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ARS Home » Southeast Area » Fort Pierce, Florida » U.S. Horticultural Research Laboratory » Subtropical Plant Pathology Research » Research » Research Project #436490

Research Project: Establishing Seedstocks for the U.S. Marine Finfish Industry

Location: Subtropical Plant Pathology Research

2020 Annual Report

The U.S. has tremendous capacity for meeting the domestic demand for seafood by expanding aquaculture in federal waters and land-based recirculating systems. As the largest importer of seafood products, expanding domestic production will reduce our reliance on imports and the trade deficit. This project will support the U.S. aquaculture industry by developing technologies that will ensure a steady supply of warm water marine fish seedstocks that are optimized for commercial production. 1. Develop year-round spawning strategies for captive broodstock and larviculture methods for seed production of marine finfish. 2. Develop methods for genetic improvement of warm water marine finfish for optimum production efficiency. 3. Increase understanding of fish physiology and enhance production efficiency through improved management strategies.

Aquaculture producers need access to seedstocks that are available year-round and optimized for the production environment. Research is needed to develop seedstocks that are bred for maximum production efficiency and have minimal impacts on the environment and native populations. Research in the disciplines of genetics, fish health, nutrition, reproductive biology, and physiology will contribute to the development of seedstocks that meet these criteria.

Progress Report
This report reflects the work done during the first year of a multi-year USDA-ARS collaborative research partnership with Florida Atlantic University’s Harbor Branch Oceanographic Institute. This project began during the second year of a standard USDA project planning cycle so there is no standard five-year plan. A five-year plan will be established “on cycle” after the first four years of the project. During these initial four years while the project is being ramped up, annually prioritized experimentation is being determined in consultation with industry stakeholders and USDA-ARS. During this first year we successfully completed reconditioning of the workspace in the campus building designated HB-36 in the Aquaculture Park at Harbor Branch Oceanographic Institute. This workspace will allow for office capacity to meet the needs of the USDA-ARS scientists and staff who will be assigned to the project in the coming years as the project continues to ramp up. This reconditioning occurred as per the lease agreement. Objective 1 Progress: Initial broodstocks of Florida pompano, including both hatchery reared and wild caught South Atlantic Coast Florida pompano, were established. An F1 hatchery stock of Florida West Coast Red Drum are on site at Harbor Branch Oceanographic Institute (HBOI). These broodstocks are currently being conditioned for spawning as the initial step to develop year-round spawning strategies for captive broodstock and larviculture methods for seed production of marine finfish. Establishing year-round spawning and efficient larviculture production will ensure steady supplies of warm water marine fish seedstocks to support commercial marine finfish production and growth of the industry. In support of Objective 1 and 3, HBOI scientists in collaboration with Proaquatix fish farm completed an experiment to understand the nutritional requirements of Florida pompano broodstock. The patterns of use and conservation of lipid components and other nutrients in eggs and larvae during early development were identified. This is an effective method to establish nutritional requirements of warm water marine fish broodstock. The results establish partial dietary lipid and protein requirements for improving spawning and the production of high quality eggs in Florida pompano. Further research on broodstock nutrient requirements and on-farm validation will provide feed manufacturers with the framework for producing high quality broodstock diets to support and contribute to the marine finfish value chain. Resulting diets will increase efficiency and profitability of marine finfish hatcheries. In support of Objectives 1 and 2, a quantitative PCR (qPCR) test was developed to target a common aquaculture parasite Amyloodinium ocellatum that causes skin disease in Florida Pompano. Outbreaks can lead to substantial fish losses and reduce product quality among consumers. Using environmental DNA (eDNA), this qPCR test will serve as a model for the development of additional eDNA monitoring techniques and enable rapid and early detection of disease before it spreads and leads to decreased production and economic losses. In direct support of Objective 2, a draft genome of the Florida pompano was sequenced and assembled using a hybrid sequencing and assembly method. This genetically important information will be used to develop a genetics-informed selective breeding program. It has been well demonstrated in terrestrial plants and terrestrial livestock that through selective breeding programs traits of interest such as increased growth rate, increased disease resistance, increased efficiency, and improved product quality lead to genetically improved strains that increase on-farm production and profits for farmers. Team members completed training in bioinformatics and utilization of cloud computing tools to facilitate further development of this genomic tool to support the selective breeding program.

1. Completion of a draft genome of Florida pompano. A hurdle in implementing a genetics-informed selective breeding program for many aquaculture species, particularly warm water marine finfish, is the lack of available genetic information. As with most warm water marine finfish, the whole genome of the Florida pompano had not previously been fully sequenced and assembled. Utilizing a hybrid sequencing method and a novel bioinformatics workflow, a complete draft genome of the Florida pompano was established by researchers at Ft. Pierce, Florida. This draft genome will allow ongoing research to identify genes associated with traits of interest in aquaculture, such as increased growth rate, increased disease resistance, and decreased inbreeding. Such traits, along with others can be actively selected for in a breeding program. Implementing a genetics-based selective breeding program allows for development of genetically improved strains of Florida pompano leading to enhanced on-farm production and greater profits for farmers.

2. Nutritional requirements of Florida pompano broodstock. The lack of optimal diets for broodstock (especially during the spawning season) continues to present an obstacle to commercial production and industry growth. Broodstock nutritional status is a powerful determinant of egg quality and successful development of both eggs and larvae. Quality broodstock diets increase reproductive success and seedstock quality increasing hatchery success, on-farm efficiencies, and farmer profitability. Understanding the nutritional status of the females during spawning overcomes this obstacle. Comprehensive and quantitative lipid analysis (lipidomics) were employed by researchers at Ft. Pierce, Florida, to determine different egg and larval lipid compositions. This baseline dataset was developed to characterize quantitative and qualitative lipid requirements for both larval development and successful reproduction of Florida pompano. Hatchery managers and marine finfish producers will benefit from efficiencies associated with meeting optimum nutritional needs for reproduction and successful seedstock production.

3. Development of a rapid disease diagnostic tool for marine fish. A principal challenge to the marine finfish aquaculture industry is the inability to detect disease outbreaks and administer an appropriate remedy in a timely manner. Identifying the presence of disease causing organisms prior to a systemic outbreak increases the potential for limiting costly mortality events. Environmental DNA (eDNA) is a noninvasive and highly accurate method for capturing the footprint of an array of disease-causing organisms at very low concentrations. Researchers at Ft. Pierce, Florida, developed a sensitive and specific quantitative PCR (qPCR) test that can detect a single copy of a genetic marker associated with the disease causing organism Amyloodinium ocellatum from the culture water, giving rapid and accurate same-day results. This qPCR test, currently undergoing validation, will provide a much needed “toolbox” for routine health monitoring and disease diagnostics on commercial aquaculture farms.