of genetic and behavioral attributes of redband trout into recovery/mgmt plans. |
Section 7. Work elements (coming back to this)
| Work element name | Work element title | Description | Start date | End date | Est budget |
|---|---|---|---|---|---|
| Produce Annual Report | Produce annual reports and publication | Results of this study will be summarized in a progress/annual completion report to BPA | 1/1/2009 | 6/30/2009 | $6,381 |
|
Biological objectives |
Metrics |
||||
| Produce/Submit Scientific Findings Report | Produce article for a peer-reviewed journal | Results of this study will be summarized through the completion of an article for a peer-reviewed journal | 3/1/2009 | 6/30/2009 | $0 |
|
Biological objectives |
Metrics |
||||
| Analyze/Interpret Data | Analyze/Interpret data for the development and validation of diagnostic SNP markers/assays | This work element will focus on the actual analysis and interpretation of genetic data to identifify diagnostic SNP markers. Following DNA sequencing of 25 nuclear DNA loci on samples from interior and coastal hatchery O. mykiss populations, genetic software programs will be used to edit and align DNA sequences and actually identify SNPs between sequences. Additional software will be used to design primers and allele-specific probes. | 7/1/2008 | 1/1/2009 | $23,200 |
|
Biological objectives |
Metrics Primary R, M, and E Type: Fish from 18 locations used as controls/treatment |
||||
| Collect/Generate/Validate Field and Lab Data | Generate data for the development and validation of diagnostic SNP markers/assays | This work element will focus on the actual generation of genetic data to identifify diagnostic SNP markers. SNP discovery will begin by the DNA sequencing of 25 nuclear DNA loci on samples from interior and coastal hatchery O. mykiss populations. Once SNPs have been identified and SNP assays developed, additional samples of interior redband trout and coastal hatchery rainbow trout will need to be screened to validate/verify the utility of identified SNPs as diagnostic markers. | 7/1/2007 | 6/30/2008 | $56,500 |
|
Biological objectives |
Metrics Primary R, M, and E Type: Fish from 18 locations used as controls/treatment |
||||
Section 8. Budgets
Itemized estimated budget
| Item | Note | FY07 | FY08 | FY09 |
|---|---|---|---|---|
| Supplies | Chemicals, pipet tips, gloves, primers, sequencing | $34,444 | $14,144 | $0 |
| Personnel | lab technician | $11,178 | $4,791 | $0 |
| Fringe Benefits | rate is 46.1% for IDFG techs | $4,650 | $1,993 | $0 |
| Overhead | 20.9% for IDFG | $10,417 | $4,464 | $0 |
| Totals | $60,689 | $25,392 | $0 | |
Total estimated FY 2007-2009 budgets
| Total itemized budget: | $86,081 |
| Total work element budget: | $86,081 |
Cost sharing
| Funding source/org | Item or service provided | FY 07 est value ($) | FY 08 est value ($) | FY 09 est value ($) | Cash or in-kind? | Status |
|---|---|---|---|---|---|---|
| Idaho Fish and Game | All genetic samples already collected by IDFG and other organizations | $0 | $0 | $0 | Cash | Confirmed |
| Totals | $0 | $0 | $0 | |||
Section 9. Project future
|
FY 2010 estimated budget: $0 FY 2011 estimated budget: $0 |
Comments: This project will only take 2 years to complete, FY07 and FY08 |
Future O&M costs:
Termination date: June 30, 2008
Comments: We propose starting funding on July 1, 2007 for FY07 dollars, in order to align the budget with State of Idaho budgeting.
Final deliverables: Quarterly reports will be produced every three months, a progress report will be produced the first year, a final report will be produced the second year to fulfill the contract, and a scientific journal article will be submitted for publication consideration that summarizes the final results.
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 | ProvinceExpense | Do Not Fund |
| NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs] | ||||||
| $0 | $0 | $0 | $0 | Basinwide | ||
| NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs] | ||||||
| $0 | $0 | $0 | $0 | ProvinceExpense | ||
ISRP PRELIMINARY REVIEW (Jun 2, 2006)
Recommendation: Fundable
NPCC comments: This project proposes to develop suites of molecular genetic markers (SNPs) 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. The project will permit identification of population’s monophyletic (unmixed) ancestry as well as those with polyphyletic (introgressed) ancestry due to recent human activities. The conservation and restoration value of such tools is high. The sponsors provided an excellent scientific background, with references, for this research project concerning a controversial and important issue. The sponsors should consult with sponsors of project 200717500 (DNA typing to identify native inland Oncorhynchus mykiss) and with the UC-Davis molecular ecology laboratory (B. May) to minimize redundancy or repetition of marker development. Ultimately this 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 although it specifically identifies needs within the Kootenai subbasin, the application is expected to be transferable to other situations. A strong argument is made for relevance of this work on hybridization of native and non-native trout and its relation to subbasin and basin plans. 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 has potential to 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 a primary objective 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. 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. The sponsors should identify also the number of SNPs 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 with 95% confidence. For characters that are not fixed for alternative alleles or forms (such as with the allozymes) an even greater number is needed. Therefore, defining the target of SNPs is important from a discriminatory power perspective. As a last 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 (SNPs) 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. The project will permit identification of population’s monophyletic (unmixed) ancestry as well as those with polyphyletic (introgressed) ancestry due to recent human activities. The conservation and restoration value of such tools is high. The sponsors provided an excellent scientific background, with references, for this research project concerning a controversial and important issue. The sponsors should consult with sponsors of project 200717500 (DNA typing to identify native inland Oncorhynchus mykiss) and with the UC-Davis molecular ecology laboratory (B. May) to minimize redundancy or repetition of marker development. Ultimately this 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 although it specifically identifies needs within the Kootenai subbasin, the application is expected to be transferable to other situations. A strong argument is made for relevance of this work on hybridization of native and non-native trout and its relation to subbasin and basin plans. 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 has potential to 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 a primary objective 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. 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. The sponsors should identify also the number of SNPs 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 with 95% confidence. For characters that are not fixed for alternative alleles or forms (such as with the allozymes) an even greater number is needed. Therefore, defining the target of SNPs is important from a discriminatory power perspective. As a last improvement, the sponsors need to more clearly describe populations to be sampled, and sampling techniques.