Epigenetics in Aquaculture

Cover
Title Page
Copyright Page
Dedication
Contents
About the Editors
List of Contributors
Preface
Acknowledgments
Part I Theoretical and Practical Bases of Epigenetics in Aquaculture
Chapter 1 The Potential Role of Epigenetics in Aquaculture: Insights from Different Taxa to Diverse Teleosts
1.1 Introduction
1.1.1 Concepts and Terminology
1.1.2 Epigenetic Mechanisms and Phenomena
1.2 Key Players of Epigenetics
1.2.1 DNMTs
1.2.2 TETs
1.2.3 KMTs/KDMs
1.2.4 HATs/KATs and HDACs
1.3 Divergent Epigenetic Mechanisms from Different Taxa to Diverse Teleosts
1.4 The Roles and Applications of Epigenetics
1.4.1 Reproduction and Early Development
1.4.2 Health and Well-Being Management
1.4.3 Nutrition and Growth Advancement
1.4.4 Sustainability Enhancement
1.5 Conclusion and Perspectives
Acknowledgments
References
Chapter 2 Transcriptional Epigenetic Mechanisms in Aquatic Species
2.1 Epigenetic Mechanisms as Modulators of Transcription
2.1.1 DNA Methylation
2.1.2 Chromatin Remodeling Through Histone Modifications
2.2 Transcriptional Epigenetic Mechanisms in Aquatic Species
2.2.1 Teleost Fish
2.2.2 Aquatic Invertebrates
2.3 Modulation of Biological Functions by Transcriptional Epigenetic Mechanisms in Aquaculture Species of Interest
2.3.1 Growth and Development
2.3.2 Nutrition and Metabolism
2.3.3 Reproduction and Broodstock Selection
2.3.4 Stress and Immune Responses
2.4 Conclusions and Perspectives
Acknowledgments
References
Chapter 3 Epigenetic Regulation of Gene Expression by Noncoding RNAs
3.1 General Introduction
3.2 Major Types of ncRNAs
3.2.1 Small Noncoding RNA (sncRNA)
3.2.2 Measurement of sncRNAs
3.2.3 Long Noncoding RNA (lncRNA)
3.3 Roles of ncRNA in Key Processes of Teleosts
3.3.1 Roles of ncRNA During Development
3.3.2 Evaluated miRNA Functions During Teleost Development
3.3.3 Roles of ncRNA During Reproduction
3.3.4 Roles of ncRNA in Immune and Stress Response
3.4 ncRNAs as Biomarkers and Future Perspectives
Acknowledgments
References
Chapter 4 Epigenetic Inheritance in Aquatic Organisms
4.1 Introduction
4.1.1 Gene–Environment Interaction and Epigenetic Inheritance
4.1.2 Key Mechanisms Underlying Epigenetic Inheritance
4.1.3 Epigenetic Inheritance of Traits
4.2 Epigenetic Reprogramming of Embryo and Germline Cells
4.2.1 Reprogramming of the Embryo
4.2.2 Reprogramming of Primordial Germ Cells
4.3 Heritable Effects of Environmental Stress
4.3.1 Developmental Effects
4.3.2 Postnatal or Parental Effects
4.3.3 Germline Transmission of Epigenetic Alterations: Experimental Evidence
4.3.4 Multigenerational Versus Transgenerational Phenotypes
4.3.5 Parent-of-Origin and Transgenerational Phenotypes
4.4 Past Exposure and Future Phenotypic Consequences in Aquatic Species
4.4.1 Effects on Fish
4.4.2 Transgenerational Fish Phenotype and Population Effects: A Perspective
4.4.3 Designing Transgenerational Laboratory Experiments
4.4.4 Transgenerational Effects on Hatchery-Raised Fish
4.4.5 Potential for the Mitigation of Epigenetically Inherited Harmful Effects on Fish
4.5 Conclusions and Perspectives
References
Chapter 5 Environmental Epigenetics in Fish: Response to Climate Change Stressors
5.1 Overview of Climate Change and Environmental Stressors
5.1.1 Temperature Rise and Extreme Weather Events
5.1.2 Acidification
5.1.3 Hypoxia
5.1.4 Phenology and Distribution
5.2 Epigenetic Response to Climate Change
5.2.1 Sex Determination and Differentiation
5.2.2 Gonadal Development and Reproduction
5.2.3 Growth, Size, and Morphology
5.2.4 Nutrition
5.2.5 Stress Response and Survival
5.3 Conclusions and Future Perspectives
Acknowledgments
References
Chapter 6 Analytical Methods and Tools to Study the Epigenome
