FY 2007 Solicitation Homepage

Project Proposal Request for FY 2007 - FY 2009 Funding

Proposal 199305600: Research to advance hatchery reform, including captive broodstocks

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Table of Contents
Part 1. Administration and Budgeting
Section 1: General Administrative
Section 2: Project Location
Section 3: Project Species
Section 4: Past Accomplishments
Section 5: Relationship to Other Projects
Section 6: Biological Objectives
Section 7: Work Elements
Section 8: Budget
Section 9: Project Future
Section 10: Documents
Part 2. Reviews
Part 1 of 2. Administration and Budgeting
Section 1: General Administrative Information
Process Information:
Date Proposal Submitted & Finalized Status Form Generator
January 10, 2006 Finalized Barry Berejikian

Proposal Type: Ongoing
Proposal Number: 199305600
Proposal Name: Research to advance hatchery reform, including captive broodstocks
BPA Project Manager: David Byrnes
Agency, Institution or Organization: Northwest Fisheries Science Center
Short Description: This project will provide guidance on management of Columbia River Basin hatcheries, including captive broodstocks. Research will focus on developing methods to improve broodstock management and fish quality and reduce negative ecological interactions.
Information Transfer: Research results and management recommendations will be transferred via peer-reviewed scientific literature, project annual reports, attendance at regional workshops and symposia, and regular attendance at Captive Broodstock Technical Oversight Committee meetings.
 
Project Proposal Contacts
Contact Organization Address Phone/Email Roles Notes
Form Submitter
Barry Berejikian NOAA Fisheries P.O. Box 130
Manchester, WA 98353
Ph: 360-871-8301
Fax: 206-842-8364
Email: barry.berejikian@noaa.gov
Form Submitter
All Assigned Contacts
Barry Berejikian NOAA Fisheries P.O. Box 130
Manchester, WA 98353
Ph: 360-871-8301
Fax: 206-842-8364
Email: barry.berejikian@noaa.gov
Form Submitter

Section 2: Project Location
Sponsor Province: Mainstem/Systemwide ARG Province: Mainstem on the ground/Multiprovince
Sponsor Subbasin: None Selected ARG Subbasin: Mainstem on the ground/Multiprovince
Location(s) at which the action will be implemented
Latitude Longitude Waterbody Location Description County/State Subbasin Primary?
47.48000 122.21300 Laboatory UW Portage Bay Hatchery King, Washington Systemwide No
47.53587 122.599055 Laboratory NOAA Fisheries, Northwest Fisheries Science Center, Manchester Research Station Kitsap, Washington Systemwide No
47.65215 122.68308 Laboratory UW Big Beef Creek Field Station Kitsap, Washington Systemwide No
47.629653 122.297527 Laboratory NOAA Fisheries, Northwest Fisheries Science Center King, Washington Systemwide Yes
45.3544 117.22861 Stream Lick Creek (Imnaha River tributary) near Joseph, Oregon Wallowa County, Oregon Imnaha Yes

Section 3: Focal Species
Focal Species:
Primary Secondary Additional Species
Chinook All Populations
Sockeye Snake River ESU

Section 4: Past Accomplishments
Past Accomplishments for Each Fiscal Year of This Project
Fiscal Year Accomplishments
2005 Published studies that determined; 1) effectiveness of different antibiotics in controlling BKD and effects on fish physiology , 2) effects of growth on early male maturation and ovarian growth, and 3) examined genetics and fitness of captive salmon.
2004 Published a review and assessment of strategies to reintroduce captively reared salmon into the wild. Published two studies that jointly evaluated the efficacy of vaccines and antibiotics in controlling bacterial kidney disease in chinook salmon.
2003 Published studies on 1) immune function and improving health of cultured chinook salmon, 2) effects of exercise and hormones on reproductive success of chinook salmon, and 3) critical periods when body growth affects maturation in chinook and coho salmon.
2002 Convened a region-wide workshop to improve the management of captive broodstock programs in the Columbia Basin. Project managers, research scientists, and BPA discussed new techniques to maximize the benefits of broodstock programs. Published proceedings
2001 Completed a review of genetic variation and fitness in salmonids. Completed a study quantifying the effects of hydraulic redd sampling on the viablity of eyed embryos. Published a study of captive and wild salmon reproductive success.
2000 Published four studies of captive chinook salmon: 1) developing assays to quantify antibodies, 2) importance of male body size on reproductive behavior, 3) genetic variation and marine survival, and 4) body fatness effects on early maturation.
1999 Published studies 1) identifying maternal effects on offspring competitive ability, growth and survival of juvenile salmon, and 2) describing the genetic bases of juvenile Chinook salmon morphometry. Continued field monitoring collaborations with IDFG.
1998 Completed studies that quantified reproductive, behavioral and morphometric differences between salmon reared to maturity in captivity and wild salmon. Profiled immune function and identified feed properties that reduce deformities in sockeye salmon.
1997 Published the results of studies demonstrating reduced reproductive performance of captively reared salmon, describing the gene conservation potential of captive broodstocks in North America, and mechanisms controlling of growth in chinook salmon.
1996 Published results of a study that developed new feeding technologies for juvenile salmon. Completed studies of cultured chinook, sockeye and coho salmon in the areas of physiology, genetics, reproductive ecology and fish health.
1995 Published a review of the role of captive broodstocks for recovery of depleted populations of Pacific Salmon. Initiated studies to determine the potential for releasing captively reared adult salmon for natural spawning.
1994 Established captive populations of Chinook and sockeye salmon for research and initiated studies on physiology, health, and genetics. Completed a comprehensive literature review of salmonid captive propagation.
1993 Conducted a comprehensive literature review of the effects and potential of captive propagation of imperiled Pacific salmon populations. The review identified information gaps and provided the foundation for a long-term research plan

