Transcript USDA ARS Aquaculture Review of Program Program Capabilities and Accomplishments

USDA ARS Aquaculture
Review of Program
Program Capabilities and Accomplishments
Objectives
 With Dr. Conte, give ARS overview
and retrospective assessment
 Describe briefly, the facilities/people
involved in ARS Aquaculture research
 Review selected research highlights
 Share the findings of the review panel
 Set the stage for breakout sessions
ARS Aquaculture Mission
 To improve the productivity and
efficiency of US producers and the
quality of seafood and other aquatic
products to reduce dependence on
imported seafood and threatened
ocean fisheries
ARS Aquaculture Locations
Aquaculture
National Program 106
 26 appropriated projects
($35M)
 Approximately 28% CM
projects
 13 U.S. Locations (62 SY)
 4 worksites
 Program Team:
Jeff Silverstein (Lead)
Cyril Gay
ARS Aquaculture Locations
Locations and Activities
 Leetown,WV- 10 SY
 NCCCWA-Rainbow Trout
 Auburn, AL- 12 SY
 AAHRU-Catfish, other warm water fish
 Stoneville, MS- 12 SY
 CGRU-Catfish
 Stuttgart, AR- 12 SY
 SNARC-Striped Bass
 FAU-HBOI-Marine species
Locations and Activities
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Franklin/Orono, ME- 1 SY
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NCWMAC-Atlantic salmon
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HFCES-Trout Grains project
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Oyster genetics and ecology
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Co-product utilization
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Yellow perch
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Product quality-off flavor
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Natural products to limit blue-green algae
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Seafood safety
Hagerman, ID- 3(5) SY
Hatfield, OR-2 SY
Fairbanks, AK- 2 SY
Milwaukee, WI- 1 SY
New Orleans, LA- 3 SY
Oxford, MS-1 SY
Dover, DE-
Cooperative Research Programs
 UAPB-Pine Bluff, AR
 Catfish, striped bass
 TCFFWI-Shepherdstown, WV
 Production systems
 HBOI-Ft. Pierce, FL
 Marine finfish production systems
 MSU-Stoneville & Starkville, MS
 Catfish research
 OI-Waimanalo, HI
 Shrimp and marine fish nutrition
 WVU-Trout genomic research
 UCONN-Disease resistance and AMP gene platform
 UAlaska-value added products from fish processing
waste
Retrospective Assessment
National Program 106 - Aquaculture
F.S. Conte
St. Louis, MO 04-15-08
Retrospective Assessment
National Program 106 - Aquaculture
Review Team:
Fred Conte, Chair
Walt Dickhoff
George Flick, Jr.
Delbert Gatlin
Tom Losordo
Jim Parsons
Terry Tiersch
Jim Winton
University of California Davis
University of Washington
Virginia Tech
Texas A&M University
University or North Carolina
Trout Lodge, Inc
Louisiana State University
U.S. Geological Survey
PROBLEM AREA RATING CRITERIA: Low, Medium, High
QUALITY
RELEVANCE
IMPACT(S)
QUALITY of the entire problem area, not projects or researchers
RELEVANCE is assessment of the relevance of the of the
identified Goals to science and industry, and does not refer to
the work actually reported
IMPACT(S) refers to the work performed as outlined in the ARS
National Program Assessment Criteria
Retrospective Assessment
National Program 106 - Aquaculture
Assessment Criteria for Aquaculture National Program
The accomplishments of the National Program is assessed
against commitments identified in the Action Plan created at the
beginning of the 5-year National Program cycle.
PROGRAM IMPACTS:
Assessment Criteria for Aquaculture National Program
Contribute to the development and/or implementation of
regulations?
Government and/or industry programs influenced by the
research?
Influence/impact other researchers conducting research in the
same or related scientific fields?
Advance knowledge?
Major agricultural problems ameliorated, mitigated, or solved?
PROGRAM IMPACTS:
Assessment Criteria for Aquaculture National Program
Resulted in technology that has been patented or licensed, and if
so, has it led to commercialization?
