USDA ARS Aquaculture Review of Program

1. USDA ARS AquacultureReview of Program Program Capabilities and Accomplishments

2. 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

3. 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

4. ARS Aquaculture Locations

5. 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

6. ARS Aquaculture Locations

7. 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

8. 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

9. 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

10. Retrospective AssessmentNational Program 106 - Aquaculture F.S. ConteSt. Louis, MO 04-15-08

11. 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 A&M University Tom Losordo University or North Carolina Jim Parsons Trout Lodge, Inc Terry Tiersch Louisiana State University Jim Winton U.S. Geological Survey

12. 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

13. 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.

14. 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?

15. 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

16. 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?

17. Genetic Improvement

18. 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

19. 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

20. 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)

21. 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

22. 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

23. 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.

24. Flavobacterium psychrophilum genome sequence Host Pathogen Environment Integrated Aquatic Animal Health

25. F TNFSF 10 A TNFSF New * TNFSF 18 * TNFSF 8 TNFSF 11 TNFSF 4 96 * 100 100 57 91 99 100 TNFSF 13b 100 100 99 100 100 100 100 100 100 61 TNFSF 5 100 100 99 86 100 B 72 100 100 77 100 * 100 100 TNFSF 13c 99 98 94 99 88 * 100 98 100 75 100 E 100 TNFSF 6 74 99 100 100 95 91 57 99 79 100 * 100 88 100 100 TNFSF 13 93 100 98 C 100 56 100 100 62 100 59 98 100 79 Ectodysplasin 100 100 99 100 99 100 100 100 99 100 98 * TNFSF 9 98 100 100 * 100 100 TNFSF 14 85 99 TNFSF 12 TNFSF 3 TNFSF 7 TNFSF 15 TNFSF 1 TNFSF 2 D 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

26. 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

27. 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

28. 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

29. 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

30. 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

31. 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?

32. 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

33. 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

34. 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

35. 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

36. 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

37. 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 & 2are 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

38. Growth, Development and Nutrition

39. 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

40. 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

41. 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

42. 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

43. 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

44. 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

45. 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

46. Aquaculture Production Systems

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

48. 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

49. 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

50. 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