Section 5: Relationships to Other Projects
Other Current Projects Related to this Project (any funding source)
Funding Source Related ID Related Project Title Relationship
BPA 198909600 Genetic M&E Prog For Sal/Steel The work in Objective 1 complements research being conducted under project 1989-096-00, which may provide estimates of the reproductive success of jack male Chinook salmon. However, the ratio of jack males allowed to spawn naturally in that study is fixed by management agreements, and the project does not quantify fertilization success, which is the data needed by fish hatchery managers to determine the use of jacks in broodstocks. Our project will complement work under on 1989-096-00 by experimentally manipulating the proportion of jack males, quantifying fertilization success, and experimentally testing the genetic quality of adopting different life history patterns.
BPA 199107200 Redfish Lake Sockeye Salmon Ca The imprinting component of our project (Objective 2) was established in response to concerns that improper imprinting was affecting the returns of sockeye released as juveniles into Stanley Basin. The sponsors of project 1991-072-00 and 1992-040-00 (Redfish Lake Sockeye Salmon Captive Broodstock Rearing and Research - NMFS) and the Stanley Basin Sockeye Technical Oversight Committee recommended that Project 1993-056-00 initiate research on the timing of imprinting in sockeye salmon. Experiments for Objective 2 have been designed to evaluate the effects on imprinting of the different “spread-the-risk “ reintroduction strategies currently being tested for Stanley Basin Sockeye.
BPA 199107200 Redfish Lake Sockeye Salmon Ca Results from research in Objective 3 on effects of artificial and natural light on reproductive performance in sockeye salmon will have direct application to Redfish Lake Captive Broodstock Program to improve qualtiy of adults produced by the program. The aim of this research is to produce adults with spawn timing, body coloration and morphology, fertility and behavior more similar to that of wild fish.
BPA 199204000 Redfish Lake Sockeye Broodstoc Objective 4 work is linked to the basic pathology services at the Manchester Research Station that are provided to Projects 1992-040-00 and 1996-067-00. All in-culture mortalities that might occur among the captive broodstock populations of ESA-listed fish held by these Projects are necropsied at Manchester to identify cause of death and treatment recommendations, if feasible, for the survivors. Prophylactic and therapeutic measures from Objective 4 that are validated are likely to be incorporating into rearing protocols for these Projects.
BPA 199204000 Redfish Lake Sockeye Broodstoc The sponsors of project 1992-040-00 (Redfish Lake Sockeye Salmon Captive Broodstock Rearing and Research - NMFS) and the Stanley Basin Sockeye Technical Oversight Committee have recommended that Project 1993-056-00 conduct research on the timing of imprinting in sockeye salmon. Experiments for Objective 2 have been designed to evaluate the effects on imprinting of the different “spread-the-risk “ reintroduction strategies currently being tested for Stanley Basin Sockeye.
BPA 199604300 Johnson Creek Artificial Propa Research under Objective 1 will provide guidelines for proper inclusion of jack male chinook salmon in broodstock management. Recommendations will apply to the majority of spring Chinook salmon hatchery programs within the basin (Project 199604300 is listed as one example).
BPA 199604300 Johnson Creek Artificial Propa Results from research proposed in Objective 3 will assist efforts to reduce age-2 maturation in spring Chinook salmon by modifying embryo incubation protocols and growth regimes to produce fish with phenotypes (age of maturity and timing of smolting) more similar to natural populations. This research will apply to the majority of spring Chinook salmon hatchery programs with the basin. (Project 199604300 is listed as an example).
BPA 199701325 Yakima/Klickitat Fisheries Pro Results from research proposed in Objective 3 will assist efforts to reduce age-2 maturation in spring Chinook salmon by modifying embryo incubation protocols and growth regimes to produce fish with phenotypes (age of maturity and timing of smolting) more similar to natural populations. This research will apply to the majority of spring Chinook salmon hatchery programs with the basin. (Project 199701325 is listed as an example).
BPA 199701325 Yakima/Klickitat Fisheries Pro Research under Objective 1 will provide guidelines for proper inclusion of jack male chinook salmon in broodstock management. Recommendations will apply to the majority of spring Chinook salmon hatchery programs within the basin (Project 199701325 is listed as one example).
BPA 199801001 Grande Ronde Captive Brood O&M The work in Objective 4 is intimately related to captive broodstock rearing activities, especially Grande Ronde Basin spring Chinook salmon (Project 1998-010-01). BKD is a persistent problem in these stocks because the source stocks have a significant infection prevalence. The co-management agencies and facilities responsible for this captive broodstock program have agreed to evaluating BKD prevention and treatment methods we developed in prior BPA funded research, including antibiotic treatment of broodstock and vaccination of collected parr. The current proposed work under Objective 4, which expands those previous findings, is likely to be evaluated by this captive broodstock rearing program.
BPA 199801001 Grande Ronde Captive Brood O&M Results from research proposed in Objective 3 will assist efforts to produce spring Chinook salmon with life history phenotype more similar to natural populations (age of maturity, adult body size, fecundity) by modifying embryo incubation protocols and growth regimes. Impacts of growth regimes to reduce early male maturity on female maturation will be assessed.
BPA 200203100 Spring Chinook Growth Modulati The research in Objective 3 largely focuses on using environmental factors (photoperiod, food availability/growth) to match life history phenotypes of hatchery-reared fish with that of wild fish, particularly age of maturity in males and reproductive fitness characters in adults. It complements research done on project #200203100 which monitors age-2 male maturation of wild and hatchery Yakima River spring Chinook salmon, and conducts hatchery scale trials of growth manipulations to reduce age-2 maturation of male hatchery fish. Results from both projects have been used to develop growth regimes and rearing environments to reduce early male maturation in hatchery-reared Chinook salmon, and can be applied to a number of spring Chinook salmon supplementation projects as mentioned above. Work in Objective 3 is unique in that it also evaluates impacts of growth regimes to females.
BPA 200501200 Sockeye Smolt Program Experiments planned under Objective 2 will examine the importance of odor exposure timing and duration in smolts and will help develop optimal imprinting release protocols for smolts released into Stanley Basin as part of the expanded Stanley Basin sockeye smolt production (project # 2005-012-00 - Sockeye Smolt Program – ODFW)