Yielded health, social or economic advantages for consumers?
Have new or improved scientific methods or technologies been
developed by ARS and adopted by others (e.g., customers,
stakeholders, consumers, and/or other scientists)?
ARS recognized as a leader in this program area?
Note: Not all criteria would apply to all National Programs or all program
components
PROGRAM IMPACTS:
Assessment Criteria for Aquaculture National Program
Question for Panel Discussion:
Does the panel feel that the research in this National Program
has the right balance of basic and applied research?
Genetic Improvement
Selected accomplishments
 Development of improved catfish and rainbow trout germplasm
 Improved growth rate in 103 line
 Improved resistance against CWD and ESC through selective breeding
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Production of tetraploid trout lines
USDA NCWMAC Atlantic Salmon Breeding Program
Candidate Gene ID in catfish, trout and oysters
Cryopreservation of germplasm at NAGP, Fort Collins, CO
Research Component I: Genetic Improvement
Genetics/Genomics
Problem Area IA – Conserve, Characterize, and Utilize Genetic Resources
Review Team Rating: Medium Quality, High Relevance, Emerging Impact
• Sperm and tissue deposited in National Animal Germplasm Program
(NAGP). Extensive interactions and linkages by NAGP with non-USDA
personnel
• Good progress, but now researchers need to utilize the molecular
tools that have been developed to quantify genetic variation
• Progress being made, but still, researchers need to clarify a system for
prioritization and selection of genetic markers
Research Component 1: Genetic Improvement Genetics/Genomics
Problem Area 1B – Breeding for Economically Important Traits
Review Team Rating: Medium Quality, High Relevance, Emerging Impacts
• Good progress relative to rainbow trout and channel catfish
• Delivery of genetically improved lines and broodstocks is still in early
stages. Focus is on selection for single traits. Correlated responses to
selection were not addressed (e.g. selection growth with reduced disease resistance)
Research Component 1: Genetic Improvement Genetics/Genomics
Problem Area IC – Genomic Resources
Review Team Rating: High Quality, High Relevance, High Impact
• Excellent progress has been made on rainbow trout and catfish
This is a highly productive area of great strength for NP 106 and should
remain a Core Area of focus and support for the development of strains
that will make domestic aquaculture competitive on a global scale
Research Component 1: Genetic Improvement Genetics/Genomics
Problem Area ID – Specific Breeding Aids (Polyploidy, Sex Control,
Cryopreservation)
Review Team Rating: Low Quality, High Relevance, Low Impact
This problem area could be eliminated and the topics redistributed to
other areas
More effort should be directed toward production of triploids and
tetraploid broodstocks
Research Component 1: Genetic Improvement Genetics/Genomics
Problem Area IE – Bioinformatics and Statistical Analysis Tools
Review Team Rating: Low quality, High Relevance, Low Impact
• Little Work Done in this Problem Area
• Little evidence that bioinformatics tools have been applied.
