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200721800 - Development of single nucleotide polymorphism (SNPs) genetic markers diagnostic between coastal rainbow trout and interior redband trout

Sponsor: Idaho Department of Fish & Game

Budgets: FY07: $60,689 | FY08: $25,392 | FY09: $0

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.

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Final Council recommendation (Nov 2006)

Funding category: Expense

Recommended budgets: FY07: $0 | FY08: $0 | FY09: $0


ISRP final recommendation: Fundable


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.

State/province recommendation: Fundable

Review group: Mtn Col

Recommended budgets: FY07: $60,689 | FY08: $25,392 | FY09: $0


State/province recommendation: MS: Recommended Action

Review group: MSRT

Recommended budgets: FY07: (n/a) | FY08: (n/a) | FY09: (n/a)

Comment: There are two projects addressing this issue. This project is focused in the Kootenai system but coordinates with other projects. If this project were funded it should be closely coordinated with project number 200717500.