Section 6: Biological Objectives
Biological Objectives of this Proposed Project
Biological Objective Full Description Associated Subbasin Plan Strategy Page Nos
Improve Fish Health and Quality Reduce morbidity and mortality among captively reared or hatchery salmon through vaccination against BKD. None This objective has basinwide relevance and addresses questions described in the NWPCC Draft Research Plan, the 2000 Council Fish and Wildlife Program, 2004 FCRPS BiOP, the 2003 ISAB supplementation review, and the 2004 APRE (see section 10 for details). Various
Improve genetic management of Chinook salmon This objective will test four null hypotheses that will provide guidance on the genetic management of Chinook salmon populations. H01: Propensity of male Chinook salmon to mature early (jacking) is not influenced by paternal genetic effects or paternal age. H02: Propensity of male Chinook salmon to mature early (jacking) is not influenced by maternal genetic or environmental effects. H03: Propensity of male Chinook salmon to mature early (jacking) is not influenced by growth rate or smolt size at release. H04: Survival and age structure of Chinook salmon is not influenced by the degree of inbreeding. None This objective has basinwide relevance and addresses questions described in the NWPCC Draft Research Plan, the 2000 Council Fish and Wildlife Program, 2004 FCRPS BiOP, the 2003 ISAB supplementation review, and the 2004 APRE (see section 10 for details). Various
Improve olfactory imprinting and reduce straying The overall goal of Objective 2 is to identify hatchery practices that influence olfactory imprinting, and thereby develop strategies to minimize straying of artificially produced salmonids. The studies conducted under Objective 2 will examine critical uncertainties about olfactory imprinting related to release strategies for reintroduction of captively-reared salmon back into their ancestral waters. None This objective has basinwide relevance and addresses questions described in the NWPCC Draft Research Plan, the 2000 Council Fish and Wildlife Program, 2004 FCRPS BiOP, the 2003 ISAB supplementation review, and the 2004 APRE (see section 10 for details). Various
Maintain adaptive life history strategies Maintain natural age-at-maturity and reproductive potential of Chinook salmon through improvements in broodstock management. We will develop empirically derived protocols for incorporating jack males in chinook salmon hatchery broodstocks. The protocols will be based on actual breeding success and genetic quality of naturally spawning jack and older Chinook salmon males. None This objective has basinwide relevance and addresses questions described in the NWPCC Draft Research Plan, the 2000 Council Fish and Wildlife Program, 2004 FCRPS BiOP, the 2003 ISAB supplementation review, and the 2004 APRE (see section 10 for details). Various
Match wild phenotypes in salmon hatchery programs The experiments proposed under this objective examine the effects two environmental factors : photoperiod/quality of light, and food availability (growth) on life history phenotypes in spring Chinook salmon and sockeye salmon. The main goal of this work is to provide new methods to produce fish from supplementation programs that have phenotypes (age of maturity, timing of smolting, adult body size and coloration, and fecundity) more similar to that of natural populations. Three experiments will be conducted under this objective. Much of the work (Experiments 1 and 2) focuses on manipulating growth regimes and altering emergence time to reduce early male maturation in hatchery spring Chinook salmon. Experiment 1 is trial run of growth regimes to reduce age-2 maturation that we would presently recommend for spring Chinook salmon supplementation programs (base on research from previous funding periods). It also examines effects of this growth regime on female reproduction, compared to a regime that supports a high rate of ovarian development. Experiment 2 examines for the first time effects of photoperiod at emergence on age of maturity in males. Experiment 3 examines affects of natural versus artificial light on development of secondary sex characters and timing of spawning in sockeye salmon with the aim of producing adults more similar in phenotype to that of natural populations. None This objective has basinwide relevance and addresses questions described in the NWPCC Draft Research Plan, the 2000 Council Fish and Wildlife Program, 2004 FCRPS BiOP, the 2003 ISAB supplementation review, and the 2004 APRE (see section 10 for details). Various