6.1 Introduction
6.2 Recommendations for Choosing a Method to Study the Epigenome
6.3 Methods and Tools to Analyze Epigenetic Modifications
6.3.1 DNA Methylation Methods According to Detection Strategy
6.3.2 DNA Methylation Methods According to Resolution Level
6.3.3 DNA Methylation Methods According to Genome Coverage
6.3.4 Histone Modifications
6.3.5 Assessment of Other Epigenetic Modifications
6.4 Bioinformatics Analysis
6.5 Databases and Other Public Resources
6.6 Conclusions and Outlook
Acknowledgments
References
Part II Epigenetics Insights from Major Aquatic Groups
Chapter 7 Epigenetics in Sexual Maturation and Gametes of Fish
7.1 Introduction
7.2 Epigenetics During Spermatogenesis and Oogenesis
7.2.1 PGCs’ Epigenetic Remodeling During Embryo Life
7.2.2 Establishing the Epigenetic Profile of Eggs and Sperm During Gametogenesis
7.2.3 The Different Actors of Chromatin Packaging During Spermatogenesis
7.2.4 Parental Imprinting in Fish Gametes
7.2.5 Fate of the Gamete Epigenome
7.3 Epigenetic Changes in the Gametes Triggered by Environmental Constraints
7.3.1 Environmental Contaminants
7.3.2 Domestication
7.3.3 Reproductive Biotechnologies
7.3.4 Transmission of Gamete Epimutations to the Following Generations
7.4 Conclusion
Acknowledgments
References
Chapter 8 Epigenetics in Sex Determination and Differentiation of Fish
8.1 Introduction
8.1.1 Sex Chromosome in Fish
8.1.2 Sex Determination and Differentiation in Fish
8.1.3 Sexual Plasticity of Fish – Gonochoristic and Hermaphroditic Species
8.1.4 Phenomenon of Sex Reversal
8.2 Epigenetics and Sex Chromosome Evolution
8.2.1 The Role of DNA Methylation in the Evolution of Sex Chromosomes
8.2.2 The Role of Histone Modifications on Sex Chromosome Evolution
8.2.3 The Role of Chromatin Structure on Sex Chromosome Evolution
8.3 Epigenetics and Sex Determination
8.3.1 Regulation Network of Sex Determination
8.3.2 Epigenetic Regulation of Sex Determination on Sex-Related Genes
8.3.3 Epigenetic Markers of Sex Determination in Fish
8.4 Epigenetic Regulation of Sex Differentiation in Gonochoristic Species and Sex Change in Hermaphrodites
8.4.1 Epigenetic Regulation of Sex Differentiation in Gonochoristic Species
8.4.2 Epigenetic Regulation of Sex Change in Hermaphroditic Species
8.5 Transgenerational Epigenetic Sex Reversal
8.5.1 Transgenerational Epigenetic Inheritance in Fish
8.5.2 DNA Methylation Reprogramming Associated with Transgenerational Inheritance
8.6 Conclusions and Future Perspectives
Acknowledgments
References
Chapter 9 Epigenetics in Fish Growth
9.1 Myogenesis in Teleosts
9.1.1 Introduction to Myogenesis, Highlighting the Peculiarities of Fish Muscle
9.1.2 Myogenesis During Early Development
9.1.3 Post-Embryonic Muscle Growth
9.2 Skeletogenesis in Teleosts
9.2.1 Mechanisms of Skeletal Formation – The Origin of Skeletal Tissues
9.2.2 Bone
9.2.3 Cartilage
9.3 Epigenetic Regulation of Sexually Dimorphic Growth
9.3.1 Ecological and Physiological Relevance of Sexual Dimorphism
9.3.2 Relationship Between Sex and Growth with an Overview of Key Molecular Networks
9.3.3 Implications of DNA Methylation and Hydroxymethylation in Growth Differences Between Males and Females
9.3.4 miRNAs Differentially Expressed with Sex and Their Role in Muscle Growth
9.4 Epigenetic Control of the Skeleton in Teleosts
9.5 Mitochondrial Epigenetics
9.5.1 Link Between Mitochondrial Function and Muscle Growth
9.5.2 Introduction to Different Types of DNA Modifications in the Mitoepigenome and Their Implications for Mitochondrial Function
9.5.3 Mitoepigenome in Fish
9.5.4 Association Between Growth, Mitochondrial Methylation, and Hydroxymethylation
