Use of Biotechnology to Improve Aquaculture

Steven Kappes

USDA-ARS

SMK@ars.usda.gov

Introduction

The consumption of aquaculture species continues to steadily increase in the United States and to meet this growing demand the U.S. imports most of its seafood products. Natural aquatic populations cannot produce sufficient quantities to meet future needs and therefore farming aquaculture species is becoming essential to meet consumer demands. Considerable progress has been made in improving livestock and poultry production systems in the last 100 years and it is likely that the same large potential exists to increase production efficiency and enhance product quality and consistency in aquaculture species. Research is desperately needed to improve production traits such as growth rate, feed efficiency, and product quality, and reduce disease susceptibility and the environmental impact of production systems. This will require research efforts in reproduction, nutrition, genetics, growth and development, immunology, water quality, and production systems.

Recent advances in biotechnology have provided scientists with many new research tools to improve agriculture systems. Biotechnology has been many times defined as new technology that is used to study genomes but biotechnology has also been developed to study proteins and many other aspects of biology. A successful research program that uses biotechnology to solve industry problems must also have a strong research program in the traditional disciplines because biotechnology is only a set of research tools that are used to address research problem areas. A multi-discipline team of researchers is needed for the major finfish, crustaceans, and mollusks species to fully realize the potential of biotechnology tools and understand the biology of the important production traits.

Genomics Research

A critical component of a highly profitable production system is the use of a specific germplasm that has been selected for high performance for certain production traits in a range of environments and under certain management systems. Very little selection has been used to improve aquaculture germplasm to date and therefore a large amount of genetic diversity is available to improve production, health, and meat traits. Genomics research is a tool to identify the genetic components of these traits but a quantitative genetics program is a prerequisite that is needed to quantify the genetic contribution to the total variation observed for a trait. Genetic selection programs based on phenotypic records not only provide the quantitative information (estimates of heritability) but also can be used for genomic research to identify genes that influence the traits of interest.

Many laboratory resources are needed to efficiently identify genes that influence traits of interest. One of the first resources needed is a road map (linkage map) of each chromosome. DNA markers are developed and ordered on each chromosome to make a linkage map. A number of types of DNA markers can be used to make a linkage map but the newest type of marker is called a Single Nucleotide Polymorphism (SNP). A linkage map needs to consist of 1000 or more DNA markers to make it useful in different populations since not every marker is informative in every family.

The second objective is to use the DNA markers to identify a chromosomal region that contains a gene(s) that influences a trait. DNA markers flanking a region containing the gene can be used to select animals (Marker Assisted Selection) that are genetically superior for that gene. Usually researchers will attempt to find the gene within the chromosomal region to improve the Marker Assisted Selection process and eventually determine the physiological and biochemical processes that control the expression of the trait. Determining the processes that influence a trait will be useful for developing pharmaceutical products that will enhance production efficiency, health status, or product quality and consistency.

Additional resources needed to efficiently identify genes are short gene sequences (Expressed Sequenced Tags), physical maps, and eventually the sequence of the genome. The ESTs can be used to compare sequences across species to build a comparative map. A comparative map allows the use of mapping information from a related species that has a well developed map (Zebra fish) to determine the relative map location of genes in a species with little mapping information. EST sequences are also used to determine when genes are active and the level of activity. Physical maps are used to determine DNA marker and gene order and some types of physical maps can be used for sequencing portions of the genome. Sequencing the genome is the ultimate physical and comparative map and should be the long-term objective for each agriculturally important species.

The process to identify genes affecting traits requires scientists from many disciplines (quantitative genetics, molecular genetics, immunology, nutrition, reproduction, and growth and development) to work together. Phenotypic and genotypic information needs to be collected on a large number (several hundred to a thousand) of animals. This effort and a DNA sequencing effort require an information management system to be developed. Bioinformatic tools also need to be developed to analyze and interpret the DNA sequence information. Scientists trained in computer science, data management and bioinformatics need to be part of the multi-discipline, genomics team.

Genomics research that will improve aquaculture production systems must also include microbial genomics research efforts. Sequencing a microbial genome has become a very common practice because the size of the genome is quite small. Over 100 microbial genomes are getting sequenced and 30 genomes have already been fully sequenced. These genome sequences have already provided many insights to the scientists on how the microbe functions. Microbial genomics with be a valuable tool for improving animal health, food safety, and production efficiency by sequencing harmful and beneficial microbes.

Functional Genomics

Genomics research is only valuable if genomic information can be tied to the biology of the organism to provide solutions to industry problems. Proteomics or functional genomics are terms used to describe the tools to study proteins and determine the function of each protein. Some of the research tools needed to study proteins in a high-through put process are still being developed. The cost of proteomics will be a magnitude higher that genomics research. Recent reports estimate that the human genome only has 30,000 to 40,000 genes but the estimated number of proteins that are generated from these genes are much higher and the proteins can be modified into several different forms.

Education and Training

There is a shortage of people trained in genomics to fill the many open genomics positions in agriculture. Agribusinesses have been hiring most of the recent graduates and many times the professor that was training them. Many genomic startup, non-agriculture companies have also been hiring students with agriculture interests. Individuals trained in computer science and bioinformatics are more difficult to find. An essential component of a successful biotechnology research effort in aquaculture will be an intensive training program.

Conclusion

There is tremendous potential for improving aquaculture production systems to meet future consumer needs with a safe and satisfying product and the use of biotechnology will increase the potential and allow the industry to realize these benefits in less time.