Section 7: Work Elements
Work Elements and Associated Biological Objectives
Work Element Name Work Element Title Description Start Date End Date Estimated Budget
1a: Mark/Tag Animals Affix Petersen Disc tags to mature Chinook salmon Affix disc tags to Chinook salmon used to quantify the breeding success of jack and older males in a natural stream 8/1/2007 8/30/2009 $24,647
Biological Objectives Metrics
Maintain adaptive life history strategies
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

1b: Collect/Generate/Validate Field and Lab Data Conduct experiments to determine the breeding success and genetic quality of jack male Chinook salmon Conduct experiments in natural streams and quasi-natural environments to test three null hypotheses. H01: Fertilization success of jack males is equal to that of older males? H02: The ratio of jacks to older males on the spawning grounds does not affect the relative fertilization success of males adopting alternative life history tactics. H03. The offspring of jack and older males exhibit similar genetic quality (equal survival through embryonic development, equal post-emergence growth rates and post-emergence survival). 6/1/2007 5/31/2010 $554,548
Biological Objectives Metrics
Maintain adaptive life history strategies
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

1c: Analyze/Interpret Data Conduct statistical analyses on jack male breeding success and genetic quality. Conduct DNA pedigree analyses and statistical analyses to test hypotheses 1 -3. Analysis of variance and multiple regression techniques will be used following appropriate assumption testing and data transformations. The analyses will include the development of empirically based models to guide broodstock management with respect to the use of jack male Chinook salmon. 10/1/2007 3/30/2010 $320,406
Biological Objectives Metrics
Maintain adaptive life history strategies
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

2a: Produce Hatchery Fish Culture sockeye salmon exposed to test odors for olfactory imprinting experiments designed to test release strategies and to test effects of light quality on reproductive performance Rear experimental sockeye salmon to maturity for behavioral testing of imprinting, reproductive performance, and behavior 6/1/2007 12/31/2009 $233,973
Biological Objectives Metrics
Improve olfactory imprinting and reduce straying
* Rearing: # smolts into program: 3800 smolts
* Rearing: # adults into program: 1000 adults
* Incubation: # fertilized eggs into incubation program.: 5000 fertilized eggs

2b: Collect/Generate/Validate Field and Lab Data Conduct experiments on sockeye salmon to assess imprinting success of juvenile and adult release strategies Conduct physiological, molecular and behavioral tests of imprinting success and reproductive behavior of sockeye salmon exposed to odors during different developmental periods paralleling release strategies 6/1/2007 5/31/2010 $272,969
Biological Objectives Metrics
Improve olfactory imprinting and reduce straying
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

2c: Analyze/Interpret Data Conduct statistical analyses on physiological, molecular and behavioral tests of imprinting success of sockeye salmon Conduct statistical analyses on physiological, molecular and behavioral tests of imprinting success and reproductive behavior 6/1/2007 5/31/2010 $191,078
Biological Objectives Metrics
Improve olfactory imprinting and reduce straying
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

3a: Produce Hatchery Fish Culture spring Chinook salmon to test effects of growth regimes and photoperiod on age of maturity, fecundity and fertility. Spring Chinook salmon will be cultured for two experiments: 1) effects of growth on age of maturity in both sexes and fecundity/fertility in females and 2) effects of photoperiod at emergence and growth postponding on early male maturation and timing of smolting. 6/1/2007 5/31/2010 $300,623
Biological Objectives Metrics
Match wild phenotypes in salmon hatchery programs
* Purpose of production program: Research described in Objective 3
* Incubation: # fry (button-up) produced.: 5000 spring Chinook salmon
* Rearing: # juveniles (presmolt) into program: 5000 spring Chinook salmon
* Rearing: # smolts into program: 4500 spring chinook salmon
* Rearing: # adults into program: 1200 spring Chinook salmon
* Incubation: # fertilized eggs into incubation program.: 6000 spring Chinook salmon

