Aquaculture Biotechnology E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Fachliteratur
• Sprache: Englisch

Seitenzahl: 930

Veröffentlichungsjahr: 2011

Beschreibung

This important book looks at a broad spectrum of biotech research efforts and their applications to the aquaculture industry. Aquaculture Biotechnology provides key reviews that look at the application of genetic, cellular, and molecular technologies to enable fish farmers to produce a more abundant, resilient, and healthier supply of seafood. Aquaculture Biotechnology is divided into seven sections and nineteen chapters that cover topics ranging from broodstock improvement to fish health and gene transfer. With chapters provided by leading researchers and skillfully edited by top scientists in the field, this will be a valuable tool to researchers, producers, and students interested in better understanding this dynamic field of aquaculture.

Leseprobe

Contents

Cover

Title Page

Copyright

Dedication

Preface

Contributors

Part 1: Broodstock Improvement

Chapter 1: Genomic Tools for Understanding the Molecular Basis of Production-Relevant Traits in Finfish

OVERVIEW

TARGETED, TRAIT-RELEVANT GENE DISCOVERY

THE APPLICATION OF MICROARRAY TECHNOLOGY IN FINFISH AQUACULTURE AND RESEARCH

Chapter 2: Advances in Genomics and Genetics of Penaeid Shrimp

INTRODUCTION

EST COLLECTION AS AN APPROACH TO GENE DISCOVERY IN SHRIMP

MEDIUM- TO HIGH-THROUGHPUT STUDIES OF DIFFERENTIAL EXPRESSION AND GENE DISCOVERY

RNAi-BASED APPLICATIONS IN SHRIMP AQUACULTURE: FROM REVERSE GENETICS TO CONTROL OF DISEASES

MARKERS, GENETIC MAPS, AND LARGE INSERT GENOMIC LIBRARIES IN SHRIMP

ANALYTICAL CHALLENGES IN GENOMICS AND GENETICS OF SHRIMP

CONCLUDING REMARKS

ACKNOWLEDGMENTS

Chapter 3: Genetic and Genomic Approaches to Atlantic Halibut Broodstock Management

INTRODUCTION

PRODUCTION OF ALL-FEMALE STOCKS OF ATLANTIC HALIBUT

PEDIGREE ANALYSIS

HALIBUT GENETIC LINKAGE MAP

QUANTITATIVE TRAIT LOCI

BROODSTOCK SELECTION

FUTURE DIRECTIONS

ACKNOWLEDGEMENTS

Chapter 4: Prospects and Pitfalls of Clonal Fishes in the Postgenomic Era

BACKGROUND

CLONAL LINES: A REPEATABLE EXPERIMENTAL SYSTEM

GENETIC ANALYSES USING CLONE CROSSES

UTILIZATION OF DNA OR RNA FROM CLONES

CASE EXAMPLES OF POTENTIAL FOR UTILIZING CLONES IN AQUACULTURE-RELATED RESEARCH

CONCLUSION

Part 2: Molecular Cytogenetics

Chapter 5: Application of Fluorescence In Situ Hybridization (FISH) to Aquaculture-Related Research

INTRODUCTION

LOCALIZATION OF REPETITIVE SEQUENCES, TRANSPOSONS, AND TRANSGENES

IDENTIFICATION AND CHARACTERIZATION OF SEX CHROMOSOMES

CHARACTERIZATION OF INTERSPECIFIC HYBRIDS AND CHROMOSOME SET MANIPULATED FINFISH

ASSIGNMENT OF GENETIC LINKAGE GROUPS TO SPECIFIC CHROMOSOMES (GENOME MAPPING)

IDENTIFICATION OF PATHOGENS IN CULTURED SHELLFISH, FISH, AND WASTEWATER GENERATED BY AQUACULTURE

FUTURE APPLICATIONS

Part 3: Fish Health

Chapter 6: The Application of Genomics, Proteomics, and Metabolomics to Studies of Fish Health

INTRODUCTION

STUDIES OF PATHOGEN BIOLOGY

HOST–PATHOGEN INTERACTIONS

APPLICATIONS OF GENOMICS AND PROTEOMICS TO VACCINE DEVELOPMENT

CONCLUDING REMARKS

Chapter 7: Antimicrobial Peptides and Their Potential as Therapeutants in Aquaculture

