USDA ARS Aquaculture Review of Program Program Capabilities and Accomplishments

USDA ARS AquacultureReview 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

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

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 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

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

Retrospective AssessmentNational Program 106 - Aquaculture

F.S. ConteSt. Louis, MO 04-15-08

Review Team:

Fred Conte, Chair University of California DavisWalt Dickhoff University of WashingtonGeorge Flick, Jr. Virginia TechDelbert Gatlin Texas A&M UniversityTom Losordo University or North CarolinaJim Parsons Trout Lodge, IncTerry Tiersch Louisiana State UniversityJim Winton 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

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?

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)?

Note: Not all criteria would apply to all National Programs or all program components

ARS recognized as a leader in this program area?

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

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/GenomicsProblem 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

• Progress being made, but still, researchers need to clarify a system for prioritization and selection of genetic markers

• Good progress, but now researchers need to utilize the molecular tools that have been developed to quantify genetic variation

Review Team Rating: Medium Quality, High Relevance, Emerging Impacts

Research Component 1: Genetic Improvement Genetics/Genomics

Problem Area 1B – Breeding for Economically Important Traits

• 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)

• Good progress relative to rainbow trout and channel catfish

Review Team Rating: High Quality, High Relevance, High Impact

Problem Area IC – Genomic Resources

• 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/GenomicsProblem 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

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 HealthFlavobacterium psychrophilum

genome sequence

PathogenHost

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

IL-lik

Mm FASL

Ip APRIL

Ga BALM

100100

100 100

TNFSF 2 TNFSF 1

TNFSF 15

TNFSF 7

TNFSF 3

TNFSF 14

TNFSF 6

TNFSF 5

TNFSF 11

TNFSF 10

TNFSF New

TNFSF 18

TNFSF 8

TNFSF 4

TNFSF 13b

TNFSF 13c

TNFSF 13

Ectodysplasin

TNFSF 9

TNFSF 12

Review Team Rating: Medium Quality, Medium Relevance, Medium Impact

Research Component II: Integrated Aquatic Animal Health Management

Problem Area IIA – Pathogen Identification and Disease Diagnosis

• 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

• 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

Problem Area IIB – Vaccines and Medicines

• 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

Problem Area IIC – Immunology and Disease Resistance

• 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

Review Team Rating: Medium Quality, Medium Relevance, Medium Impact

Problem Area IID – Mechanism of Disease

• Some progress to develop models to assess pathogenesis of disease

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

Problem Area IIE – Epidemiology

Team Rating: Medium Quality, Medium Relevance, Low Impact

• Few actual epidemiological analyses conducted – is this a research need?

• Limited progress in economic impact of trematode infection

Problem Area IIF – Microbial Genomics

• 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

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 Hybrid catfish researchHybrid 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

• Little progress documented

• Example-gonadotropin-releasing hormone (GnRH) work with Florida pompano is more transfer of technology than research, this technology is decades old

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

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 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

• 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

Review Team Rating: Medium Quality, Low/Med Relevance, Medium Impact

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

Problem Area IVC – Sustainable Sources of Nutrients

Problem Area IVD – Nutrient Use and Feed Evaluation

• 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

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

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

Problem Area IVG – Effective Probiotics

Review Team Rating: Unable to rate quality due to lack of information, Medium Relevance, Low Impact

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 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

• 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

• Many achievements were through development of management practices rather than new technology. However, the outcome will be a more competitive aquaculture production system

Problem Area VB – Production Intensity

Review Team Rating: Med/High Quality, High Relevance, Medium Impact

• 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

•Improved tank based aquaculture technology has been achieved.

Problem Area VB – Production Intensity (Cont)

• No research to develop models of fish farming systems that could assist producers in decision-making

• No progress was made in this area

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

•Research assessed existing technologies, rather than developing new, improving existing, or adapting alternative techniques and technology

Problem Area VD – Predator and Fowl Control

Review Team Rating: Low Quality, High Relevance, Low Impact.

• The review panel also recommend strong collaboration with the USDA APHIS program as this is an area key to their mission

• Few farms in the direct project adopted management strategies or technologies to address the problem

• The goal of assessing the population of fish-eating birds was accomplished

• Focused almost exclusively on pond harvesting technology

Problem Area VE – Live Aquatic Animal Handling, Transport, and Inventory

• 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

• Most efforts reported cut across broad categories of technology development. The common thread appears to be developing components and systems for low-salinity aquaculture

Problem Area VF – Culture of Marine Species in Low-Salinity Water

Review Team Rating: Medium Quality, Medium Relevance, Emerging/Medium Impact

• 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

Some redundancy with other components 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

• Most work was covered in Component IV

• 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

Problem Area VIB – Water Use and Reuse

Review Team Rating: Medium Quality, High Relevance, Medium Impact

• 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

• 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

Problem Area VIC – Effluent Management Control

Review Team Rating: Medium Quality, High Relevance, Medium/High Impact

• No documented monitoring projects were found

• No documented progress

• The review team suggest that this problem area be rewritten with researchable objectives

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

•Little progress was made

Problem Area VIE – Environmental Sustainability

•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 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

Goal 1: All objectives with regard to catfish and shrimp addressed

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

• Harvesting and Transport Environmental Effects on Meat Quality Elucidated in Catfish

Problem Area VIIA – Tissue Quality (Cont)

• 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

• 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

Problem Area VIIB – Interaction of Genetics and Nutrition

• The Review team recommends to integrate this topic under Nutrition (Component IV) or Genomics (Component II)

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

Review Team Rating: Medium Quality, High Relevance, Low Impact

Problem Area VIIC – Predicting Product Quality or Defects

• 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)

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)

Problem Area VIIE – Off-Flavor Methodology (6 Components)

Review Team Rating: High Quality, High Relevant, Low Impact

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

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

Problem Area VIIE – Off-Flavor Methodology (Cont)

Though overall the current results were disappointing, the project activities are worth pursuing

3. Off-flavor Methodologies Evaluated for Catfish Production

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

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

Problem Area VIIF – New Uses for Byproducts (10 Components)

Goal 1. Extensive publication record to support productive activity

Review Team Rating: High Quality, High Relevance, Medium Impact

Problem Area VIIG – Processing

• No documentation provided for this section

Review Team Rating: No Quality rating due to lack of information, High Relevance, no Impact rating due to lack of information.

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 AssessmentNational 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

Retrospective AssessmentNational Program 106 – Aquaculture

General Recommendations

USDA ARS Aquaculture Review of Program Program Capabilities and Accomplishments

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