Background

There has been limited genetic improvement of aquaculture stocks so there are major opportunities for improvement through traditional animal breeding, broodstock development, germplasm preservation, molecular genetics, and allied technologies.  Research will address improvement of growth rates, feed efficiency, survival, disease resistance, fecundity, yield, and product quality; genetic characterization and gene mapping; and conservation and utilization of important aquatic germplasm.

Vision

Genetically efficient, sustainable, and humane production of food from aquatic organisms will be the goal.

Mission

Accelerate genetic improvement of aquatic species leading to more efficient and profitable production of healthy, nutritious and palatable aquatic products.

Impact

Reduced production costs and losses for farmers, creation and maintenance of globally competitive aquatic products in diverse production environments, increasing consumer choice and reducing consumer costs.

Linkages

USDA-ARS National Programs: 101 Food Animal Production; 103 Animal Health; 105 Animal Well-Being and Stress Control Systems; 107 Human Nutrition; USDA, ARS National Animal Germplasm Repository (NAGP)

Other Agencies and Departments: U.S. Colleges of Agriculture and State Agricultural Experiment Stations, U.S. Fish and Wildlife Service, U.S. Geological Survey

Private Sector: U.S. Aquaculture and Grower Associations, U.S. Aquatic Animal Farmers

Problems to be addressed

a.  Conserve, characterize, and utilize genetic resources

U.S. aquaculture production occurs in a wide array of environments and management systems.  The efficiency of livestock and poultry production has dramatically improved due to advances in genetic selection programs; however, genetic improvement of cultured aquatic species has lagged behind traditional livestock species.  Maintaining genetic diversity will be essential for providing a diverse genetic basis for current and future breeding programs that will develop stocks with efficient performance in different climates and production systems, when exposed to new diseases, and provide quality products that meet the changing demands of consumers.  As breeding programs develop and progress, research is needed to determine physical and genetic characteristics of domestic and wild species, develop the means to identify and protect improved stocks from foreign encroachment, and conserve valuable germplasm.  DNA of relevant germplasm will be stored and provided to researchers for genomic characterization and analysis.  The National Animal Germplasm Program will assist in conservation efforts for future use, and the information will be stored in the animal component of the GRIN (Genetic Resources Information Network) database.

Goals

1.      Isolate and maintain genetic resources (sperm and eggs, DNA, tissue and genomic information) in a repository for potential use by industry and research.

2.      Quantify genetic variation and genetic distance between and within strains of aquaculture species.

3.      Identify phenotypic and molecular differences between stocks and species, which will be used to characterize and develop markers for unique traits or characteristics identified or developed within the U.S.

Approach

1.      Sample and characterize current stock resources by quantitative genetic analysis and molecular experimentation.

2.      Survey genetic resources of the different available species and strains and assess their potential for development.

3.      Identify distinct morphology or DNA sequences specific to developed stocks or traits and use these to establish rights for the protection of germplasm and stocks.

4.      Evaluate species and strains for economically relevant traits including disease resistance, environmental tolerance, and adaptation to production systems.

Outcomes

• Quantify the status of the nation’s available aquatic genetic resources. 
• Enhance and improve the development of strains and stocks for commercial production. 
• Protect and conserve developed strains. 
• Recommend to industry how to utilize diverse genetic resources in different production systems and environments and maintain genetic diversity.

ARS Locations

• Stoneville, MS 
• Leetown, WV 
• Stuttgart, AR 
• Newport, OR 
• Orono/Franklin, ME

b.  Selective breeding for economically important traits

Improving biological efficiency and reducing production losses is achieved through selective breeding.  There has been limited improvement of aquaculture stocks so major opportunities exist to improve methods of genetic evaluation, genetic characterization, and understanding of genotype by environment interactions of economically important traits.  Applied breeding programs for aquatic species are critically needed to accelerate selection response toward efficient and profitable production of healthy, nutritious, and palatable aquatic products and improve the health and well-being through enhanced adaption to different production environments and with greater resistance to disease.

Goals

1.      Clearly define target species and economically important traits for genetic improvement of aquaculture stocks.

2.      Initiate applied breeding programs for genetic improvement and evaluation of aquaculture stocks in multiple environments.

3.      Identify genes controlling relevant traits and the genetic correlations of economically important traits.

4.      Increase biological efficiency through selective breeding.

Approach

1.      Analysis of farm level production problems and consumer needs to identify selection goals for genetic improvement.

2.      Develop methodologies that are useful across multiple environments for collecting performance information on genetic groups of aquatic species.

3.      Define the quantitative and molecular genetic relationships among traits.

4.      Assess direct and correlated responses to selection.

5.      Evaluate and implement as needed multiple methods for genetic improvement such as selection, crossbreeding, and hybridization in breeding programs.

Outcomes

• Relative economic values for traits of importance in aquaculture stocks will be identified. 
• Improved systems for regional and national evaluations of aquaculture stocks. 
• Technologies for accelerating genetic improvement in efficiency and profitability will be delivered to aquaculture producers. 
• Deliver genetically improved lines or broodstocks to producers and consumers.