OVERVIEW

PHYSICAL PROPERTIES OF ANTIMICROBIAL PEPTIDES

DISTRIBUTION OF ANTIMICROBIAL PEPTIDES

EXPRESSION OF ANTIMICROBIAL PEPTIDES

ACTIVITIES OF ANTIMICROBIAL PEPTIDES

THERAPEUTIC POTENTIAL OF ANTIMICROBIAL PEPTIDES

FUTURE DEVELOPMENTS

ACKNOWLEDGMENTS

Chapter 8: Adaptive Immunity in Finfish: A Physiological Perspective

INTRODUCTION

THE IMMUNE SYSTEM AS A WHOLE INTEGRATIVE DEFENCE MECHANISM

MH RECEPTORS

ANTIGEN PRESENTATION IN THE ADAPTIVE IMMUNE RESPONSE

MH SEQUENCES AND THEIR APPLICATIONS

CYTOKINES AND CHEMOKINES AS MEASURES OF IMMUNE RESPONSES

KNOWLEDGE OF FISH IMMUNITY AND WHAT IT MEANS FOR VACCINES

qPCR: A TECHNIQUE TO ASSESS ADAPTIVE IMMUNE RESPONSE

ENHANCING IMMUNE RESPONSES: IMMUNOSTIMULANTS

MONITORING OF HEALTH STATUS

IMPROVING BROODSTOCK AND BREEDING PRACTICES

THE FUTURE OF BIOTECHNOLOGY AND IMMUNOLOGY IN AQUACULTURE

SUMMARY

Part 4: Viral Pathogens and Diseases

Chapter 9: Structural Biology and Functional Genomics of the Shrimp White Spot Syndrome Virus and Singapore Grouper Iridovirus

INTRODUCTION

PROTEOMICS STUDIES ON WSSV AND SGIV

FUNCTIONAL ANALYSIS OF SGIV GENES USING MORPHOLINOS

STRUCTURAL CHARACTERIZATION OF NOVEL VIRAL PROTEINS

SUMMARY

ACKNOWLEDGMENTS

Chapter 10: DNA Vaccines for Viral Diseases of Farmed Fish and Shellfish

INTRODUCTION

DNA VACCINE DEVELOPMENT CRITERIA

VACCINE CANDIDATES

VACCINE FORMULATIONS

CYTOKINES AS ADJUVANTS FOR DNA VACCINES

DELIVERY METHODS

THE RESPONSE OF THE IMMUNIZED HOST

REGULATORY CONSTRAINTS

PUBLIC OPINION

Conclusions and Future Directions

Part 5: Embryogenesis and Stem Cells

Chapter 11: Egg Transcriptome, the Maternal Legacy to the Embryo

INTRODUCTION

MOLECULAR PORTRAIT OF THE FISH OOCYTE

ROLE OF MATERNAL mRNAS IN OOCYTE QUALITY AND EARLY EMBRYONIC DEVELOPMENT

CONCLUSION

Chapter 12: Application of Fish Stem Cell Technology to Aquaculture and Marine Biotechnology

INTRODUCTION

DERIVATION OF ZEBRAFISH ES CELL CULTURES

GENETIC MANIPULATION OF FISH ES CELL CULTURES

DERIVATION OF ZEBRAFISH PGC CULTURES

GERM-LINE CHIMERA PRODUCTION FROM ZEBRAFISH PGC CULTURES

APPLICATION OF STEM CELL TECHNOLOGY TO MARINE BIOTECHNOLOGY

ACKNOWLEDGMENTS

Chapter 13: Culture of Fish Head Kidney Mononuclear Phagocytes and Muscle Satellite Cells: Valuable Models for Aquaculture Biotechnology Research

INTRODUCTION

MONONUCLEAR PHAGOCYTES IN FISH

TROUT MUSCLE SATELLITE CELLS

Chapter 14: Germ Cell Transplantation in Fish: Basic Biology and Biotechnological Applications

INTRODUCTION

VASA GENE IS SPECIFICALLY EXPRESSED IN GERM CELLS

NEWLY HATCHED EMBRYOS ARE IMMUNOLOGICALLY IMMATURE

GERM CELLS CAN SEEK OUT THE GONADS AND MIGRATE TO THEM

TRANSDIFFERENTIATION OF SPERMATOGONIA FROM ADULT FISH INTO EGGS

TRIPLOID FISH ARE STERILE, BUT THEIR SOMATIC CELLS ARE NORMAL

CONCLUSION AND PERSPECTIVES

Part 6: Gene Transfer

Chapter 15: Spatial and Temporal Regulation of Transgene Expression in Fish

INTRODUCTION

TRANSGENIC FISH

PRIMARY TRANSGENIC ANIMALS AND ESTABLISHED TRANSGENIC LINES

TRANSPOSASE-MEDIATED TRANSGENESIS

LIMITATIONS IN TRANSGENESIS EFFICIENCY

REGULATION OF TRANSGENE EXPRESSION

IDENTIFICATION OF DNA REGULATORY ELEMENTS

HOMOLOGOUS AND HETEROLOGOUS REGULATORY SEQUENCES

INDUCIBLE GENE EXPRESSION SYSTEMS

CONCLUSION

Chapter 16: Antifreeze Protein Gene Transfer—Promises, Challenges, and Lessons from Nature