Integrated Aquatic Animal Health
Flavobacterium
psychrophilum genome
sequence
Host
Pathogen
Environment
Selected Accomplishments
 Compound Evaluation/Strategies for Disease Control
 Identification and functional analysis of immune genes
 Improved resistance against F. psychrophilum and E. ictaluri
through selective breeding
 Characterization of Yersinia ruckeri bacteriophage
 Vaccines against ESC, columnaris, Strep. Iniae, S. agalactiae
 Microbial genomics
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Research Component II: Integrated Aquatic Animal Health
Management
Problem Area IIA – Pathogen Identification and Disease Diagnosis
Review Team Rating: Medium Quality, Medium Relevance, Medium Impact
• Substantial redundancy with academic research, and few peer-reviewed
publications for some assays
• Serological tools were not developed, and non-lethal assays were not
developed
• Validation of assays are needed, not just initial development
Research Component II: Integrated Aquatic Animal Health Management
Problem Area IIB – Vaccines and Medicines
Review Team Rating: High Quality, High Relevance, High Impact
• Successfully developed ESC and columnaris vaccines for catfish have
been commercialized. Good progress has been made on vaccines for
other diseases and for other species
• Accomplished a potentially important breakthrough in mass delivery
approaches for immunization of fish (in-ovo administration primarily in
catfish and tilapia)
• High quality and high impact research on immune response genes of
trout and catfish was conducted
Research Component II: Integrated Aquatic Animal Health Management
Problem Area IIC – Immunology and Disease Resistance
Review Team Rating: High Quality, High Relevance, High Impact
• This is a Core Area of strength for aquatic animal health that should be
emphasized and continued
• Good collaboration with others, and important crosstalk with broodstock
improvement and genomics
Research Component II: Integrated Aquatic Animal Health Management
Problem Area IID – Mechanism of Disease
Review Team Rating: Medium Quality, Medium Relevance, Medium Impact
• Some progress to develop models to assess pathogenesis of disease
Research Component II: Integrated Aquatic Animal Health Management
Problem Area IID – Mechanism of Disease (Cont)
• Laboratory challenge models are important for several lines of research,
but duplication of ‘farm conditions’ will be problematic and has to be
addressed
Research Component II: Integrated Aquatic Animal Health Management
Problem Area IIE – Epidemiology
Team Rating: Medium Quality, Medium Relevance, Low Impact
• Limited progress in economic impact of trematode infection
• Few actual epidemiological analyses conducted – is this a research
need?
Research Component II: Integrated Aquatic Animal Health Management
Problem Area IIF – Microbial Genomics
Review Team Rating: High Quality, High Relevance, High Impact
• Strong progress made in all goals
•Genetic information on pathogens
•Developing bioinformatic tools
•Applying functional genomic approaches
• This should also continue to be a Core Area for ARS aquaculture
research
Research Component II: Integrated Aquatic Animal Health Management
Problem Area IIG – Aquatic Animal Health Management
Review Team Rating: Low Quality, Medium Relevance, Low Impact
• Strong recommendation to add Animal Health and Well Being (i.e.
animal welfare) as a new activity that should be the basis for a new or
revised Problem Area
Reproduction and Early Development
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Hybrid catfish research
Reproductive control and performance
Nutrient and energy partitioning
Optimized fry production of HSB without rotifers
Improved management of dissolved oxygen in catfish hatcheries
Research Component III: Reproduction and Early
Development
Problem Area IIIA – Control of Reproduction
Review Team Rating: Low Quality, High Relevance, Low Impact
• Little progress documented
• Example-gonadotropin-releasing hormone (GnRH) work with Florida
pompano is more transfer of technology than research, this technology is
decades old
Research Component III: Reproduction and Early Development
Problem Area IIIB– Control of Gender and Fertility
IIIC – Gamete and Zygote Quality
IIID – Gamete and Embryo Storage, Cryopres. and Use
Review Team Rating: Little information provided to ascertain Quality
rating; High Relevance, No Impact
• Few or no accomplishments listed for any goal in this problem area
Research Component III: Reproduction and Early Development
Problem Area IIIE – Early Life Stage Development and Survival
Review Team Rating: Medium Quality, High Relevance, Medium Impact
• Goals 1 & 2 are being thoroughly addressed, primarily in catfish,
somewhat in striped bass, but other species not well represented
• Focus appears to be exclusively on hatchery practices rather than on
underlying mechanisms of the science
Growth, Development and Nutrition
Selected Accomplishments
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Barley and oat protein concentrates (>70%) were developed.
New vitamin premix for plant based feeds was developed and
commercialized (ARS 702).
Genes for growth metabolism, muscle development, and fish health
have been identified.