3b: Mark/Tag Animals Implant Pit-Tags into spring Chinook salmon juvenile spring Chinook salmon will be Pit-tagged, fin-clips taken and genetic sex determined using PCR from DNA samples. 2/15/2008 3/15/2008 $9,751
Biological Objectives Metrics
Match wild phenotypes in salmon hatchery programs
Primary R, M, and E Type: 1200 PitTagged Chinook salmon presmolts.
Focal Area: Hatchery, Systemwide

3c: Collect/Generate/Validate Field and Lab Data Conduct experiments to test effects of growth and photoperiod on age of maturity, fecundity and fertility in spring Chinook salmon and light quality on reproductive performance in sockeye salmon. Experiments spring Chinook salmon will test 1) effects of growth on age of maturity, fecundity and fertility 2) effects of photoperiod at emergence and growth post ponding on early age of maturity & smolt timing. Experiments in sockeye salmon will examine effects of artificial versus natural light on adult reproductive performance. 6/1/2007 5/31/2010 $527,632
Biological Objectives Metrics
Match wild phenotypes in salmon hatchery programs
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

3d: Analyze/Interpret Data Conduct statistical analyses to test effects of growth and photoperiod on age of maturity, fecundity and fertility in spring Chinook salmon and light quality on reproductive performance in sockeye salmon. Data analyses for effects of environmental treatments in three different experiments on life history phenotype (e.g. age of maturity, timing of smolting, fecundity, spawning time, and body morphology of adults). 8/1/2007 5/31/2010 $241,691
Biological Objectives Metrics
Match wild phenotypes in salmon hatchery programs
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

4a: Produce Hatchery Fish Culture Chinook salmon for immunization and challenge experiments for treatment and prevention of BKD Obtain and rear juvenile chinook salmon for testing with modified strains of R. salmoninarum and R. salmoninarum antigens. 12/1/2007 1/31/2010 $240,903
Biological Objectives Metrics
Improve Fish Health and Quality
* Rearing: # juveniles (presmolt) into program: 2,000 chinook
* Rearing: # eggs into program: 2,000 chinook
* Rearing: # smolts into program: 2,000 chinook under quarantine conditions

4b: Collect/Generate/Validate Field and Lab Data Generate MSA null mutant of R. salmoninarum and evaluate virulence, host response, and protective capabilities against BKD Create R. salmoninarum strain that lacks the MSA protein; test the strain’s pathogenicity and vaccine potential in chinook salmon; assess chinook salmon immune response to strain. 6/1/2007 1/31/2010 $142,821
Biological Objectives Metrics
Improve Fish Health and Quality
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

4c: Analyze/Interpret Data Conduct analysis of experiments evaluating MSA null mutant of R. salmoninarum Analyze and interpret results for experiments with R. salmoninarum strain lacking the MSA protein. 5/1/2008 5/31/2010 $55,063
Biological Objectives Metrics
Improve Fish Health and Quality
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

4d: Collect/Generate/Validate Field and Lab Data Generate library of R. salmoninarum antigens and evaluate for protection against BKD by genetic immunization Create collection of plasmids containing potential R. salmoninarum antigens; test collection for protective immunity in chinook salmon; test duration of protective immunity in chinook salmon. 5/1/2008 5/31/2010 $142,821
Biological Objectives Metrics
Improve Fish Health and Quality
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

4e: Analyze/Interpret Data Conduct analysis of experiments evaluating library of R. salmoninarum antigens Analyze and interpret results for experiments with collection of R. salmoninarum antigens for protective immunity. 1/1/2010 5/31/2010 $55,063
Biological Objectives Metrics
Improve Fish Health and Quality
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

5a: Produce Hatchery Fish Culture Chinook salmon for male jacking and inbreeding experiments Culture juvenile Chinook salmon as per experimental designs to evaluate genetic and environmental factors influencing male jacking and inbreeding depression. 12/1/2007 5/31/2010 $179,073
Biological Objectives Metrics
Improve genetic management of Chinook salmon
* # of Female ad-clip (hatchery origin) fish: 180
* # of Male ad-clip (hatchery origin) fish: 165
* # of Jack ad-clip (hatchery origin) fish: 15
* Broodstock collection: # of ad-clip (hatchery origin) fish : 360
* Incubation: # fertilized eggs into incubation program.: 720000
* Incubation: # fry (button-up) produced.: 570000
* Production: # smolts released from program: 165000
* Purpose of production program: Research

5b: Mark/Tag Animals Mark experimental Chinook salmon by treatment group Mark experimental Chinook salmon by family and by inbreeding line with sequential coded-wire tags. 3/1/2008 5/1/2010 $77,858
Biological Objectives Metrics
Improve genetic management of Chinook salmon
Primary R, M, and E Type: Uncertainties Research
Focal Area: Hatchery, Systemwide