INTRODUCTION

THE DANGER POSED TO FISH BY LOW SEA WATER TEMPERATURES

ANTIFREEZE PROTEINS

WINTER FLOUNDER: A MODEL FOR ANTIFREEZE PROTEIN FREEZE RESISTANCE STRATEGIES

LOW TEMPERATURE LIMITATIONS TO SEA CAGE AQUACULTURE

ANTIFREEZE PROTEIN GENE TRANSFER; PROGRESS TO DATE

FUTURE DIRECTIONS IN THE PRODUCTION OF FREEZE-RESISTANT SALMON

SUMMARY AND CONCLUSIONS

Chapter 17: Potential Applications of Transgenic Fish to Environmental Monitoring and Toxicology

INTRODUCTION

SMALL FISH MODELS AS SENTINELS IN AQUATIC TOXICOLOGY: ZEBRAFISH AND MEDAKA

MODELS OF BIOMONITORING FISH

TOXICITY SCREENING OF COMPOUNDS USING FLUORESCENT TRANSGENIC EMBRYOS AND LARVAE

ADVANTAGES OF TRANSGENIC BIOMONITORING FISH

PERSPECTIVES

Chapter 18: Transgenic Tilapia for Xenotransplantation

INTRODUCTION

HISTORY OF THE TG FISH PROJECT (FUNDING AND PATENT ISSUES)

PRODUCTION OF TG TILAPIA

STATUS OF THE BREEDING PROGRAM

FUTURE IMPROVEMENTS TO TG TILAPIA

CONCLUSIONS

Chapter 19: The Potential of Enhancing Muscle Growth in Cultured Fish through the Inhibition of Members of the Transforming Growth Factor-β Superfamily

INTRODUCTION

MYOSTATIN DEFICIENCY AND INHIBITION

MYOSTATIN AND FISH

PRODUCTION OF TRANSGENIC TROUT OVEREXPRESSING FOLLISTATIN

FOLLISTATIN OVEREXPRESSION IN TROUT INFLUENCES MUSCLE GROWTH

DISCUSSION

ACKNOWLEDGMENTS

Part 7: Cryopreservation

Chapter 20: Fish Gamete and Embryo Cryopreservation: State of the Art

BASIC PRINCIPLES OF CELL CRYOPRESERVATION

GAMETE CRYOPRESERVATION

EMBRYO CRYOPRESERVATION

BLASTOMERE AND PRIMORDIAL GERM CELL CRYOPRESERVATION

APPLICATIONS

Part 8: Environmental Considerations

Chapter 21: The Potential Ecological and Genetic Impacts of Aquaculture Biotechnologies: Eco-Evolutionary Considerations for Managing the Blue Revolution

INTRODUCTION

GENETIC BACKGROUND

PHENOTYPIC EXPRESSION

DOMESTICATION SELECTION AND DIVERGENCE

EFFECTS IN NONNATIVE HABITATS

EFFECTS WITHIN NATIVE HABITATS

CASE STUDY OF SALMONID GROWTH ENHANCEMENT

CONCLUSION

ACKNOWLEDGMENTS

Part 9: Ethical Issues

Chapter 22: Aquaculture Ethics in the Biotechnology Century

INTRODUCTION

DOES AQUACULTURE BIOTECHNOLOGY RAISE AN ETHICAL DILEMMA?

MODERN AQUACULTURE AS A FOCAL POINT

FEATURES OF A CONTROVERSY

FROM FACTS TO ETHICAL ISSUES

CONCLUSION

ACKNOWLEDGMENTS

Color Plates

Index

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Aquaculture biotechnology / edited by Garth L. Fletcher, Matthew L. Rise. p. cm. Includes bibliographical references and index. ISBN-13: 978-0-8138-1028-7 (hard cover : alk. paper) ISBN-10: 0-8138-1028-0 (hard cover : alk. paper) 1. Aquacultural biotechnology. I. Fletcher, G. L. II. Rise, Matthew L. SH136.B56A73 2012 578.76–dc23 2011028323

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Dedication

In memory of

Kenjiro Ozato

1938–2006

This monograph on aquaculture biotechnology is dedicated to the memory of Professor Kenjiro Ozato. He was one of the first pioneers to exploit the use of gene transfer to fish as a means of altering phenotypes and, thus, helped to pave the way to greater understanding of tissue-specific gene expressions.

At the time of his passing, in 2006, Kenjiro Ozato was Emeritus Professor at Nagoya University. He retired in 2002 and became an honorary member of his former laboratory, the Laboratory of Freshwater Fish Stocks at the Bioscience and Biotechnology Center of Nagoya University, where he continued his research on medaka.

