Epigenetics in Aquaculture

About the Editors xvii List of Contributors xix Preface xxiii Acknowledgments xxv Part I Theoretical and Practical Bases of Epigenetics in Aquaculture 1 1 The Potential Role of Epigenetics in Aquaculture: Insights from Different Taxa to Diverse Teleosts 3 Han-Ping Wang and Zhi-Gang Shen 1.1 Introduction 3 1.2 Key Players of Epigenetics 4 1.3 Divergent Epigenetic Mechanisms from Different Taxa to Diverse Teleosts 10 1.4 The Roles and Applications of Epigenetics 11 1.5 Conclusion and Perspectives 25 2 Transcriptional Epigenetic Mechanisms in Aquatic Species 45 Laia Navarro-Martín, Jan A. Mennigen, and Jana Asselman 2.1 Epigenetic Mechanisms as Modulators of Transcription 45 2.2 Transcriptional Epigenetic Mechanisms in Aquatic Species 51 2.3 Modulation of Biological Functions by Transcriptional Epigenetic Mechanisms in Aquaculture Species of Interest 54 2.4 Conclusions and Perspectives 57 3 Epigenetic Regulation of Gene Expression by Noncoding RNAs 65 Elena Sarropoulou and Ignacio Fernández 3.1 General Introduction 65 3.2 Major Types of ncRNAs 65 3.3 Roles of ncRNA in Key Processes of Teleosts 76 3.4 ncRNAs as Biomarkers and Future Perspectives 84 4 Epigenetic Inheritance in Aquatic Organisms 95 Ramji K. Bhandari 4.1 Introduction 95 4.2 Epigenetic Reprogramming of Embryo and Germline Cells 101 4.3 Heritable Effects of Environmental Stress 104 4.4 Past Exposure and Future Phenotypic Consequences in Aquatic Species 108 4.5 Conclusions and Perspectives 114 5 Environmental Epigenetics in Fish: Response to Climate Change Stressors 127 Zhi-Gang Shen, Yue Yu, and Han-Ping Wang 5.1 Overview of Climate Change and Environmental Stressors 127 5.2 Epigenetic Response to Climate Change 129 5.3 Conclusions and Future Perspectives 137 6 Analytical Methods and Tools to Study the Epigenome 149 Oscar Ortega-Recalde and Timothy A. Hore 6.1 Introduction 149 6.2 Recommendations for Choosing a Method to Study the Epigenome 150 6.3 Methods and Tools to Analyze Epigenetic Modifications 150 6.4 Bioinformatics Analysis 165 6.5 Databases and Other Public Resources 166 6.6 Conclusions and Outlook 166 Part II Epigenetics Insights from Major Aquatic Groups 175 7 Epigenetics in Sexual Maturation and Gametes of Fish 177 Marta Lombó Alonso, Audrey Laurent, María Paz Herráez, and Catherine Labbé 7.1 Introduction 177 7.2 Epigenetics During Spermatogenesis and Oogenesis 177 7.3 Epigenetic Changes in the Gametes Triggered by Environmental Constraints 181 7.4 Conclusion 186 8 Epigenetics in Sex Determination and Differentiation of Fish 193 Qian Wang, Qian Liu, Xiaona Zhao, Wenxiu Ma, Lili Tang, Bo Feng, and Changwei Shao 8.1 Introduction 193 8.2 Epigenetics and Sex Chromosome Evolution 195 8.3 Epigenetics and Sex Determination 198 8.4 Epigenetic Regulation of Sex Differentiation in Gonochoristic Species and Sex Change in Hermaphrodites 199 8.5 Transgenerational Epigenetic Sex Reversal 201 8.6 Conclusions and Future Perspectives 203 9 Epigenetics in Fish Growth 209 Jorge M.O. Fernandes, Artem V. Nedoluzhko, Ioannis Konstantinidis, and Paulo Gavaia 9.1 Myogenesis in Teleosts 209 9.2 Skeletogenesis in Teleosts 213 9.3 Epigenetic Regulation of Sexually Dimorphic Growth 215 9.4 Epigenetic Control of the Skeleton in Teleosts 218 9.5 Mitochondrial Epigenetics 219 9.6 Conclusion 221 10 Epigenetics in Fish Nutritional Programming 231 Kaja H. Skjærven, Anne-Catrin Adam, Takaya Saito, Rune Waagbø, and Marit Espe 10.1 Epigenetic Basis of Nutritional Programming 231 10.2 Nutritional Programming 233 10.3 Key Nutrients and Metabolites for Epigenetic Mechanisms 235 10.4 Case Examples 237 10.5 Conclusions and Perspectives for Nutritional Programming in Aquaculture 239 11 