Fish meal free diet supports growth equal to fish meal diets
Determined pompano nutrient requirements at 3 ppt salinity
Research Component IV: Growth, Development and
Nutrition
Problem Area IVA – Regulating Feed Intake
Review Team Rating: Medium Quality, Low/Med Relevance, Medium
Impact
• Some activity in this area directly relates to the development of the USDA
103 line of channel catfish, whose faster growth rate is largely attributed
to increased feed intake
• Basic insights provided about factors controlling feed
Problem Area IVB – Tissue Growth and Development
Rating: Medium Quality, Med/High Relevance, Medium Impact
• Significant impacts have been demonstrated in catfish; solid set of
papers in the peer-reviewed literature
• Addressed as it related specifically to myostatin gene in relation to body
composition and molecular expression; pursued at the tissue level but not
at the cellular level
Research Component IV: Growth, Development and Nutrition
Problem Area IVC – Sustainable Sources of Nutrients
Problem Area IVD – Nutrient Use and Feed Evaluation
Review Team Rating: High Quality, High Relevance, High Impact
• Evidence of good progress is apparent
• ARS could look into resolutions identified by National Organic
Standards Board (NOSB) and possible relationships that may influence
ARS research
Research Component IV: Growth, Development and Nutrition
Problem Area IVE – Interaction of Gene Regulation and Nutrition
Review Team Rating: Unable to rate quality due to lack of information,
High Relevance, Low Impact
• ARS should look into reference diets to be used in genomics research
• This research should be applied across disciplines, beyond nutrition
Research Component IV: Growth, Development and Nutrition
Problem Area IVF – Interactions Affecting Reproduction
Review Team Rating: Unable to rate quality due to lack of information,
High Relevance, Low Impact
This problem area should be redirected into the Reproduction
research component (Component III)
• This is an important area for future research: increase emphasis on this
activity, it is a long-term effort
• Ensure that this is not left out of the genomic approaches as stated
previously in this report
Research Component IV: Growth, Development and Nutrition
Problem Area IVG – Effective Probiotics
Review Team Rating: Unable to rate quality due to lack of information,
Medium Relevance, Low Impact
Research Component IV: Growth, Development and Nutrition
Problem Area IVH – Immune System Enhancement (Nutrients and
Immunostimulants)
Review Team Rating: High Quality, High Relevance, Medium Impact
• Significant progress noted for all goals
• Expand research beyond catfish and tilapia
• Establish cross discipline research with genomics and aquatic animal
health
Aquaculture Production Systems
Selected Accomplishments
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Aerator placement reduces costs up to 20%
Intensive recirculating systems technologies
Cobia production in RAS
Remote sensing to detect harmful algal blooms
Research Component V: Aquaculture Production
Systems
Problem Area VA – Biosecurity
Review Team Rating: Low Quality, High Relevance, Low Impact
• No progress in defining the engineering or biological components of a
bio-secure facility
• No quarantine protocols were reported
• No strategies for pathogen detection or monitoring was reported
Research Component V: Aquaculture Production Systems
Problem Area VB – Production Intensity
Review Team Rating: Med/High Quality, High Relevance, Medium Impact
• Many achievements were through development of management
practices rather than new technology. However, the outcome will be a
more competitive aquaculture production system
• Much of the research focused on this goal bordered on farm based
demonstration type work that changed management strategies (i.e.,
moving aerator placement, tested stocking strategies) rather than
developing and testing new technologies with hypothesis-based
projects
Research Component V: Aquaculture Production Systems
Problem Area VB – Production Intensity (Cont)
•Improved tank based aquaculture technology has been achieved.
• No research to develop models of fish farming systems that could
assist producers in decision-making
Research Component V: Aquaculture Production Systems
Problem Area VC – Integrated Production Systems
Review Team Rating: Unable to assess quality due to lack of evidence of
work in this area, Medium Relevance, No Impact
• No progress was made in this area
Research Component V: Aquaculture Production Systems
Problem Area VD – Predator and Fowl Control
Review Team Rating: Low Quality, High Relevance, Low Impact.