9.6 Conclusion
Acknowledgments
References
Chapter 10 Epigenetics in Fish Nutritional Programming
10.1 Epigenetic Basis of Nutritional Programming
10.1.1 DNA Methylation
10.1.2 Histone Modifications and Chromatin Structure
10.1.3 Noncoding RNAs in Epigenetic Inheritance
10.2 Nutritional Programming
10.2.1 Definition
10.2.2 Critical Windows
10.3 Key Nutrients and Metabolites for Epigenetic Mechanisms
10.4 Case Examples
10.4.1 Programming of Broodstock to Affect the Offspring
10.4.2 Programming of Larvae to Affect Later Stages of Development
10.5 Conclusions and Perspectives for Nutritional Programming in Aquaculture
Acknowledgments
References
Chapter 11 Microbiome, Epigenetics and Fish Health Interactions in Aquaculture
11.1 Introduction
11.2 The Fish Microbiome in Aquaculture
11.2.1 The Fish Microbiome Diversity and Composition
11.2.2 Extrinsic and Intrinsic Factors that Affect Fish Microbiome Composition
11.2.3 Microbiome Interaction with Fish Health and Immunity
11.2.4 Microbiome Engineering
11.3 Microbiome-Epigenome Interactions
11.3.1 Mammals and Model Species
11.3.2 Microbiome and Epigenetic Interactions in Aquaculture
11.4 Gaps in Knowledge and Future Research Avenues
11.5 Conclusions
References
Chapter 12 Epigenetics of Stress in Farmed Fish: An Appraisal
12.1 Introduction
12.2 Stress and Stress Response
12.2.1 Stress
12.2.2 HPI/HPA Axis and the Stress Hormones
12.2.3 Stress Responses
12.2.4 Individual Differences in Stress Response and Coping Styles
12.2.5 Common Measurements of the Stress Response
12.3 Is There an Epigenetics of Stress in Cultured Fish?
12.3.1 A Brief State of the Art
12.3.2 Unbalances and Misperceptions
12.4 The Neuroepigenetics of Stress: Fishing with Mammalian Models
12.4.1 Rationales and Limitations
12.4.2 Immediate Early Genes in the Hippocampus
12.4.3 Brain-Derived Neurotrophic Factor
12.4.4 Serotonin Signaling
12.4.5 Hypothalamic Connections
12.4.6 Other Hypothalamic and Pituitary Candidates
12.5 Epigenetic Biomonitoring of Stress
12.5.1 Tracking Changes
12.5.2 Tissue Dependency
12.5.3 Time-Dependency
12.5.4 Critical Period
12.6 Conclusions
Acknowledgments
References
Chapter 13 Epigenetics in Hybridization and Polyploidization of Aquatic Animals
13.1 Hybridizing and Hybridization
13.2 Polyploidy and Polyploidization
13.3 Epigenetic Changes and Effects During Hybridization and Polyploidization in Aquatic Animals
13.3.1 Epigenetic Reprogramming During Hybridization and Polyploidization
13.3.2 Nonadditive Gene Expression
13.3.3 DNA Methylation
13.3.4 Histone Modification and Other Epigenetic Changes
13.4 Association of Epigenetic Changes with Heterosis
13.5 Conclusions and Future Perspectives
Acknowledgments
References
Chapter 14 Epigenetics in Aquatic Toxicology
14.1 Introduction
14.2 Epigenetic Endpoints in Aquatic Toxicology Studies
14.2.1 DNA Methylation in Relation to Aquatic Toxicology
14.2.2 Histone Modification in Relation to Aquatic Toxicology
14.2.3 Noncoding RNA in Relation to Aquatic Toxicology
14.3 Epigenetics During Early Development Related to Toxicology
14.4 Multigenerational and Transgenerational Toxicology
14.5 Epigenetics in Ecological Risk Assessment
14.6 Rapid Evolution
14.7 Epigenetics in Aquaculture
14.8 Conclusion and Perspectives
References
Chapter 15 Epigenetics in Mollusks
15.1 Introduction
15.1.1 Definition and Presentation of Mollusks
15.1.2 Mollusks’ Place in Aquaculture
15.1.3 Sensitivity of Mollusks to Environmental Changes and Anthropogenic Pressures
15.2 DNA Modifications in Mollusk Species
15.3 Chromatin Conformation and Histone Modifications/Variants in Mollusks
15.4 Noncoding RNAs in Mollusks