5c: Collect/Generate/Validate Field and Lab Data Collect and summarize data on performance of experimental Chinook salmon Collect and summarize data on survival, growth, age, and life history of experimental Chinook salmon.ent Description 6/1/2007 5/31/2010 $124,572
Biological Objectives Metrics
Improve genetic management of Chinook salmon
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

5d: Analyze/Interpret Data Conduct analysis of experiments evaluating effects of inbreeding and parental phenotype on Chinook salmon performance Analyze and interpret results for experiments evaluating effects of level of inbreeding and male and female parental phenotype on survival, age, and life history of Chinook salmon. 3/1/2008 4/30/2010 $90,834
Biological Objectives Metrics
Improve genetic management of Chinook salmon
Focal Area: Hatchery, Systemwide
Primary R, M, and E Type: Uncertainties Research

7: Produce/Submit Scientific Findings Report Produce project annual reports covering all five objectives and publish scientific results in peer-reviewed journals Produce an Annual Report covering background, methods, results, and discussion and recommendations for each objective of the the project. A draft document describing work completed within two months of the end of the annual performance period The document will be organized by each of the five major objectives. Within each objective the document will be organized in sections as follows: The documents will be organized in sections as follows • Abstract (limit 600 words) • Introduction • Description of project area • Methods and materials by objective • Results and discussion of results by objective • Data management activities by objective (where not discussed in results) • Summary and conclusions • Summary of expenditures, including major purchases • Supplemental volume or appendices detailing summaries of data Within one month of receiving BPA comments on the draft, the document will be edited and republished as the Annual Report. The Annual Report will be provided in electronic formats. The electronic version will be prepared consistent with instructions for preparing and submitting electronic reports and publications (http://www.efw.bpa.gov/cgi-bin/FW/PublicationsHowTo.cgi) ready for posting on the BPA Web site. Manuscripts submitted for publication in a peer-reviewed journal may be substituted for a technical section within the Annual Report, with prior BPA approval. Regardless, we expect to submit an average of three to four manuscripts for peer-reviewed publication in scientific journals on an annual basis. 3/1/2007 8/15/2010 $441,185
Biological Objectives Metrics
Improve Fish Health and Quality
Improve genetic management of Chinook salmon
Improve olfactory imprinting and reduce straying
Maintain adaptive life history strategies
Match wild phenotypes in salmon hatchery programs
No Metrics for this Work Element

8: Coordination Coordinate research activities within and among all objectives Principal investigators will attend regional captive broodstock Technical Oversight Committee meetings and other meetings that pertain to Hatchery Reform within the Columbia Basin. As each Objective described in this SOW requires highly specialized research, certain aspects of research plans, approaches, and findings can only best be described by the respective PI. Therefore, attendance by an individual PI enables productive dialogue between broodstock program managers and scientists to help set future directions for the implementation programs. This research project and the implementation programs have been well served by information exchanged through the TOC process, and continued attendance is critical. Financial support is requested for project personnel to attend scientific meetings and symposia to disseminate research methodologies and project findings to the broader fisheries community. Participation in such meetings enables direct consultation with peers conducting research in the same fields, and for each PI to acquire information on new techniques and data sources not yet published in the primary literature. These benefits will improve the overall quality of the final research product. The total amount budgeted for all Coordination activities is less than 4% of the overall budget amount. 6/1/2007 5/31/2010 $234,220
Biological Objectives Metrics
Improve Fish Health and Quality
Improve genetic management of Chinook salmon
Improve olfactory imprinting and reduce straying
Maintain adaptive life history strategies
Match wild phenotypes in salmon hatchery programs
No Metrics for this Work Element

8: Manage and Administer Projects Manage and administer research projects This work element covers project management and administrative work related to the contract excluding environmental compliance. Project PIs will meet approximately bi-monthly to discuss progress on the various aspects of the research project. Discussions will include on-going efforts to maintain cost-effectiveness and synergy among the project components. Portions of the work under each of the Objectives will be completed by subcontractors. Regular schedules will be established for communication and research planning between lead scientists and subcontractors. Other management and administration tasks include tracking budget expenditures, managing performance of subcontracts, communicating with the BPA Project Manager to track progress and identify any potential problems. The project may require within-year modifications (through the NPCC modification process) depending on research findings o or unexpected difficulties. 6/1/2007 5/31/2010 $92,251
Biological Objectives Metrics
Improve Fish Health and Quality
Improve genetic management of Chinook salmon
Improve olfactory imprinting and reduce straying
Maintain adaptive life history strategies
Match wild phenotypes in salmon hatchery programs
No Metrics for this Work Element


