FY 2002 Innovative proposal 34005

Section 1. Administrative

Project location

Reasonable and Prudent Alternatives (RPAs)

Section 2. Past accomplishments

Section 3. Relationships to other projects

Section 4. Budget for Planning and Design phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Planning and Design phase

Section 5. Budget for Construction and Implementation phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Construction and Implementation phase

Section 6. Budget for Operations and Maintenance phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Operations and Maintenance phase

Section 7. Budget for Monitoring and Evaluation phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Monitoring and Evaluation phase

Section 8. Estimated budget summary

Itemized budget

Total estimated budget

Cost sharing

Reviews and recommendations

This information was not provided on the original proposals, but was generated during the review process.

Comment:

A similar proposal was submitted for the FY2001 innovative solicitation and was ranked 15 out of 66 proposals submitted. This proposal is improved from the earlier version, and they have adopted the ISRP suggestion to focus on a few stocks. Specifically, this incarnation focuses on four specific chinook stocks as a proof of concept that the microarray technique will permit users to identify fish with particular stocks or groups—obviating much of the need for tags and marks. In theory this technique could perhaps be valuable in assessing success of YKFP supplementation, as they claim, but reviewers would have to take that on faith because details are not provided.

Microarrays, one of the newest technologies to hit molecular biology, have been developed to assess the expression of many genes at once in response to a given stimulus. The technology has been used extensively in pharmacogenetics and bioinformatics, where a large literature base has developed. However, developing DNA libraries for fish populations and then using them to identify individuals in this way is not proven. Fundamentally, microarrays are better suited for the comparative expression of genes and for mutation detection than for population genetics applications. The researchers appear to be competent in microarray development for cryptosporidians and bacteria in general, but do not seem particularly strong in use of this technique for fish. The literature cited on DNA fingerprinting and its use in salmon populations is not entirely up-to-date. In the early 90s, the basin investigated the utility of the multi-locus DNA fingerprinting approach to addressing management concerns for chinook salmon. The effort did not yield much useful information due in part to the polyploidy nature of salmonids, which generated gels with overlapping confounding banding patterns. The subsequent use of single-locus probes overcame these problems, but few single-locus probes have been developed specifically for salmonids.

The authors argue that the technology has potential for clearly distinguishing separate breeding groups of fish and that assignment of individuals to specific stocks can occur rapidly; they intend to demonstrate these applications. The authors also argue that the technology has potential for helping to address some of the important questions concerning the Basin's fisheries. Most of the important questions concerning hatchery and wild fish require quantitative information related to fitness. How will this "new" technology help to answer questions concerning effects of habitat degradation and hatchery fish interbreeding on the fitness of endemic fish populations? Additionally, it is not clear how quantitative levels of divergence can be generated from the microarray data, and how the microarray data analysis can deal with issues of non-Mendelian inheritance and the occurrence of null alleles. The latter two issues have been dealt with extensively in the salmonid allozyme literature and are being addressed with the burgeoning microsatellite literature.

Comment:

Comment:

Comments
The proposal would use microarray technology to obtain genetic fingerprints of chinook salmon with the purpose of identifying the population or origin of individual fish. This approach contrasts with gel based methods used to collect allozyme and microsatellite data. This technique is unproven for this application, but after sufficient development might be quicker and less expensive than microsatellite approaches.

Already ESA Required?
No

Biop?
No

Comment:

Comments
This proposal would use microarray technology to obtain genetic fingerprints of chinook salmon with the purpose of identifying the population or origin of individual fish. This approach contrasts with gel based methods use to collect allozyme and microsatellite data. This technique is unproven for this application, but after sufficient development might be quicker and less expensive than microsatellite approaches.

Already ESA Req? No

Biop? No

Comment: