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Resilient Coastal Communities and Economies

Description:

Topic 8.1: Resilient Coastal Communities and Economies

Subtopic 8.1.1F Improving Outcomes of Marine Aquaculture via Genomic Approaches

Summary: In comparison to human medicine or land based agriculture, the genomic basis for improving marine aquaculture breeding outcomes is in its infancy. Most aquaculture facilities rely on batch spawning and trial and error. There is little chance of identifying individual parents and the specific genetic traits that provide eggs and larvae with superior qualities of growth, feed conversion and disease resistance. The sequencing of the human genome took 10 years and 3 billion dollars. The cost of genome sequencing has declined to <10 days and < 1,000 per human genome. Perhaps more important non-model genomes such as abalone, yellowtail (Seriola sp.) bluefin tuna, and rock scallop can be developed based on linkages to data bases from better studied biomedical model organisms such as the zebrafish. NOAA resource managers and the aquaculture industry seeks assistance in developing high-throughput, low cost methods to conduct pedigree analyses, and to identify and routinely screen for functional genes associated with favorable growth characteristics and genes associated with disease sensitivity and resistance.

Project Goals: Genetic trait selection is an integral part of land based agriculture and has revolutionized the production of corn, rice and soybeans. Atlantic salmon is the only marine species to undergo extensive selective breeding. Concerns over escapement from offshore farms, the need to recover endangered species via hatchery rearing, as well as consumer preference, dictates that the domestication of newer aquaculture species such as yellowtail and the stock enhancement of natural populations of depleted abalone must rely on a full understanding and the retention of mostly wild genetic characters, but it must also weed out the inferior spawning stock with each broodstock collection and spawning event. Assistance from the private biotech community is critical to developing rapid, cost-effective screening procedures designed for pedigree analysis, genomic trait selection to improve outcomes of aquaculture, and monitor the success of out-planting as a means of wild stock recovery. While the ultimate goal might be commercial biotech kits that could be sold to hatchery managers (similar to a modern pregnancy kit), the immediate and perhaps longer term economic model would be to provide a continuing fee-for-service business to support hatchery managers.

Phase I Activities and Expected Deliverables:

Activities Include:

  • Identification of a family of single nucleotide polymorphisms (SNPs), to allow parent-offspring and kinship analyses in a candidate aquaculture species among the tuna family (Scombridae), jack family (Carangidae), the drum and croaker family (Sciaenidae), or the abalone genus (Haliotis). This could include Pacific bluefin tuna, yellowtail jack, white seabass, or red abalone.
  • Genetic screening of existing data bases for identification of trait-associated genes in a candidate aquaculture species among the tuna family (Scombridae), jack family (Carangidae), the drum and croaker family (Sciaenidae) or the abalone genus (Haliotis). This could include Pacific bluefin tuna, yellowtail jack, white seabass or red abalone.

Deliverables include:

  • A next-generation SNP assay or similar approach to identify parent-offspring relationships that is not dependent on conventional micro-satellite or sequence based approaches.
  • A roadmap to the development of a high-throughput, low cost automated assay of parent-offspring relationships in a hatchery environment.
  • A roadmap to the development of a SNP chip or similar approach to allow rapid and low cost screening for hatchery managers for favorable and unfavorable genetic traits.

Phase II Activities and Expected Deliverables:

Activities Include:

  • Development and testing of a market ready technique for high-throughput, automated screening of parent stock and eggs for paternity analysis
  • Development and testing of a prototype chip for screening polymorphic genes associated with desirable and undesirable traits in an aquaculture setting. Design should be flexible to allow the addition of new markers as our understanding of the underlying genomes improves.

Deliverables include:

  • Market ready technique for high-throughput, automated screening of parent stock and eggs for paternity analysis
  • Prototype chip for screening polymorphic genes associated with desirable and undesirable traits in an aquaculture setting. Prototype should be designed to be flexible to allow the addition of new markers as our understanding of the underlying functional genomes improves.

NOTE: Even though a prototype may be required to be delivered for the project, it is important to note that this prototype is still the property of the offeror. NOAA would only do field or lab testing on that product to see its feasibility in a production (or development) environment.

 

Subtopic 8.1.2F Developing Technologies for Offshore Aquaculture in The United States

Summary: Offshore aquaculture refers to aquaculture in the waters between state maritime boundaries and the end of the Exclusive Economic Zone (EEZ). Offshore aquaculture has the potential to complement wild harvest fisheries, increase our domestic supply of safe, healthy seafood and contribute to resilient coastal communities and economies. There is huge opportunity for offshore aquaculture development in the United States. The U.S. EEZ is the largest in the world, spanning a wide range of ocean conditions and habitats. Less than 0.01% of the U.S. EEZ could potentially produce up to 600,000 metric tons or more per year of an equally wide range of farmed aquatic species. Dozens of commercial operations around the world currently use offshore aquaculture technologies, and U.S. companies, investors, and farmers have participated in this global aquaculture industry by exporting technology, equipment, seedstock, services, investment and feed. With the development and impending implementation of the Fishery Management Plan for Regulating Offshore Aquaculture in the Gulf of Mexico, the United States is poised to grow its domestic offshore aquaculture industry. With this growth will come new challenges to working in remote, offshore environments, and a range of technologies will be needed to address logistical and environmental issues. Proposals are requested for research towards innovative products and services to specifically develop offshore aquaculture capabilities for finfish, shellfish, or seaweeds. Priority is given to research that addresses technology bottlenecks to developing domestic offshore aquaculture operations and in turn increase our sustainable seafood supply, protect our ocean resources, and create economic opportunities for coastal communities.

Project Goals: New technologies, products and methods are needed to address challenges in developing offshore aquaculture for finfish, shellfish, and seaweeds. Projects that would support production improvements can include but are not limited to: technologies, methods or products that address offshore farming technologies , preventing risks from escapes (such as sterile stock), development of tools for management, remote and/or real-time monitoring, transportation, facility maintenance, and harvest, feeds for offshore culture, preventing disease transfer, and hatchery technology. Priority will be given to proposals that specifically target and address issues associated with offshore aquaculture and the unique challenges it presents.

Phase I Activities and Expected Deliverables:

Activities Include:

  • Develop high probability solutions to key bottleneck issues.
  • Execute research and development of techniques and management measures to address these bottlenecks.
  • Explore commercialization opportunities (preliminary business planning)

Deliverables include:

  • Proof of concept at the lab or bench scale
  • Refinement of products or solutions
  • Commercialization plan with permit requirements, preliminary enterprise budgets and business plan
  • Technical Report showing commercial application of developed technology/technique and research results.

Phase II Activities and Expected Deliverables:

Activities Include:

  • Prototype or pilot scale trials of the techniques and products developed in Phase I.
  • Further refinement and/or expansion of product or solutions
  • Refinement of profit/loss models, enterprise budgets and business plan

Deliverables include:

  • Detailed report on developed technology/technique showing biological, legal and economic feasibility under commercial conditions

NOTE: Even though a prototype may be required to be delivered for the project, it is important to note that this prototype is still the property of the offeror. NOAA would only do field or lab testing on that product to see its feasibility in a production (or development) environment

References:

  • Overcoming Technical Barriers to the Sustainable Development of Competitive Marine Aquaculture in the United States (2008) http://www.nmfs.noaa.gov/aquaculture/docs/aquaculture_docs/noaanist_techbarriers_final.pdf
  • NOAA Marine Aquaculture Policy (2011) http://www.nmfs.noaa.gov/aquaculture/docs/policy/noaa_aquaculture_policy_2011.pdf
  • Department of Commerce Aquaculture Policy (2011) http://www.nmfs.noaa.gov/aquaculture/docs/policy/doc_aquaculture_policy_2011.pdf

 

Subtopic 8.1.3F Orthogonal Stereo Camera System for Visual Fish Surveys

Summary: NOAA Fisheries is mandated to provide the best scientific information available to establish conservation and management measures for the sustainability of our Nation’s living marine resources and healthy oceans. One national priority relevant to this mission is the need resolve data-limited fish assessments. Many of the data-limited assessments result directly from the inability to effectively sample rocky and reef habitats. The scientific community has relied on camera systems deployed along the bottom to provide counts and measures for assessments. One research approach is the accurate synchronization of paired stereo cameras which provide the counts and precise length measurements of fish during camera surveys. Another research approach is the use of multiple synchronized pair stereo cameras where their view fields are orthogonally arranged and stitched to provide a 360 degree horizontal view to eliminate double counting targets while providing accurate length measures (to 0.5 cm accuracy). Research has demonstrated that the use of paired stereo cameras with sufficient accuracy in “synchronization” and “stitched view fields” have significantly improved abundance estimates for assessments; however to date, commercially available stereo camera systems lack the accuracy in “synchronization” and “stitched view fields” for scientific data collections. There is consensus (and market) among fisheries scientists within the agency and among the international scientific community regarding a need for an off-the-shelf (easy to use turn-key) orthogonal stereo camera system with accurate “synchronization” and “stitched view field” capabilities that could be widely deployed to improve visual fish survey operations to resolve data-limited stock assessments in difficult to sample reef and rocky habitats.

Project Goals: An orthogonal stereo camera system needs to be designed and commercialized to provide accurate “synchronization” and “stitched view fields” among multiple stereo cameras to enable accurate counting and measuring (length to within 0.5 cm) of fish during scientific underwater visual surveys. Researchers have investigated the applicability of using accurately synchronized stereo cameras for measuring fish length and recommend arranging multiple pairs of synchronized stereo cameras orthogonally and horizontally to stitch the stereo view fields together to provide a horizontal 360 degree sampling field will prevent double counting of fish. Although there are underwater stereo cameras and spherical cameras that are commercially available, there are no commercial products that provide sufficiently accurate “stereo camera synchronization” and accurate “stitching between multiple synchronized stereo cameras” that can be utilized for visual fish surveys providing precise fish length measurements to the nearest 0.5 cm. There is a need to develop and commercialize an orthogonal stereo camera system with these features that is easily to deploy and use, including clear protocols for its calibration, operation, and performance metrics. Another system feature that researchers have investigated is an optional fish detection trigger (through active acoustic and/or far-field infrared detection) which minimizes data collect for only detected targets having applicability for prolonged deployments. Although this is not a requirement for this SBIR, it is important to recognize this might be an optional feature that is desired by the scientific community. There is sufficient research published to guide the specifications of developing and commercializing a standardized low-cost stereo camera system with these requirements that will be widely used for visual fish surveys both domestically and internationally. This orthogonal stereo camera system will wide international applicability for the data-limited regions that require stakeholder engagement, therefore its operation must be relatively simple and reliable. The goal of commercializing this portable underwater stereo camera system is to provide a low cost and reliable tool that will be widely deployed in standardized visual fish surveys to resolve data-limited stock assessments. There is a need to commercialize an orthogonal stereo camera system for visual fish surveys to accurately identify, count, measure fish per unit sampling volume. Underwater stereo cameras have recently become available as commercial products; however none of these existing products are designed with accurate “synchronization of stereo cameras” and accurate “stitching of view fields of multiple stereo camera units” for providing accurate fish length measures (to the nearest 0.5 cm) from scientific visual fish surveys. Therefore, the NOAA mission and the wider scientific community would benefit from the development and commercial availability of an orthogonal stereo camera system with accurate “synchronization” and “view field stitching” that can be deployed for visual fish surveys.

An orthogonal stereo camera system with accurate “synchronization between stereo cameras” and accurate “stitching of stereo camera view fields” to count fish and accurately measure fish length to the nearest 0.5 cm within a 360 degree horizontal view around the system to be deployed on the seafloor (to depths of 500 meters) during visual fish surveys. This orthogonal stereo camera arrangement should have the ability to capture high definition (HD) video (at least 1080p at 30 f/s) or capture HD still images (at least 6 megapixels) to count, identify, and accurately measure fish (accuracy within 0.5 cm) in the 360 degree sampling volume around the system with the intent of reducing double counting of fish. Camera must have minimal lens distortion to obtain accurate fish length measurements using stereo camera imaging. The cameras must have low light sensitivity (at least 0.2 lux @ f 1.4). An optional feature that enables a fish detection trigger is desirable to capture digital fish images. The system could include an optional feature of synchronized lighting or strobed modules synchronized to the stereo camera units for capturing digital fish images at night or low light conditions. The system should be relatively user-friendly turn-key operation with clear operational instructions. Software needed for calibration of stereo camera modules and lens distortion compensation to achieve accurate and precise fish length measurements to the nearest 0.5 cm within the sampling volume at various angles of fish orientation. Software interface for accurate synchronization, operation data collection and data storage. Software is needed for data export with metadata and post processing (i.e., stitching sampling fields of the orthogonal stereo cameras, fish counts and length measurements). The system must contain sufficient data storage capacity for continuous HD video recording for duration of 2 hours with data downloading capability.

Phase I Activities and Expected Deliverables:

Activities include:

  • Explore the feasibility in building out an orthogonal stereo camera for visual fish surveys to accurately identify, count, measure fish per unit sample volume.
  • Provide proof of concept in ensuring the stereo cameras (either two or more) is synchronized.

Deliverables include:

  • Progress Reports and Detailed Final Report as outlined in solicitation
  • Provide design and technical report for (and any white papers associated with) the camera
  • Provide prototype buildout specification and blueprint for camera, ensuring the details outlined above is taken into consideration.

Phase II Activities and Expected Deliverables:

Activities include:

  • Prototype or pilot scale trials of the techniques and products developed in Phase I.
  • Further refinement and/or expansion of product or solutions
  • Refinement of profit/loss models, enterprise budgets and business plan

Deliverables include:

  • Progress Reports and Detailed Final Report on developed technology/technique of the low cost stereo camera system for visual fish surveys showing the accuracy, precise, and reliability of measures, and the economic feasibility under commercial conditions

NOTE: Even though a prototype may be required to be delivered for the project, it is important to note that this prototype is still the property of the offeror. NOAA would only do field or lab testing on that product to see its feasibility in a production (or development) environment

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