Section 8: Budget

Itemized Estimated Budget
Item Note FY 2007 Cost FY 2008 Cost FY 2009 Cost
Personnel Part time salaries for 12 different NOAA FTE (5 project principal investigators and 7 biological staff) $320,372 $339,594 $359,969
Fringe Benefits Benefits for NOAA employees $159,873 $169,466 $179,634
Supplies Supplies and materials for field and laboratory experiments (Objectives 1-5) $120,761 $120,761 $120,761
Travel Local travel for scientific research. Non-local travel for coordination and management meetings and conferences $30,967 $30,967 $30,967
Capital Equipment Spectroradiometer and ultrasound equipment $16,320 $ 0 $ 0
Overhead Overhead on NOAA salaries and benefits $251,588 $266,683 $282,684
Other Utilities costs for operating pumps, chillers, and other equipment $20,160 $20,160 $20,160
Other Subcontracts for personnel services (University of Washington, Pacific States Marine Fisheries Commission, Oregon Department of Fish and Wildlife, and miscellaneous maintenance) $554,004 $564,882 $573,249
Totals $1,474,045 $1,512,513 $1,567,424

Total Estimated FY 2007-2009 Budgets
Total Itemized Budget$4,553,982
Total Work Element budget$4,553,982

Cost sharing
Funding Source or Organization Item or Service Provided FY 2007 Est Value ($) FY 2008 Est Value ($) FY 2009 Est Value ($) Cash or in-kind? Status
NOAA Fisheries Personnel $200,000 $212,000 $225,000 In-Kind Confirmed
Totals $200,000 $212,000 $225,000

Section 9: Project Future
Project Future Costs and/or Termination
FY 2010 Est Budget FY 2011 Est Budget Comments
$1,600,000 $1,600,000 We expect the region will continue to rely heavily on this project to guide hatchery reform in the Columbia River Basin for the forseeable future.
Future Operations & Maintenance Costs
Future operations and maintenance costs will be similar to those in the current proposal for this 'uncertainties research' project.
 
Termination Date Comments
None This project will continue to reduce uncertainties regarding the most beneficial use of artificial production in the Columbia River Basin. The goals of maximizing benefits (and minimizing risks) for ESA-listed population and will be served by continuation of a broad-based, multidisciplinary research program.
 
Final Deliverables
This project will continue to deliver management guidance through project annual reports, publications in the peer-reviewed scientific literature, and presentation of research findings at regional oversight committee meetings and scientific symposia.

Section 10: Narrative
Document Type Size Date

Part 2 of 2. Reviews of Proposal
Administrative Review Group (ARG) Results
Account Type:
Expense
Location:
Province: Mainstem on the ground/Multiprovince
Subbasin: Mainstem on the ground/Multiprovince
Primary Focal Species
No Change
ARG Comments: [none]


NPCC Final Funding Recommendations (October 23, 2006) [Full NPCC Council Recs]

FY 2007 Budget
$1,000,000
FY 2008 Budget
$1,000,000
FY 2009 Budget
$1,000,000
Total NPCC Rec
$3,000,000
Budget Type:Expense
Budget Category:Multi-province
Recommendation:Fund
Comments: Reduce the work elements to priority elements.


NPCC Draft Funding Recommendations (September 15, 2006) [Full NPCC Council Recs]

FY 2007 Budget
$1,000,000
FY 2008 Budget
$1,000,000
FY 2009 Budget
$1,000,000
Total NPCC Rec
$3,000,000
FY 2007 MSRT Rec
$ 0
FY 2008 MSRT Rec
$ 0
FY 2009 MSRT Rec
$ 0
Total MSRT Rec
$ 0
Budget Category:Multi-province
Comments: Reduce the work elements to priority elements. Need to confirm what work can be accomplished at this budget level.
NPCC Staff Comments: MSRT recommends $1,468,100.

Local or MSRT Comments: The MSRT considered this proposal while reviewing the research projects in the basinwide category.

MSRT General Comments: This project has provided core research evaluating captive broodstock methodologies. Some MSRT members expressed concern that BPA is funding some research that may be more appropriately funded within NOAA's congressional budget. Cost share? The project appears to be a grab bag of important research items. Some research items may be more important than others. The MSRT ranked the project as High Priority without a clear understanding of the importance of each question the project is attempting to address. Although this is an ongoing project, some of the tasks proposed are new. The proposal merits additional scrutiny to determine high priority research topics and reduction in budget. The MSRT would like to see better integration with project number 200203100 and 200733500. There appears to be some lack of coordination and possibly some duplication between this older "parent" project and several of the new NOAA proposals in this group.


Independent Scientific Review Panel Final Review (August 31, 2006) [Download full document]

Recommendation: Fundable (Qualified)
NPCC Comments: Although the various components of this complex project will all provide valuable results, the ISRP wishes to express its concerns. A strategy of increasing the costs over time to support research to learn about hatchery reform may result only in incrementally small changes in the nature of the hatchery product. "Hatchery reform" is an endpoint that still may fall short of producing hatchery-origin fish whose integration with wild populations would not cause significant fitness decreases.

