Preface

Aquaculture is the fastest food production sector in the world and prospects are that this position will be maintained for years to come. According to data from the Food and Agriculture Organization (FAO) of the United Nations, in 2020 global aquaculture production reached a record of 122.6 million tons worth USD 281.5 billion. Animals accounted for 87.5 million tons while algae comprised 35.1 million tons. However, aquaculture must become more sustainable to meet the growing demand for aquatic foods of an ever-increasing human population. Thus, improved aquaculture production requires further technical innovations, including more focus on breeding programs, feed utilization, well-being, and disease control. Similar to any other food production system, aquaculture is about producing the phenotypes with superior value. In this endeavor, new advances on our understanding of the epigenetic regulation of the phenotype have the potential to play an increasing role in achieving aquaculture production sustainability.

The term "epigenetics" was coined by Conrad Waddington in the 1940s, but with a meaning different from how it is understood today. Initially, it was essentially related to what today is understood as the field of developmental biology and how the phenotype comes into being. However, the modern concept of epigenetics, i.e., "the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence," arose in the mid-1990s and around the turn of this century. The field has largely benefited especially from the advancements made after the sequence of the human genome, the characterization of the regulatory elements, and all emerging technologies to interrogate different aspects of the genome and epigenome.

Epigenetics is now considered one of the "hot topics" in biology. Epigenetic modifications or "marks" can be easily identified, and they constitute therapeutic approaches for the treatment of an increasing number of diseases. Thus, there is a lot of research ongoing in the epigenetics of cancer, for example.

There are three very important aspects to take into account when dealing with epigenetics. First, epigenetics integrates genomic and environmental influences to bring about the phenotype. Second, there is a fraction of the phenotypic variance that cannot be explained solely on genetic variation, but that can be explained by taking into account epigenetic variation. Third, epigenetic changes can be inherited and thus passed from parents to offspring into the following generations. Combined, this has prompted the implementation of epigenetic research, not only in ecology and evolution for its contribution to adaptation to new environments, but also into agriculture and livestock for improved food production. Consequently, recently there has been both a clear interest in marine epigenetics and in the application of epigenetics in aquaculture. One of the main reasons is that aquatic organisms are quite susceptible to environmental cues since, for example, temperature in a cold-blooded animal influences growth rates more strongly than in a warm-blooded animal. Further, in contrast to mammals, fishes seem to have less reprogramming and erasing of epigenetic marks after fertilization, thus facilitating epigenetic transmission of environmental influences to the next generation. Thus, there is a lot of interest for the application of epigenetics in aquaculture. However, and to the best of our knowledge, there are currently no books that address this need.

"Epigenetics in Aquaculture" consists of 20 chapters and is arranged into three parts: Part I: Theoretical and practical bases of epigenetics in aquaculture; Part II: Epigenetics insights from major aquatic groups; and Part III: Implementation of epigenetics in aquaculture. All chapters are written by top specialists with ample experience and at the forefront in their respective research fields.

Part I contains six chapters (Chapters 1-6) and provides the necessary background to understand what epigenetics is about and what are the major mechanisms and phenomena. The first chapter covers the overall roles and the diversity of epigenetic mechanisms across major taxa and provides insights into their potential applications in aquaculture and aquatic animals. The following two chapters are devoted to the three main epigenetic mechanisms regulating gene expression, namely, DNA methylation, histone modifications, and non-coding RNAs. The next two chapters are devoted to two key aspects of epigenetics. One explains how epigenetic modifications can be inherited across different generations, a hot topic in different areas of biology, and the other elucidates the role of epigenetics in integrating environmental cues as a powerful mechanism in the adaptation and the basis of organismal plastic responses to rapid environmental change. The last chapter of Part I presents the currently available methods to analyze the epigenetic modifications including the latest developments, as well as some basic resources for the bioinformatics analysis of the data. It also explains how to choose among the different approaches based on the type of question that one aims to answer.

Part II contains 11 chapters (Chapters 7-17) and constitutes the bulk of the book. These chapters explore the roles of epigenetic regulatory mechanisms in key biological process and their relevance for aquatic production. The first two chapters deal with epigenetic sex determination and differentiation as well as the dynamics of epigenetic marks during gametogenesis and early development. The following two chapters are devoted to growth, with one focusing on skeletal muscle and the other emphasizing nutritional programming. The next two chapters of Part II are devoted to the epigenetics of stress response, immune response, and the emerging topic of the role of the microbiome in shaping epigenetic responses of the host. Additionally, one chapter is focused on epigenetics in hybridization and polyploidy and another on how epigenetics can contribute to explain organismal responses to toxins present in the aquatic environment. Many of the above-cited chapters of Part II focus on fish, where considerable work has been carried out so far. Thus, this part ends with three chapters dedicated to the epigenetics of other taxa that are also very important for aquaculture production, namely mollusks, crustaceans, and algae, where interesting discoveries related to similarities and differences with the situation in vertebrates are being made.

Finally, Part III includes the final three chapters (Chapters 18-20), dealing with the actual integration of epigenetics into aquaculture practice. For this, the development of biomarkers and their applications in aquaculture is discussed. Particular attention is then paid on the integration of epigenetic selection into current genetic breeding programs. The final chapter identifies knowledge gaps, discusses challenges that must be overcome, and outlines future prospects on the application of epigenetics in aquaculture. In addition to tables, figures, and abundant bibliography, each chapter contains a glossary of terms used with pertinent definitions.

Thus, this book provides an update on the state-of-the-art on the knowledge of epigenetic regulatory mechanisms in major taxa of aquatic organisms including algae, crustaceans, mollusks, and fish and how this new knowledge can be applied to increase aquaculture production. It covers both basic and applied aspects of epigenetics related to reproduction, development, growth, nutrition, and disease of aquatic species, which we hope will benefit the aquatic scientific community and the aquaculture sector.

This book will be appealing to anyone interested in knowing all major aspects related to epigenetics, including mechanisms, inheritance, methodology, etc. Information contained within will be particularly useful to researchers working on epigenetics in aquatic animals and aquaculture, including basic aspects of fish and shellfish epigenetics, reproductive endocrinology, genetics, and evolutionary and environmental biology. It will also appeal to PhD and MSc students and biologists working in hatcheries or in breeding companies, who will all benefit from reading about epigenetics and the opportunities it can provide. More broadly, aquatic biologists, including fisheries managers and conservation biologists, will also benefit from clear and practical information in epigenetics. The epigenetic insights from fish, shellfish, and aquatic model species will attract readers from other disciplines as well, who might find inspiration in findings made on epigenetics of aquatic organisms.

Our previous book, "Sex Control in Aquaculture," was based on knowledge accumulated after decades of applying sex control techniques to improve aquatic productivity. In contrast, the present book is based on research that is just a few years old because the study of epigenetics in aquatic organisms and its application in aquaculture is still in its infancy. Thus, a lot remains to be done. We hope that our efforts in providing a comprehensive picture of the current situation will be of much help and foster future research. The well-known British zoologist D'Arcy Thompson (1860-1948) wrote in the preface of his most famous book "On Growth and Form" that "this book of mine has little need of preface, for indeed it is 'all preface' from beginning to end." Given...