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.