Epigenetics in Aquaculture

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.

Francesc Piferrer is Research Professor and Head of the Reproductive Physiology and Environmental Epigenetics Group at the Institute of Marine Sciences, Spanish National Research Council, Barcelona, Spain.

Han-Ping Wang is Principal Scientist, Research Professor, and Director of the Ohio Center for Aquaculture Research and Development at The Ohio State University, Piketon, Ohio, USA.

Table of Contents

List of Contributors

Preface

Acknowledgements

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 

Han-Ping Wang

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 TET

1.2.3 KMT and KDM

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

1.4.1.1 The potential roles of epigenetics in early development

1.4.1.2 The potential applications of epigenetics in reproduction and breeding

1.4.2 Health and wellbeing management 

1.4.2.1   The roles of epigenetics in controlling stress and disease

1.4.2.2   The potential applications of epigenetics in health and wellbeing management 

1.4.3        Nutrition and growth advancement 

1.4.3.1   The roles of epigenetics in nutrition and growth 

1.4.3.2 The potential applications of epigenetics in nutrition and growth 

1.4.3        Sustainability enhancement

1.4.4.1 The roles of epigenetics in adaption and sustainability

1.4.4.2 The potential applications of epigenetics in sustainability enhancement

1.5 Conclusion and perspectives

2             Transcriptional epigenetic mechanisms in aquatic species 

Laia Navarro-Martín, Jan A. Mennigen, Jana Asselman

2.1.        Epigenetic mechanisms as modulators of transcription 

2.1.1.     DNA methylation: 

2.1.1.1. Regulation of DNA methylation status by key enzymes 

2.1.1.2. Methylation changes translated into functional states in the genome 

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 

2.5.        Acknowledgments 

2.6.        References 

3             Epigenetic regulation of gene expression by non-coding RNAs  

Elena Sarropoulou and Ignacio Fernández

3.1.        General introduction

3.2.        Major types of ncRNAs

3.2.1.     Small non-coding RNA (sncRNA)

3.2.1.1. MicroRNA (miRNA)

3.2.1.2. P-element–induced wimpy testis (Piwi)-interacting RNA (piRNA)

3.2.1.3. Small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA)

3.2.1.4. Transfer RNA (tRNA)-derived fragments (tRFs)

3.2.2.     Measurement of sncRNAs

3.2.2.1. Methods for sncRNA detection

3.2.2.2. sncRNA expression 13 3.2.3 long non-coding RNA (lncRNA)

3.2.3.1. circRNAs 16 3.2.3.2 Large intergenic noncoding RNAs (lincRNAs)

3.3.        Roles of ncRNA in key processes of teleosts

3.3.1.     Roles of ncRNA during development

3.1.1.     Evaluated miRNA functions during teleost development

3.3.2.     Roles of ncRNA during reproduction

3.3.3.     Roles of ncRNA in immune and stress response

3.4.        ncRNAs as Biomarkers and Future perspectives

4             Epigenetic inheritance in aquatic organisms 

Ramji K. Bhandari

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 exposures 

4.3.1.     Developmental exposure effects 

4.3.2.     Postnatal or parental exposure 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 in hatchery-raised fish: Authors’ view 

4.4.5.  Potential for the Mitigation of Epigenetically Inherited Harmful Effects in Fish 

4.5.        Conclusions and Perspectives 

5             Environmental epigenetics in fish: Response to climate change stressors

             Zhi-Gang Shen, Yue Yu

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   

6             Analytical methods and tools to study the epigenome  

            Oscar Ortega-Recaldeand Timothy A. Hore

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  

6.3.1.1. Enzyme-based methods  

6.3.1.2. Affinity-based methods  

6.3.1.3. Bisulfite-based methods 

6.3.1.4. Direct detection methods 

6.3.2.     DNA methylation methods according to resolution level  

6.3.2.1. Low resolution 

6.3.2.2. Medium resolution 

6.3.2.3. Single-nucleotide resolution 

6.3.3. DNA methylation methods according to genome coverage 

6.3.3.1. Targeted approaches 

6.3.3.2. Genome-wide 

6.3.3.3. Whole genome        

6.3.4. Histone modifications 

6.3.4.1. Chromatin immunoprecipitation 

6.3.4.2. CUT&RUN And CUT&Tag 

6.3.5. Assessment of other epigenetic modifications  

6.4. Bioinformatic analysis  

6.5. Databases and other public resources  

6.6. Conclusions and outlook 

Part II: Epigenetics insights from major aquatic groups

7             Epigenetics in sexual maturation and gametes of fish 

Lombó Alonso Marta, Laurent Audrey, Herráez Maria Paz, Labbé Catherine 

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

7.3.1.1. DNA methylation

7.3.1.2. Histone modifications

7.3.2.     Domestication

7.3.3.     Reproductive biotechnologies

7.3.3.1. Biotechnologies targeting the gametogenesis stages

7.3.3.2. Biotechnologies targeting the gametes

7.3.4. Transmission of gamete epimutations to the following generations

7.3.4.1. Transmission of epigenotoxic effect

7.3.4.2. Transmission of biotechnological clues

7.4. Conclusion

8             Epigenetics in sex determination and differentiation of fish

        Qian Wang, Qian Liu, Xiao-Na Zhao, Wen-Xiu Ma, Li-Li Tang, Bo Feng, Chang-Wei Shao