•Research assessed existing technologies, rather than developing
new, improving existing, or adapting alternative techniques and
technology
• Few farms in the direct project adopted management strategies or
technologies to address the problem
• The review panel also recommend strong collaboration with the USDA
APHIS program as this is an area key to their mission
• The goal of assessing the population of fish-eating birds was
accomplished
Research Component V: Aquaculture Production Systems
Problem Area VE – Live Aquatic Animal Handling, Transport, and
Inventory
Review Team Rating: Low Quality, High Relevance, Low Impact
• Focused almost exclusively on pond harvesting technology
• Incremental progress was reported on improvements in seine
technology in farm-based demonstration type projects. New thinking
and more basic, replicated research was demonstrated with the effort to
create an electrically enhanced seine
Research Component V: Aquaculture Production Systems
Problem Area VF – Culture of Marine Species in Low-Salinity Water
Review Team Rating: Medium Quality, Medium Relevance,
Emerging/Medium Impact
• Most efforts reported cut across broad categories of technology
development. The common thread appears to be developing
components and systems for low-salinity aquaculture
• Efforts to date appear to be tank-centric, as opposed to pond-based,
but good technical transfer observed
Sustainability and Environmental
Compatibility of Aquaculture
Selected Accomplishments
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Some redundancy with other components
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Sustainable feeds, Reducing water use, Concentrating waste
Environmental Best Management Practices
Management of oyster pests through IPM
Research Component VI: Sustainability and Environmental
Compatibility of Aquaculture
Problem Area VIA – Aquaculture Feeds
Review Team Rating: High Quality, High Relevance, High Impact
• Most work was covered in Component IV
Research Component VI: Sustainability and Environmental
Compatibility of Aquaculture
Problem Area VIB – Water Use and Reuse
Review Team Rating: Medium Quality, High Relevance, Medium Impact
• A good body of work relating to solids removal, nutrient flocs and
recirculating aquaculture system design was noted, but no documented
work for flow-through aquaculture systems was found related to
improving current system design to improve effluent quality
• Solids removal and RAS research is on target, but there was no
documentation or published work relating to net pen and/or flowthrough systems
• Overall, there is good, well published research relating to removal of
Total Suspended Solids and Phosphorus. However, cost effectiveness
of such practices not summarized
Research Component VI: Sustainability and Environmental
Compatibility of Aquaculture
Problem Area VIC – Effluent Management Control
Review Team Rating: Medium Quality, High Relevance, Medium/High
Impact
• The research and practices evaluated and developed for the catfish
industry are well documented and laudable. However, no reported
practices were evaluated or developed for other species or systems
• No documented monitoring projects were found
Research Component VI: Sustainability and Environmental
Compatibility of Aquaculture
Problem Area VID – Social Sustainability
Review Team Rating: Unable to evaluate Quality due to lack of
information, High Relevance, unable to evaluate impact due to lack of
information
• No documented progress
• The review team suggest that this problem area be rewritten with
researchable objectives
Research Component VI: Sustainability and Environmental
Compatibility of Aquaculture
Problem Area VIE – Environmental Sustainability
Review Team Rating: Low Quality, High Relevance, Low Impact
•Little progress was made
•Work on integrated pest management in oysters is useful and well
documented. This is also true for the reported eelgrass studies. The
Western Regional Aquaculture Center funding supported this work for
over 8 years.