Kenjiro graduated from the Department of Zoology in the Faculty of Science at Kyoto University in 1962 and joined the Graduate School of Science to study chicken embryogenesis under the tutelage of Dr. Tokindo S. Okada. In 1967, he was awarded an Assistant Professorship at the Biological Laboratory, Yoshida College, Kyoto University. Shortly after taking up this position, he spent a period of time studying cell culture techniques under the tutelage of Dr. James D. Ebert, a renowned embryologist at the Carnegie Institute. Upon returning to Japan, he was encouraged by Dr. Tokindo S. Okada to study the developmental biology of fish. Dr. Okada was convinced that “[t]he time of fish biology will come in 15 years.” At that time (1970s), this aspect of fish biology was in its infancy. There is no question that tremendous advances have been made in molecular and developmental biology since that time. Kenjiro Ozato became a pioneer in this field.

Kenjiro established an in vitro cell culture system for fish pigment cells using goldfish and attempted to understand the molecular mechanisms associated with pigment cell transformation in the Xiphophorus fish-hybrid melanoma system. However, Xiphophorus, being viviparous, complicated in vitro analyses of the cellular mechanisms. Consequently, he shifted his attention to medaka, an oviparous fish, and developed methods to introduce foreign genes into medaka eggs in order to elucidate gene function in vivo. In 1986, he successfully demonstrated the expression of the chick δ-crystalline gene in medaka embryos (Ozato et al. 1986). This was the first direct evidence for transgene expression in fish: a demonstration that helped encourage a fledgling group of like-minded biologists to follow in his footsteps. Subsequently, Kenjiro produced a great volume of work in the field of fish developmental biology using transgenic and nuclear transfer techniques.

In 1994, Kenjiro moved to the Laboratory of Freshwater Fish Stocks at the Bioscience Centre of Nagoya University, where he began his genetic studies of Professor Hideo Tomita’s collection of living natural medaka mutants. During this time, he successfully helped establish a strain of transparent medaka, “see-through medaka,” within which the internal organs could be observed without the need for dissection (Wakamatsu et al. 2001). Kenjiro was also eager to advance the use the medaka as a disease model as evidenced by his final contribution to fish biology with his research on polycystic kidney disease, which was well received by researchers in a variety of medical fields (Mochizuki et al. 2005).

Kenjiro introduced medaka as an animal model for research around the world (Ozato et al. 1992). He collaborated with other investigators in assessing the influence of endocrine disrupters on wild animal taxa using medaka (Wakamatsu and Ozato 2002) and contributed to research efforts involving the use of this model for research on space exploration. He helped convene two international symposia on medaka research and was very active in encouraging and supporting Asian scientists in the development of their research programs on fish by visiting them in their own countries and welcoming them to participate in workshops at Nagoya University (Japan 1996).

Kenjiro was a kind, generous gentleman who showed true humility with regard to his many accomplishments. His considerable achievements and gentle manner earned him high regard and endearment from researchers worldwide.

Excerpted from The Fish Biology Journal MEDAKA (2007), Vol 11, pp 1–4, with permission. Yuko Wakamatsu Laboratory of Freshwater Fish Stocks, Bioscience and Biotechnology Center Nagoya University, Nagoya, Japan

REFERENCES

Japan 1996. Japan Society for the Promotion of Science, Asian Science Seminar, Reproductive Biology and Biotechnology in Aquatic Animals-Asia ‘96. March 16–28, 1996, Nagoya University.

Mochizuki E, Fukuta K, Tada T, Harada T, Watanabe N, Matsuo S, Hashimoto H, Ozato K, and Wakamatsu Y. 2005. Fish mesonephric model of polycystic kidney disease in medaka (Oryzias latipes) pc mutant. Kidney Int. 68: 23–34.

Ozato K, Kondoh H, Inohara H, Iwamatsu T, Wakamatsu Y, and Okada TS. 1986. Production of transgenic fish: introduction and expression of chicken δ–crystalline gene in medaka embryos. Cell Differ. 19: 237–244.

Ozato K, Inoue K, and Wakamatsu Y. 1992. Medaka as a model of transgenic fish. Mol Mar Biol Biotechnol. 1: 346–354.

Wakamatsu Y, Pristyazhnyuk S, Kinoshita M, Tanaka M, and Ozato K. 2001. The see-through medaka: a fish model that is transparent throughout life. Proc Natl Acad Sci USA. 98: 10046–10050.

Wakamatsu Y and Ozato K. 2002. Medaka (Oryzias latipes) as a fish model for endocrine-disrupting substance testing. Environ Sci. 9: 419–426.