8.1. Introduction

8.1.1. Sex chromosome in fish

8.1.2. Sex determination and sex 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 in sex chromosome evolution

8.2.3. The role of chromatin structure in 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. Epigenetics and sex differentiation

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

9             Epigenetics in fish growth  

Jorge M.O. Fernandes, Artem V. Nedoluzhko, Ioannis Konstantinidis and Paulo Gavaia

9.0.        Synopsis 

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. Implication 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 to mitochondrial function

9.5.3.     The mitoepigenome in fish

9.5.4.     Association between growth, mitochondrial methylation and hydroxymethylation

9.6.        Conclusion

10           Epigenetics in fish nutritional programming

            Kaja H. Skjærven, Anne-Catrin Adam, Takaya Saito, Rune Waagbø, and Marit Espe

10.1 Epigenetic basis of nutritional programming

10.1.1 DNA methylation

10.1.2 Histone modifications and chromatin structure

10.1.3 Non-coding 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

10.2.1 Programming of broodstock to affect the offspring

10.2.2 Programming of larvae to affect later stages

10.5 Conclusions and perspectives for nutritional programming in aquaculture

10.6 Acknowledgements

11          Microbiome, epigenetics, and fish health interactions in aquaculture

Sofia Consuegra, Tamsyn Uren Webster, Ishrat Anka

Introduction

11.1. The fish microbiome in aquaculture

11.1.1. The fish microbiome diversity and composition

11.1.2. Extrinsic and intrinsic factors that affect fish microbiome composition

11.1.2.1. Extrinsic factors (habitat, diet, stress)

11.1.2.2. Intrinsic factors (host genetics, age)

11.1.3. Microbiome interaction with fish health and immunity

11.1.4. Microiome manipulations

11.2. Miscrobiome-epigenome intractions

11.2.1. Microbiome-epigenome interactions in mammals and model species

11.2.2. Microbiome and epigenetic interactions in aquaculture

11.3. Conclusions

12   The epigenetics of stress in farmed fish – an appraisal

Bruno Guinand and Athanasios Samaras

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. 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 (BDNF)            

12.4.4. Serotonin signaling

12.4.5. Hypothalamic connections

12.4.5. 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

13           Epigenetics in hybridization and polyploidization of aquatic animals 

               Li Zhou and Jian-Fang Gui 

13.1. Hybridizing and Hybridization  

13.2. Polyploidy and Polyploidization  

13.3. Epigenetic changes 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 

14.         Epigenetics in aquatic toxicology 

               Sara J. Huttonand Susanne M. Brander 

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.  Non-coding 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.      Conclusions and perspective

15           Epigenetics in molluscs 

Manon Fallet 

15.1       Introduction

15.1.1. Definition and presentation of mollusks

15.1.2. Molluscs’ place in aquaculture

15.1.3. Sensitivity of mollusks to environmental changes and anthropogenic pressures

15.2. DNA modification in mollusc species

15.3. Chromatin conformation and histone modifications/variants in molluscs

15.4. Non-coding RNAs in molluscs

15.5. Epigenetic responses to environmental fluctuations in molluscs

15.6. Mechanisms of meiotic epigenetic inheritance in molluscs and their impact in evolution

15.7. Perspectives

15.7.1. Remaining challenges in molluscs epigenetics

15.7.2. Application of epigenetic markers in aquaculture and aquatic species conservation

15.8. General conclusions

16          Epigenetics in crustaceans  

Günter Vogt 

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 in crustaceans  

16.8.      Potential application of epigenetics in crustacean aquaculture 

17          Epigenetics in algae

Christina R. Steadman 

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 algae species, Chlamydomonas reinhardtii 

17.2.8 Histone modifications in other microalgae  

17.3 Environmental stress alters microalgae epigenomes 

17.4 Conclusions and perspectives  

Part III:  Implementation of epigenetics in aquaculture

18          Development of epigenetic biomarkers in aquatic organisms 

            Dafni Anastasiadiand Anne Beemelmanns

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. Non-coding 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

18.3.3.2. Procedure step-by-step

18.3.4. Machine learning methods for epigenetic biomarkers

18.3.4.1. Classification of machine learning methods

18.3.4.2. Sample size determination

18.3.4.3. Machine learning workflow

18.3.5. Examples of machine learning methods for epigenetic biomarker discovery in aquatic organisms

18.3.5.1. Sex: a classification problem

18.3.5.2. Age: a regression problem

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

18.4.7.1. Temperature

18.4.7.2. Hypoxia

18.4.7.3. Temperature and Hypoxia combined

18.4.7.4. Salinity

18.4.8. Aquatic contaminants

18.4.9. Adaptation and speciation

18.5. Future perspectives

18.6. Concluding remarks

19           Genetics and epigenetics in aquaculture breeding 

Shokouoh Makvandi-Nejad and Hooman Moghadam

19.1 Overview

19.2 Breeding in Aquaculture & 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 & search for Epigenetic Biomarkers

19.7 Concluding Remarks

20           Epigenetics in aquaculture: knowledge gaps, challenges and future prospects

Francesc Piferrer

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

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