ARS Locations

• Stoneville, MS 
• Leetown, WV 
• Newport, OR 
• Stuttgart, AR 
• Orono/Franklin, ME

c.  Genomic resources

Animal genomics will play an increasingly important role in assuring the continued profitability and competitiveness of U.S. agriculture.  Advances in the field of genomics are rapidly being implemented in strategies aimed at the genetic improvement of all agricultural species.  The United States aquaculture industry is an important segment of U.S. agriculture, yet genomic resources are currently underdeveloped for most aquaculture species.  Identifying, mapping, and understanding the function and control of genes will permit the utilization of new genetic technologies and increase our ability to realize the full genetic potential of important aquaculture species.  Efficient use of genomic technologies will also require the development of specific molecular genetic resources for each species of interest.  Genomic information will be integrated with genetic selection programs to increase genetic gains, develop new products for aquaculture production, and provide new management tools to increase production efficiency.

Goals

1.   Obtain suitable high-density genetic linkage maps for aquaculture species.

2.   Initiate physical maps for aquaculture species; yielding integrated physical/genetic maps that serve as comprehensive maps for comparative mapping with whole genome sequences of model organisms. 

3.   Develop genomic resources (molecular markers) for integrating functional genomics into existing aquaculture research programs.

Approach

1.   Develop and map microsatellite and single nucleotide polymorphisms in well-characterized reference populations.

2.   Develop bacterial artificial chromosome physical (contig) maps for aquaculture species that integrate with the genetic linkage maps through common markers.

3.   Develop tissue specific cDNA libraries and sequences for inclusion in the construction of microarrays and other functional genomic technologies.

4.   Correlate phenotypic information with genetic markers in resource populations to identify quantitative trait loci for use in breeding programs.

5.   Utilize novel molecular genetic techniques (knockouts or insertions) or organisms to investigate the biological activity of specific genes and proteins for commercially important traits.

Outcomes

• Microsatellite/single nucleotide polymorphism genetic linkage maps with sufficient marker coverage to choose subsets of markers for the identification of quantitative traits in resource families.  
• Physical bacterial artificial chromosome maps anchored to genetic linkage maps, with integrated comprehensive maps serving as comparative maps with whole genome sequences of model species. 
• Uniquely expressed transcripts and microarrays containing subsets of those transcripts for functional genomic experiments will be identified. 
• Biochemical pathways and their modulation through controlled manipulation of genes will be defined.

ARS Locations

• Stoneville, MS 
• Leetown, WV 
• Orono/Franklin, ME

d.  Specific breeding aids

In addition to traditional selective breeding methodologies, specific breeding aids can be used to further genetic progress following application to breeding programs.  Specific breeding aids typically focus on chromosome set manipulations to alter phenotypes (sex), produce inbred lines, and impact reproduction.  Control of reproduction is also a critical limitation for most aquaculture species.  There are problems related to enabling reproduction in hard to spawn species and throughout the year in seasonal spawners, and conversely to limiting reproduction in animals at risk of escaping to the wild.  Cryopreservation of gametes and embryos is also a critical need for both germplasm conservation and applied breeding programs.  Cryopreservation may allow year round availability of gametes and permit crosses between animals that do not spawn contemporaneously.

Goals

1.      Induce spawning in hard to reproduce species.

2.      Enable year-round production of gametes.

3.      Limit reproduction and control sex (e.g. chromosome set manipulation, sex reversal)

4.      Suitable cryopreservation of gametes and embryos.

Approaches

1.      Identify neuroendocrine limitations preventing spawning.

2.      Identify and replicate environmental cues needed for spawning induction.

3.      Develop techniques of meiotic and mitotic disruption (polyploidy, androgenesis, gynogenesis) resulting in chromosome set manipulations, highly inbred lines, or other methods of disrupting sexual development, and methods for production of single sex populations. 

4.     Determine optimum cryoprotectants, and rates of freezing and thawing for gametes and embryos.

Outcomes

• Year round availability of seed for aquaculture animals will be accomplished. 
• Reduced risk associated with commercial culture near natural populations of aquatic species. 
• Unrestricted availability of gametes, especially sperm will be realized.

ARS Locations

• Stoneville, MS 
• Leetown, WV 
• Stuttgart, AR

e.  Bioinformatics and statistical analysis tools

Genomic and proteomic technologies used in breeding programs create large datasets that quickly outpace simple genetic analysis methods.  Bioinformatics tools are needed to assimilate and process information into functional components in breeding programs.  Statistical analysis software needs to be developed to interpret results from genomic/proteomic data and integrate this information into selective breeding programs.  Bioinformatics and statistical analysis tools specific for aquacultured species are poorly developed.  However, the types and format of molecular data from aquatic species are similar to those of other species.  Therefore researchers can integrate and optimize existing bioinformatics tools for aquaculture genomics and proteomics data.

Goals

1.      Relational databases containing genomic and physiological data.

2.      Computer software for analysis and application of molecular data.

Approach

1.      Develop relational databases to integrate molecular and physiological data.

2.      Integrate and optimize existing data analysis software.

3.      Develop software to facilitate comparative genomic analyses between species.

4.      Develop software for implementation of molecular data into genetic selection programs.

Outcome

• Genomic/proteomic information for aquaculture species and software for data management and application will be publicly available.

ARS Locations

• Stoneville, MS 
• Leetown, WV