Technical and scientific background: This is a huge project, which makes its review cumbersome and difficult. It takes some review effort just to determine how all of the components fit together and are coordinated, especially how all of them fit in with various monitoring and evaluation (M&E) efforts to assess success. The multiple components fit into these five objectives:

1. Maintain adaptive life history strategies in hatchery Chinook salmon;

2. Improve olfactory imprinting and reduce straying in hatchery salmon;

3. Use environmental factors to match wild phenotypes in Chinook and sockeye reared in hatchery supplementation programs;

4. Improve Fish Health and Quality by Prevention and Treatment of Bacterial Kidney Disease; and

5. Identify genetic and environmental factors influencing male precocity and fitness in hatchery Chinook salmon.

The technical and scientific background used to set up the objectives and the entire proposal is very extensive.

Rationale and significance to subbasin plans and regional programs: This multi-faceted project has clear significance to hatchery reform, which is critical to continued use of this technology as a management tool. The rationale and significance are laid out well - by objective - and explain how each relates to the 2004 APRE, the 2000 Fish and Wildlife Program, the 2004 BiOp, and the 2006 Council’s Draft Research Plan.

Relationships to other projects: The linkages to other projects are evident in the proposal.

Project history: The past accomplishments are well summarized and demonstrate how the project has evolved over time.

Objectives: The biological objectives are extensive, but largely task oriented. An overarching biological objective is needed.

Tasks (work elements) and methods: The methods are detailed and useful, although we question the value of the experiments on determining the consequences of inbreeding. While quantifying the consequences of inbreeding would be beneficial, it is well recognized that inbreeding is to be avoided. The provided methods are extraordinarily detailed and complete, almost more than a reviewer can deal with.

Monitoring and evaluation: This project is more experimental in nature than on-the-ground. So, data analysis and interpretation are more appropriate terms here. As such, that activity is documented well.

Facilities, equipment, and personnel: The facilities, equipment and personnel are excellent in all regards.

Information transfer: This is outlined adequately; project proponents have published in the peer reviewed literature and presented at regional and national conferences.

Benefits to focal and non-focal species: The results of the proposed research would likely decrease the negative impact of artificial production programs on natural populations. This project should do little harm to non-focal species, and some findings may translate to other species.


Independent Scientific Review Panel Preliminary Review (June 2, 2006) [Download full document]

Recommendation: Fundable (Qualified)
NPCC Comments: Although the various components of this complex project will all provide valuable results, the ISRP wishes to express its concerns. A strategy of increasing the costs over time to support research to learn about hatchery reform may result only in incrementally small changes in the nature of the hatchery product. "Hatchery reform" is an endpoint that still may fall short of producing hatchery-origin fish whose integration with wild populations would not cause significant fitness decreases.

Technical and scientific background: This is a huge project, which makes its review cumbersome and difficult. It takes some review effort just to determine how all of the components fit together and are coordinated, especially how all of them fit in with various monitoring and evaluation (M&E) efforts to assess success. The multiple components fit into these five objectives:

1. Maintain adaptive life history strategies in hatchery Chinook salmon;

2. Improve olfactory imprinting and reduce straying in hatchery salmon;

3. Use environmental factors to match wild phenotypes in Chinook and sockeye reared in hatchery supplementation programs;

4. Improve Fish Health and Quality by Prevention and Treatment of Bacterial Kidney Disease; and

5. Identify genetic and environmental factors influencing male precocity and fitness in hatchery Chinook salmon.

The technical and scientific background used to set up the objectives and the entire proposal are very extensive.

Rationale and significance to subbasin plans and regional programs: This multi-faceted project has clear significance to hatchery reform, which is critical to continued use of this technology as a management tool. The rationale and significance are laid out well - by objective - and explain how each relates to the 2004 APRE, the 2000 Fish and Wildlife Program, the 2004 BiOp, and the 2006 Council’s Draft Research Plan.

Relationships to other projects: The linkages to other projects are evident in the proposal.

Project history: The past accomplishments are well summarized and demonstrate how the project has evolved over time.

Objectives: The biological objectives are extensive, but largely task oriented. An overarching biological objective is needed.

Tasks (work elements) and methods: The methods are detailed and useful, although we question the value of the experiments on determining the consequences of inbreeding. While quantifying the consequences of inbreeding would be beneficial, it is well recognized that inbreeding is to be avoided. The provided methods are extraordinarily detailed and complete, almost more than a reviewer can deal with.

Monitoring and evaluation: This project is more experimental in nature than on-the-ground. So, data analysis and interpretation are more appropriate terms here. As such, that activity is documented well.

Facilities, equipment, and personnel: The facilities, equipment and personnel are excellent in all regards.

Information transfer: This is outlined adequately; project proponents have published in the peer reviewed literature and presented at regional and national conferences.

Benefits to focal and non-focal species: The results of the proposed research would likely decrease the negative impact of artificial production programs on natural populations. This project should do little harm to non-focal species, and some findings may translate to other species.

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