Microbiome, Epigenetics, and Fish Health Interactions in Aquaculture 245 Sofia Consuegra, Tamsyn Uren Webster, and Ishrat Anka 11.1 Introduction 245 11.2 The Fish Microbiome in Aquaculture 245 11.3 Microbiome-Epigenome Interactions 252 11.4 Gaps in Knowledge and Future Research Avenues 255 11.5 Conclusions 255 12 Epigenetics of Stress in Farmed Fish: An Appraisal 263 Bruno Guinand and Athanasios Samaras 12.1 Introduction 263 12.2 Stress and Stress Response 264 12.3 Is There an Epigenetics of Stress in Cultured Fish? 267 12.4 The Neuroepigenetics of Stress: Fishing with Mammalian Models 269 12.5 Epigenetic Biomonitoring of Stress 273 12.6 Conclusions 274 13 Epigenetics in Hybridization and Polyploidization of Aquatic Animals 287 Li Zhou and Jian-Fang Gui 13.1 Hybridizing and Hybridization 287 13.2 Polyploidy and Polyploidization 287 13.3 Epigenetic Changes and Effects During Hybridization and Polyploidization in Aquatic Animals 289 13.4 Association of Epigenetic Changes with Heterosis 292 13.5 Conclusions and Future Perspectives 293 14 Epigenetics in Aquatic Toxicology 301 Sara J. Hutton and Susanne M. Brander 14.1 Introduction 301 14.2 Epigenetic Endpoints in Aquatic Toxicology Studies 303 14.3 Epigenetics During Early Development Related to Toxicology 310 14.4 Multigenerational and Transgenerational Toxicology 311 14.5 Epigenetics in Ecological Risk Assessment 313 14.6 Rapid Evolution 314 14.7 Epigenetics in Aquaculture 315 14.8 Conclusion and Perspectives 316 15 Epigenetics in Mollusks 325 Manon Fallet 15.1 Introduction 325 15.2 DNA Modifications in Mollusk Species 328 15.3 Chromatin Conformation and Histone Modifications/Variants in Mollusks 330 15.4 Noncoding RNAs in Mollusks 331 15.5 Epigenetic Responses to Environmental Fluctuations in Mollusks 336 15.6 Mechanisms of Meiotic Epigenetic Inheritance in Mollusks and Their Impact in Evolution 340 15.7 Perspectives 345 15.8 General Conclusions 346 16 Epigenetics in Crustaceans 355 Günter Vogt 16.1 Introduction 355 16.2 Epigenetics Research with Brine Shrimps and Copepods 356 16.3 Epigenetics Research with Water Fleas 359 16.4 Epigenetics Research with Amphipods 363 16.5 Epigenetics Research with Freshwater Crayfish 363 16.6 Epigenetics Research with Shrimps and Crabs 371 16.7 State of the Art of Epigenetics in Crustaceans 373 16.8 Potential Application of Epigenetics in Crustacean Aquaculture 374 17 Epigenetics in Algae 383 Christina R. Steadman 17.1 Introduction: What Are Algae 383 17.2 Algae Epigenetics 388 17.3 Environmental Stress Alters Microalgae Epigenomes 404 17.4 Conclusions and Perspectives 405 Part III Implementation of Epigenetics in Aquaculture 413 18 Development of Epigenetic Biomarkers in Aquatic Organisms 415 Dafni Anastasiadi and Anne Beemelmanns 18.1 Biomarkers 415 18.2 Epigenetic Biomarkers 415 18.3 Development of Epigenetic Biomarkers 417 18.4 Epigenetic Biomarkers in Aquatic Organisms and their Applications in Aquaculture 425 18.5 Future Perspectives 431 18.6 Concluding Remarks 432 19 Genetics and Epigenetics in Aquaculture Breeding 439 Shokouoh Makvandi-Nejad and Hooman Moghadam 19.1 Overview 439 19.2 Breeding in Aquaculture and Evolution of Genetic Markers 440 19.3 Epigenetics and Missing Heritability 442 19.4 Transgenerational Inheritance of Epigenetic Marks 444 19.5 Epigenetic Marks -- Possible Biomarkers to Improve Breeding 444 19.6 Association Analysis and Search for Epigenetic Biomarkers 445 19.7 Concluding Remarks 446 20 Epigenetics in Aquaculture: Knowledge Gaps, Challenges, and Future Prospects 451 Francesc Piferrer 20.1 Introduction 451 20.2 Knowledge Gaps 452 20.3 Challenges 456 20.4 Prospects 458 Acknowledgments 461 References 461 Index-Species 465 Index-Subjects 469