Preface

The culture of fish began in ancient Egypt and China several thousand years ago. However, it was not until the 1950s and 1960s that modern aquaculture for food and profit had its beginnings (Beveridge and Little 2002). Today, it is the fastest growing animal food production sector worldwide. This rapid expansion of aquaculture was, and still is, a boon to biologists as well as engineers because of its requirements for highly qualified personnel with the skill sets required to solve problems essential to the development of this important and essential food resource.

A sustainable and profitable aquaculture industry is technology and innovation driven. The rapid expansion of the industry motivated by increasing demands for product and profit required the development of appropriate low-cost feeds, efficient feeding systems, and increasingly sophisticated culture facilities on land and in the water to ensure containment and to minimize environmental contamination.

All cultured food fish and shellfish were at some point captured in the wild, and many are only now going through the process of domestication: selection of the fittest to survive, grow, and reproduce in an aquaculture environment. Not all genotypes lend themselves to survival in contained culture facilities, let alone reproduce successfully and grow at a cost-effective rate sufficient to satisfy investors. This general issue led to the first successful innovation of benefit to aquaculture: the introduction of selective crossbreeding programs for Atlantic salmon in Norway in the early 1970s (Gjedrem 1997). This program clearly demonstrated that fish, in common with other domesticated animals, had desirable traits with strong heritable components.

The first major biotechnology products to prove essential to industry were antibiotics, where they were credited with preventing a total crash of the salmon culture industry in Norway in the 1980s. This technology has, to a large extent, been superseded by the development of efficacious vaccines; the first ones being simple products consisting of inactivated bacterial cultures that eventually gave way to the use of live attenuated vaccines and more recently subunit or recombinant vaccines (Sommerset et al. 2005).

A quantum leap in interest by the scientific community to look for biotechnological ways to improve aquaculture production took place with the 1982 publication by Palmiter and colleagues, demonstrating that the addition of a few extra growth hormone genes could dramatically increase the growth rates of mice. This prompted a number of scientists to try and duplicate this success by experimenting with gene transfer in fish. However, at that time, very few fish genes were available, so most researchers had to resort to the use of the available mammalian, chicken, bacterial, and viral nucleotide sequences to build gene constructs. The only exception was the Davies, Hew, and Fletcher group, who were fortunate enough to be conducting research on fish antifreeze protein genes (Fletcher and Davies 1991). Few of these early gene transfer studies proved of value to aquaculture. However, they did serve as a “proof of concept” by showing that genes could be transferred to fish, expressed appropriately, and inherited in a stable Mendelian fashion.

In addition to the paucity of knowledge about genes in fish in the 1980s, the lack of a simple and effective method for detecting transgene integrants in tissues served as a second major bottleneck to the successful development of biotechnology tools for the benefit of aquaculture. The only reliable technique available during those early years was genomic Southern blotting; a difficult and slow procedure when one considers that there can be hundreds to thousands of samples to screen. This particular hurdle was overcome by a key technological leap in the 1980s: the invention and widespread application of PCR techniques. This revolutionized the field of molecular biology and provided an effective and essential technique to genetic engineers for the detection of transgene integrants.

The next advancement of considerable value to the development of biotech tools for aquaculture was the establishment of zebrafish as a vertebrate model in the 1990s (Grunwald and Eisen 2002). Although this development did not take place with aquaculture in mind, it did bring widespread international attention to the value of research on fish.

Once zebrafish and later the Japanese Medaka were established as important vertebrate models, all of the discoveries in molecular biology that occurred in the 1970s (e.g., reverse transcriptase, restriction enzymes, recombinant DNA, and DNA sequencing technologies), the 1980s (e.g., automated DNA sequencing), and the 1990s (e.g., DNA microarrays, cDNA, and genomic DNA libraries) were widely applied to the study of fish. These developments helped train a “critical mass” of scientists that could apply their expertise to solving problems.

Today, genome sequences are available for five model fish species (fugu, tetraodon, zebrafish, medaka, and stickleback), and genome sequencing projects for aquaculture species such as Atlantic salmon and catfish are well underway (Davidson et al. 2010; Liu 2011). These genomic technologies show great promise with regard to the discovery of genes that could alleviate aquaculture production constraints such as growth rates, disease and stress resistance, low or high temperature tolerance, and for the carnivorous species, the ability to utilize plant sourced feeds. Such discoveries could be used to modify the genome and phenotype of the animal, or facilitate the development of molecular markers for selecting broodstock with production-relevant traits.

