USDA ARS Aquaculture Review of Program

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USDA ARS AquacultureReview of Program

• Program Capabilities and Accomplishments

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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

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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

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ARS Aquaculture Locations
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AquacultureNational 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

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ARS Aquaculture Locations
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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

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Locations and Activities

• Franklin/Orono, ME- 1 SY
• NCWMAC-Atlantic salmon
• Hagerman, ID- 3(5) SY
• HFCES-Trout Grains project
• Hatfield, OR-2 SY
• Oyster genetics and ecology
• Fairbanks, AK- 2 SY
• Co-product utilization
• Milwaukee, WI- 1 SY
• Yellow perch
• New Orleans, LA- 3 SY
• Product quality-off flavor
• Oxford, MS-1 SY
• Natural products to limit blue-green algae
• Dover, DE-
• Seafood safety

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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

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Retrospective AssessmentNational Program 106 -
Aquaculture
F.S. ConteSt. Louis, MO 04-15-08
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Retrospective AssessmentNational Program 106 -
Aquaculture
Review Team Fred Conte, Chair University of
California Davis Walt Dickhoff University of
Washington George Flick, Jr. Virginia
Tech Delbert Gatlin Texas AM University Tom
Losordo University or North Carolina Jim
Parsons Trout Lodge, Inc Terry Tiersch Louisiana
State University Jim Winton U.S. Geological
Survey
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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
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Retrospective AssessmentNational 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.
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PROGRAM IMPACTSAssessment 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?
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PROGRAM IMPACTSAssessment 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
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PROGRAM IMPACTSAssessment 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?
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Genetic Improvement
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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
• 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

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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

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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)

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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
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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 areasMore effort
should be directed toward production of triploids
and tetraploid broodstocks
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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.

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Integrated Aquatic Animal Health
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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

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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

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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

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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

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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

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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?

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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

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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

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Reproduction and Early Development

• 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

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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

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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

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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

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Growth, Development and Nutrition
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Selected Accomplishments

• Barley and oat protein concentrates (gt70) 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

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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

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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

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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

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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

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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
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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

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Aquaculture Production Systems
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Selected Accomplishments

• Aerator placement reduces costs up to 20
• Intensive recirculating systems technologies
• Cobia production in RAS
• Remote sensing to detect harmful algal blooms

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Research Component V Aquaculture Production
SystemsProblem 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

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Research Component V Aquaculture Production
SystemsProblem 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

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Research Component V Aquaculture Production
SystemsProblem 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

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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

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Research Component V Aquaculture Production
SystemsProblem 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

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Research Component V Aquaculture Production
SystemsProblem 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

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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

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Sustainability and Environmental Compatibility of
Aquaculture
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Selected Accomplishments

• Some redundancy with other components
• Sustainable feeds, Reducing water use,
  Concentrating waste
• Environmental Best Management Practices
• Management of oyster pests through IPM

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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

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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 flow-through 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

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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

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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

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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.

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Quality, Safety, and Variety of Aquaculture
Products
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Selected Accomplishments

• 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

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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

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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

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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)

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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)

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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)

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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
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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
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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
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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
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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

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Retrospective AssessmentNational Program 106
AquacultureGeneral 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
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Retrospective AssessmentNational Program 106
AquacultureGeneral 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
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