This essential guide will allow you to understand how new developments in our knowledge of epigenetic mechanisms and epigenetic inheritance can be applied to improve aquaculture production and aquatic resource management and conservation.
Epigenetics is the study of heritable changes in gene expression that are independent of alterations in the nucleotide sequence. It integrates genomic and environmental influences to shape the phenotype. Epigenetics is a field with particular relevance to aquaculture and aquatic organisms, since it underpins acclimatory responses to diverse and changing environments and inheritance of desired phenotypes.
Epigenetics in Aquaculture provides a comprehensive introduction to epigenetics, epigenetic mechanisms, epigenetic inheritance, and research methods. It also provides the current state of the art on research and development on epigenetics in the major functions of aquatic organisms in the framework of aquaculture production. The fact that aquaculture is the fastest-growing sector of food production makes the book especially timely.
Readers will also find: - Detailed treatment of subjects including aquatic faunal reproduction, sex determination, growth regulation, nutritional programming, disease resistance, stress response and much more - Survey of current research lacunae and the projected future of the discipline - An authorial team of internationally renowned experts
Epigenetics in Aquaculture is a valuable reference for researchers, biologists and advanced students in any area of marine science, oceanography, aquaculture, environmental science, and food production.
Table of Contents
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