At present, the practical application of gene biotechnologies to commercial aquaculture that bring a return on the investment in research is largely restricted to the development of vaccines, broodstock selection markers, and disease diagnostics. This is, to a large extent, due to difficulties government agencies have had in developing an acceptable process for the approval of animal food products developed by biotechnological means. Observe the fact that it took from 1994, when Aqua Bounty Technologies first met with FDA USA, until 2009 for the agency to codify the procedures required to review an application to market a growth hormone transgenic salmon product (FDA 2009). It took another year for the agency to announce that the product was safe to eat (FDA 2010). However, at the time of writing this book, the FDA has yet to approve the product for sale. Investment by the company in this product is in excess of $20 million; much of it is attributable to the lack of regulatory precedents. Therefore, it is apparent that, once the guidelines for the approval of aquaculture biotechnological products have been established, they will serve as a road map for corporate researchers to follow.

This will provide investors with the confidence that investment in such endeavors is worthwhile.

This monograph brings together the major biotechnological advances that are relevant to the enhancement of aquaculture to date. It is divided into nine parts. Part 1, consisting of four chapters, deals with genomic approaches to improving fish and shellfish broodstock. Genomics is, in essence, fundamental to identifying functional genes that can be used as markers for selective breeding programs and/or genetic modification.

Part 2 deals with cytogenetic tools for genome mapping and the localization of protein-coding genes and transgenes on fish and shellfish chromosomes.

Part 3 concentrates on fish health with chapters on the physiological aspects of adaptive immunity in fish, the application of genomics to understand the health of fish, and the discovery of fish antimicrobials that could serve as therapeutants.

Part 4 consists of two chapters. The first chapter deals with proteomics and structural biology techniques, mass spectrometry in particular, that can be used to study the viral protein structure, function, and virus–host interactions. The second chapter outlines progress toward the development of DNA vaccines for viral diseases of farmed fish and shellfish.

Part 5 consists of four chapters on the fundamental issues concerning fish embryogenesis and stem cells that range from the egg transcriptome to germ cell transplantation.

Part 6 deals with issues pertinent to gene transfer. Despite the 30-year history behind the application of this technique to aquaculture, there have been few advances. The efficiency of gene transfer is still very low; targeted integration of single copy genes has yet to be achieved and the ability to accurately predict expression levels at the transcription and translation level is nonexistent. At present, our hopes lie in research on model fish, such as zebrafish, that could point to ways of resolving these issues. It is for this purpose that this part begins with a chapter on the regulation of transgene expression in zebrafish. The remaining four chapters present examples of the range of research that is currently being carried out using gene transfer techniques. The first chapter points to the difficulties involved in producing freeze-resistant fish, and the remaining three chapters outline progress toward the generation of zebrafish for environmental monitoring, tilapia for the production of human insulin expressing islets for xenotransplantation, and follistatin transgenic trout to understand fish muscle growth.

Part 7 deals with cryopreservation, a technique that is essential for the preservation of unique genotypes.

The monograph is completed with two chapters on environmental and ethical issues (Parts 8 and 9, respectively) that should be considered when planning to apply biotechnological advances to aquaculture.

REFERENCES

Beveridge MCM and Little DC. 2002. The history of aquaculture in traditional societies. In: Ecological Aquaculture, The evolution of the blue evolution (ed. Costa-Pierce BA). Blackwell Publishing Ltd., Oxford, UK. pp 3–29.

Davidson WS, Koop BF, Jones SJM, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, and Omholt SW. 2010. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol. 11: 403.

FDA. 2009. Genetically engineered animals. http://www.fda.gov/AnimalVeterinary/DevelopmentApprovalProcess/GeneticEngineering/GeneticallyEngineeredAnimals/default.htm.

FDA. 2010. AquAdvantage Salmon. Briefing Packet. Food and Drug Administration, Centre for Veterinary Medicine, Veterinary Medicine Advisory Committee. http://www.fda.gov/downloads/AdvisoryCommittees/CommitteesMeetingMaterials/ VeterinaryMedicineAdvisoryCommittee/UCM224762.pdf.

Fletcher GL and Davies PL. 1991. Transgenic fish for aquaculture. In: Genetic Engineering, Principles and Methods (ed. Setlow J). Plenum Press, New York. Vol 13. pp 331–370.

Gjedrem T. 1997. Selective breeding to improve aquaculture production. World Aquacult. 28(1): 33–45.

Liu Z. 2011. Development of genomic resources in support of sequencing, assembly, and annotation of the catfish genome. Comp Biochem Physiol. 6 (Part D): 11–17.

Palmiter RD, Brinster RL, Hammer RE, Trumbauer ME, Rosenfeld MG, Birnberg NC, and Evans RM. 1982. Dramatic growth of mice that develop from eggs microinjected with metallothionein−growth hormone fusion genes. Nature. 300: 611–615.

