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.