15.5 Epigenetic Responses to Environmental Fluctuations in Mollusks
15.6 Mechanisms of Meiotic Epigenetic Inheritance in Mollusks and Their Impact in Evolution
15.7 Perspectives
15.7.1 Remaining Challenges in Mollusk Epigenetics
15.7.2 Application of Epigenetic Markers in Aquaculture and Aquatic Species Conservation
15.8 General Conclusions
References
Chapter 16 Epigenetics in Crustaceans
16.1 Introduction
16.2 Epigenetics Research with Brine Shrimps and Copepods
16.3 Epigenetics Research with Water Fleas
16.4 Epigenetics Research with Amphipods
16.5 Epigenetics Research with Freshwater Crayfish
16.6 Epigenetics Research with Shrimps and Crabs
16.7 State of the Art of Epigenetics Research in Crustaceans
16.8 Potential Application of Epigenetics in Crustacean Aquaculture
References
Chapter 17 Epigenetics in Algae
17.1 Introduction: What Are Algae
17.1.1 Algae’s Prominent Role in the Environment
17.1.2 Algae in Aquaculture
17.2 Algae Epigenetics
17.2.1 DNA Methylation and Associated Chromatin Modifying Enzymes in Other Organisms
17.2.2 DNA Methylation in the Model Algae Species, Chlamydomonas reinhardtii
17.2.3 Chlorophyte DNA Methylation
17.2.4 Stramenopile (Heterokont) DNA Methylation
17.2.5 Other Types of DNA Methylation
17.2.6 Histone Modifications and Associated Chromatin-Modifying Enzymes in Other Organisms
17.2.7 Histone Modifications in the Model Alga Species, C. reinhardtii
17.2.8 Histone Modifications in Other Microalgae
17.3 Environmental Stress Alters Microalgae Epigenomes
17.4 Conclusions and Perspectives
References
Part III Implementation of Epigenetics in Aquaculture
Chapter 18 Development of Epigenetic Biomarkers in Aquatic Organisms
18.1 Biomarkers
18.1.1 General Concepts and Definitions of Biomarkers
18.1.2 Biomarkers in Aquatic Organisms
18.2 Epigenetic Biomarkers
18.2.1 DNA Methylation
18.2.2 Histone Modifications
18.2.3 Noncoding RNAs
18.3 Development of Epigenetic Biomarkers
18.3.1 Considerations for the Design of Experiments for Biomarker Discovery
18.3.2 Epigenetic Biomarker Discovery Procedure in the Era of Omics
18.3.3 General Systematic Approach
18.3.4 Machine Learning Methods for Epigenetic Biomarkers
18.3.5 Examples of Machine Learning Methods for Epigenetic Biomarker Discovery in Aquatic Organisms
18.4 Epigenetic Biomarkers in Aquatic Organisms and their Applications in Aquaculture
18.4.1 Hatchery Rearing and Fitness
18.4.2 Developmental Processes, Maturation, and Growth
18.4.3 Sex Ratios
18.4.4 Nutrition and Nutritional Programming
18.4.5 Aging
18.4.6 Health and Disease Resistance
18.4.7 Stress Due to Environmental Factors
18.4.8 Aquatic Contaminants
18.4.9 Adaptation and Speciation
18.5 Future Perspectives
18.6 Concluding Remarks
Acknowledgments
References
Chapter 19 Genetics and Epigenetics in Aquaculture Breeding
19.1 Overview
19.2 Breeding in Aquaculture and Evolution of Genetic Markers
19.3 Epigenetics and Missing Heritability
19.4 Transgenerational Inheritance of Epigenetic Marks
19.5 Epigenetic Marks – Possible Biomarkers to Improve Breeding
19.6 Association Analysis and Search for Epigenetic Biomarkers
19.7 Concluding Remarks
References
Chapter 20 Epigenetics in Aquaculture: Knowledge Gaps, Challenges, and Future Prospects
20.1 Introduction
20.2 Knowledge Gaps
20.2.1 Phylogenetic Considerations
20.2.2 Epigenetic Mechanisms
20.2.3 Methodological Aspects
20.2.4 Epigenetic Inheritance
20.2.5 Environmental Influences
20.3 Challenges
20.3.1 Overall Challenge
20.3.2 Methodological and Technical Challenges
20.3.3 Challenges Related to Data Analysis
20.4 Prospects
20.4.1 Epigenetic Markers
20.4.2 Technical Advances and Training
Acknowledgments
References
Index-Species
Index-Subjects
EULA