Sommerset I, Krossøy B, Biering E, and Frost P. 2005. Vaccines for fish in aquaculture. Exper Rev Vaccines. 4(1): 89–101.

Garth L. Fletcher Matthew L. Rise

Contributors

Leandro A. Becker Department of Biology University of Waterloo Waterloo, ON, Canada

Tillmann Benfey Department of Biology University of New Brunswick Fredericton, NB, Canada

Julien Bobe Institut National de la Recherche Agronomique INRA SCRIBE—Campus de Beaulieu Rennes, France

Marije Booman Ocean Sciences Centre Memorial University of Newfoundland St. John's, NL, Canada

Terence M. Bradley Department of Fisheries Animal and Veterinary Science University of Rhode Island Kingston, RI, USA

Craig L. Browdy Novus International Inc., Charleston, SC, USA

Laura L. Brown Pacific Biological Station Department of Fisheries and Oceans Nanaimo, BC, Canada

Elsa Cabrita Institute of Marine Sciences of Andalusia—ICMAN Spanish National Research Council—CSIC Puerto Real, Cádiz, Spain

Robert W. Chapman Marine Resources Research Institute South Carolina Department of Natural Resources Charleston, SC, USA

Paul Collodi Department of Animal Sciences Purdue University West Lafayette, IN, USA

Peter L. Davies Department of Biochemistry Queen's University Kingston, ON, Canada

Enrique de la Vega CI OCEANOS Cartagena, Colombia

Mònica Díaz Departament de Fisiología Facultat de Biologia Universitat de Barcelona Barcelona, Spain

Brian Dixon Department of Biology University of Waterloo Waterloo, ON, Canada

Susan E. Douglas Institute of Marine Biosciences National Research Council Halifax, NS, Canada

Zhi-Qiang Du Department of Animal Science and Center for Integrated Animal Genomics Iowa State University Ames, IA, USA

Marc Ekker Centre for Advanced Research in Environmental Genomics Department of Biology University of Ottawa Ottawa, ON, Canada

Oystein Evensen Department of Basic Sciences and Aquatic Medicine Norwegian School of Veterinary Science Oslo, Norway

Ian A. Fleming Ocean Sciences Centre Memorial University of Newfoundland St. John's, NL, Canada

Garth L. Fletcher Ocean Sciences Centre Memorial University of Newfoundland St. John's, NL, Canada

Alexis Fostier Institut National de la Recherche Agronomique INRA SCRIBE—Campus de Beaulieu Rennes, France

Frederick W. Goetz School of Freshwater Sciences University of Wisconsin-Milwaukee Milwaukee, WI, USA

Zhiyuan Gong Department of Biological Sciences and NUS Graduate School National University of Singapore Singapore

Danielle M. Gorbach Department of Animal Science and Center for Integrated Animal Genomics Iowa State University Ames, IA, USA

Paz Herráez Department of Molecular Biology Faculty of Biology University of León León, Spain

Choy L. Hew Department of Biological Sciences National University of Singapore Singapore

Olga Hrytsenko Department of Biology Dalhousie University Halifax, NS, Canada

Dimitar B. Iliev Norwegian College of Fishery Science University of Tromsø Tromsø, Norway

Stewart C. Johnson Pacific Biological Station Department of Fisheries and Oceans Nanaimo, BC, Canada

Yannick Labreuche Marine Biomedicine and Environmental Sciences Center Medical University of South Carolina Charleston, SC, USA

IFREMER Département Lagon Ecosystèmes et Aquaculture Durable en Nouvelle-Calédonie Station de Saint-Vincent Noumea cedex, New Caledonia

Siew Hong Lam Department of Biological Sciences National University of Singapore Singapore

Jo-Ann C. Leong Hawai'i Institute of Marine Biology School of Ocean and Earth Science and Technology University of Hawaii Kaneohe, HI, USA

Lyne Létourneau Faculté des sciences de l’agriculture et de l’alimentation Département des sciences animals Pavillon Paul-Comtois Quebec, QC, Canada

Zhengjun Li Department of Biological Sciences National University of Singapore Singapore

Ryan MacDonald Centre for Advanced Research in Environmental Genomics Department of Biology University of Ottawa Ottawa, ON, Canada

Simon MacKenzie Institute of Biotechnology and Biomedicine Universitat Autonoma de Barcelona Barcelona, Spain

Debbie Martin-Robichaud Fisheries and Oceans Canada St. Andrews Biological Station St. Andrews, NB, Canada

Darek T.R. Moreau Ocean Sciences Centre Memorial University of Newfoundland St. John's, NL, Canada

Hwee Boon Grace Ng Department of Biological Sciences and NUS Graduate School National University of Singapore Singapore