Quality, Safety, and Variety of
Aquaculture Products
Selected Accomplishments
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rapid test to identify Ictalurus (i.e., channel, blue and hybrid catfish)* to combat
product mislabeling
Bacteria to remove off-flavor compounds from ponds
Dogs trained to identify off-flavors
Over 1.1 million MT of fish coproducts
Research Component VII: Quality, Safety, and Variety of
Aquaculture Products for Consumers
Problem Area VIIA – Tissue Quality
Review Team Rating: Medium Quality, High Relevance, Medium/High
Impact
Goal 1: All objectives with regard to catfish and shrimp addressed
• Harvesting and Transport Environmental Effects on Meat Quality
Elucidated in Catfish
Research Component VII: Quality, Safety, and Variety of Aquaculture
Products for Consumers
Problem Area VIIA – Tissue Quality (Cont)
• Results reported that reduced protein as well as the substitution of
plant protein resulted in no reduction of filet yield, but no information
was provided on how the quality of the filet was impacted by the
various diets
• A significant number of publications have appeared in the literature on
this identical research effort, making it difficult to determine how this
research advanced knowledge from the previous research
Research Component VII: Quality, Safety, and Variety of Aquaculture
Products for Consumers
Problem Area VIIB – Interaction of Genetics and Nutrition
Review Team Rating: Quality cannot be assessed due to lack of
information reported, High Relevance (when moved to research
component IV), Impact cannot be assessed due to lack of information
• The Review team recommends to integrate this topic under Nutrition
(Component IV) or Genomics (Component II)
Research Component VII: Quality, Safety, and Variety of Aquaculture
Products for Consumers
Problem Area VIIC – Predicting Product Quality or Defects
Review Team Rating: Medium Quality, High Relevance, Low Impact
• Beyond product substitution, no other work was performed to show that
Goal 2 has been achieved (pre- and post-harvest techniques and systems to ensure
product quality)
Research Component VII: Quality, Safety, and Variety of Aquaculture
Products for Consumers
Problem Area VIID – Off-Flavor Delayed Harvesting
Review Team Rating: Quality cannot be assessed due to lack of
information reported, High Relevance, Impact cannot be assessed
due to lack of information
• Consider moving this section to Production Systems (component V)
Research Component VII: Quality, Safety, and Variety of Aquaculture
Products for Consumers
Problem Area VIIE – Off-Flavor Methodology (6 Components)
Review Team Rating: High Quality, High Relevant, Low Impact
1. Identifying and Characterizing Genes and Enzymes Involved in the
Biosynthesis of Off-flavor Metabolites
No publications were reported
2. Bacteria to Remove Off-flavor Compounds from Catfish Ponds
A continuing, long-term effort, which the second phase to remove
flavor/odor compounds by microorganisms will require several
characteristics that are impacted by the environment and the
competing microbiota
Research Component VII: Quality, Safety, and Variety of Aquaculture
Products for Consumers
Problem Area VIIE – Off-Flavor Methodology (Cont)
3. Off-flavor Methodologies Evaluated for Catfish Production
Though overall the current results were disappointing, the
project activities are worth pursuing
4. Evaluation of Sensory Versus Analytical Detection of Off-flavors
It is difficult to determine how this method differed substantially from
other methods produced in the literature
Research Component VII: Quality, Safety, and Variety of
Aquaculture Products for Consumers
Problem Area VIIE – Off-Flavor Methodology (Cont)
5. Trophic Relationships in Catfish Production Ponds
Results demonstrated a relationship between pond age and the potential
for off-flavor production, which has potential for pond managers to
modify the pond environment favorably. No publications were reported
6. Dogs Trained to Detect Off-flavor Compounds in Water & Fish Filet
The project was successfully performed. However, the research does
not relate the ability of the dogs to correlate their perception of the
compounds with the acceptance or rejection of the product by a
sensory panel, either at the pond level or at the processing facility
Research Component VII: Quality, Safety, and Variety of Aquaculture
Products for Consumers
Problem Area VIIF – New Uses for Byproducts (10 Components)
Review Team Rating: High Quality, High Relevance, Medium Impact
Goal 1. Extensive publication record to support productive activity
Research Component VII: Quality, Safety, and Variety of Aquaculture
Products for Consumers
Problem Area VIIG – Processing
Review Team Rating: No Quality rating due to lack of information,
High Relevance, no Impact rating due to lack of information.
•
No documentation provided for this section
Retrospective Assessment
National Program 106 – Aquaculture
General Recommendations
1. Long-term research is a critical responsibility for ARS
because of their potential for sustained effort and infrastructure
2. Expand research efforts to include additional species
3. Tools that are developed such as genetic markers, physical
maps, should be made available for industry driven and
academic research
Retrospective Assessment
National Program 106 – Aquaculture
General Recommendations
4. Develop and strengthen programmatic linkages among researchers
and species groups to enable integration across disciplines and
commodities
5. Integrate activities with other agencies such as CSREES, APHIS,
FDA, NOAA International Barcode and CITES whenever appropriate