Tomoyuki Okutsu Japan International Research Center for Agricultural Science Tsukuba, Ibaraki, Japan

Nuala A. O’Leary Marine Biomedicine and Environmental Sciences Center Medical University of South Carolina Charleston, SC, USA

Michael P. Phelps Department of Fisheries Animal and Veterinary Science University of Rhode Island Kingston, RI, USA

Ruth B. Phillips School of Biological Sciences Washington State University-Vancouver Vancouver, WA, USA

Josep V. Planas Departament de Fisiologia Facultat de Biologia Universitat de Barcelona Barcelona, Spain

Bill Pohajdak Department of Biology Dalhousie University Halifax, NS, Canada

Darrin Reid Institute for Marine Biosciences National Research Council Halifax, NS, Canada

Michael Reith Institute for Marine Biosciences National Research Council Halifax, NS, Canada

Matthew L. Rise Ocean Sciences Centre Memorial University of Newfoundland St. John's, NL, Canada

Javier Robalino Facultad de Ingeniería Marítima y Ciencias del Mar Escuela Superior Politécnica del Litoral Prosperina, Guayaquil, Ecuador

Barrie D. Robison Department of Biological Sciences University of Idaho Moscow, ID, USA

Vanesa Robles Indegsal and Department of Molecular Biology University of León León, Spain

Kristine Romoren GE Healthcare AS—Oslo Oslo, Norway

Max F. Rothschild Department of Animal Science and Center for Integrated Animal Genomics Iowa State University Ames, IA, USA

Hendrian Sukardi Department of Biological Sciences National University of Singapore Singapore

Yutaka Takeuchi Research Center for Advanced Science and Technology Tokyo University of Marine Science and Technology Tateyama, Chiba, Japan

Gary H. Thorgaard School of Biological Sciences Washington State University Pullman, WA, USA

Juan Martin Traverso Institut National de la Recherche Agronomique SCRIBE—Campus de Beaulieu Rennes, France

Gregory W. Warr Marine Biomedicine and Environmental Sciences Center Medical University of South Carolina Charleston, SC, USA Division of Molecular and Cellular Biosciences National Science Foundation Arlington, VA, USA

Ten-Tsao Wong Department of Animal Sciences Purdue University West Lafayette, IN, USA

James R. Wright Jr. Department of Pathology and Laboratory Medicine University of Calgary/Alberta Health Services-Calgary Zone Calgary Laboratory Services—Diagnostic and Scientific Centre Calgary, Alberta, Canada

Jinlu Wu Department of Biological Sciences National University of Singapore Singapore

Goro Yoshizaki Department of Marine Biosciences Tokyo University of Marine Science and Technology Minato-ku, Tokyo, Japan

Part 1

Broodstock Improvement

Chapter 1

Genomic Tools for Understanding the Molecular Basis of Production-Relevant Traits in Finfish

Marije Booman and Matthew L. Rise

OVERVIEW

Significant genomic resources (e.g., expressed sequence tag (EST) databases, DNA microarrays, single nucleotide polymorphism (SNP) genotyping platforms, bacterial artificial chromosome (BAC) libraries and BAC end sequences, genetic linkage maps, and physical maps) have been generated for several finfish species of importance to global aquaculture. Over the last few years, numerous articles (e.g., Cerdá et al. 2008; Koop et al. 2008), reviews (e.g., Douglas et al. 2006; Canario et al. 2008; Goetz and MacKenzie et al. 2008; Martin et al. 2008), and book chapters (e.g., Palti 2009; Rise et al. 2009; and several chapters in book Aquaculture Genome Technologies, 2007, edited by Z. Liu) have been published on the creation and application of finfish genomics resources. With the advent of next-generation sequencing (NGS) technologies, it is anticipated that finfish genomic resources will continue to expand.

For species of key importance to global aquaculture and fisheries (e.g., Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), Atlantic cod (Gadus morhua), channel catfish (Ictalurus punctatus), and common carp (Cyprinus carpio)), complete “genomics toolboxes” will be needed in order to take full advantage of the power of genomics in aquaculture research (e.g., for marker-assisted selection (MAS) of superior broodstock, development of optimal and sustainable feed formulations, development of maximally effective vaccines and therapeutants, etc.). Complete, high-quality reference genome sequences are critically important components of these toolboxes, and whole-genome sequencing projects are already underway for Atlantic salmon (Davidson et al. 2010) and catfish (Lu et al. 2011). As aquaculture finfish species’ genomes are sequenced and assembled, and as we move into a postgenomics era for these species, bioinformatics will undoubtedly play an ever-increasing role in the success of aquaculture genomics research.

Table 1.1 Expressed Sequence Tag (EST) Collections of Selected Aquaculture Fish Species.

Selected Orders of Teleosts