Recent developments in DNA marker technologies, in particular the emergence of Single Nucleotide Polymorphism (SNP) discovery, have rendered some of the traditional methods of genetic research outdated. Next Generation Sequencing and Whole Genome Selection in Aquaculture comprehensively covers the current state of research in whole genome selection and applies these discoveries to the aquaculture industry specifically. The text begins with a thorough review of SNP and transitions into topics such as next generation sequencing, EST data mining, SNP quality assessment, and whole genome selection principles. Ending with a discussion of the technology's specific applications to the industry, this text will be a valuable reference for those involved in all aspects of aquaculture research. Special Features: Unique linking of SNP technologies, next generation sequencing technologies, and whole genome selection in the context of aquaculture research Thorough review of Single Nucleotide Polymorphism and existing research 8-page color plate section featuring detailed illustrations

Genomics in Aquaculture is a concise, must-have reference that describes current advances within the field of genomics and their applications to aquaculture. Written in an accessible manner for anyone—non-specialists to experts alike—this book provides in-depth coverage of genomics spanning from genome sequencing, to transcriptomics and proteomics. It provides, for ease of learning, examples from key species most relevant to current intensive aquaculture practice. Its coverage of minority species that have a specific biological interest (e.g., Pleuronectiformes) makes this book useful for countries that are developing such species. It is a robust, practical resource that covers foundational, functional, and applied aspects of genomics in aquaculture, presenting the most current information in a field of research that is rapidly growing. - Provides the latest scientific methods and technologies to maximize efficiencies for healthy fish production, with summary tables for quick reference - Offers an extended glossary of technical and methodological terms to help readers better understand key biological concepts - Describes state-of-the-art technologies, such as transcriptomics and epigenomics, currently under development for future perspective of the field - Covers minority species that have a specific biological interest (e.g., Pleuronectiformes), making the book useful to countries developing such species

Tag-based approaches were originally designed to increase the throughput of capillary sequencing, where concatemers of short sequences were first used in expression profiling. New Next Generation Sequencing methods largely extended the use of tag-based approaches as the tag lengths perfectly match with the short read length of highly parallel sequencing reactions. Tag-based approaches will maintain their important role in life and biomedical science, because longer read lengths are often not required to obtain meaningful data for many applications. Whereas genome re-sequencing and de novo sequencing will benefit from ever more powerful sequencing methods, analytical applications can be performed by tag-based approaches, where the focus shifts from 'sequencing power' to better means of data analysis and visualization for common users. Today Next Generation Sequence data require powerful bioinformatics expertise that has to be converted into easy-to-use data analysis tools. The book's intention is to give an overview on recently developed tag-based approaches along with means of their data analysis together with introductions to Next-Generation Sequencing Methods, protocols and user guides to be an entry for scientists to tag-based approaches for Next Generation Sequencing.

Fish have been a major component of our diet and it has been suggested that fish/seafood consumption contributed to the development of the human brain, and this together with the acquisition of bipedalism, perhaps made us what we are. In the modern context global fish consumption is increasing. However, unlike our other staples, until a few years back the greater proportion of our fish supplies were of a hunted origin. This scenario is changing and a greater proportion of fish we consume now is of farmed origin. Aquaculture, the farming of waters, is thought to have originated in China, many millennia ago. Nevertheless, it transformed into a major food sector only since the second half of the last century, and continues to forge ahead, primarily in the developing world. China leads the global aquaculture production in volume, in the number of species that are farmed, and have contributed immensely to transforming the practices from an art to a science. This book attempts to capture some of the key elements and practices that have contributed to the success of Chinese aquaculture. The book entails contributions from over 100 leading experts in China, and provides insights into some aquaculture practices that are little known to the rest of the world. This book will be essential reading for aquaculturists, practitioners, researchers and students, and planners and developers.

The book is divided into two sections and represents the current trend of research in aquatic bioresource. In the section "Biology, Ecology and Physiological Chemistry", high-impact articles are contributed on reproduction, population genetics, evolution, biodiversity, biology and ecology of different aquatic faunas. Physiological chemistry of lipid, bioactive pharmaceuticals and chemical ecological aspects of aquatic organisms were discussed. In the section entitled "Conservation and Sustainable Management", authors highlighted conservation- and management-related issues of various bioresources in different regions of the earth. The book mentions the biological, ecological, physiological and genetic significance of aquatic organisms with resource potential. The authors stressed on rational utilisation and management of bioresource ensuring minimal damage of the aquatic ecosystem. This book would provide a direction towards sustainable ecological management of bioresource.

Genomics has revolutionized biological research over the course of the last two decades. Genome maps of key agricultural species have offered increased understanding of the structure, organization, and evolution of animal genomes. Building upon this foundation, researchers are now emphasizing research on genome function. Published with the World Aquaculture Society, Functional Genomics in Aquaculture looks at the advances in this field as they directly relate to key traits and species in aquaculture production. Functional Genomics in Aquaculture opens with two chapters that provide a useful general introduction to the field of functional genomics. The second section of the book focuses on key production traits such as growth, development, reproduction, nutrition, and physiological response to stress and diseases. The final five chapters focus on a variety of key aquaculture species. Examples looking at our understanding of the functional genomes of salmonids, Mediterranean sea bass, Atlantic cod, catfish, shrimp, and molluscs, are included in the book. Providing valuable insights and discoveries into the functional genomes of finfish and shellfish species, Functional Genomics in Aquaculture, will be an invaluable resource to researchers and professionals in aquaculture, genetics, and animal science.

Bioinformatics derives knowledge from computer analysis of biological data. In particular, genomic and transcriptomic datasets are processed, analysed and, whenever possible, associated with experimental results from various sources, to draw structural, organizational, and functional information relevant to biology. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics in Aquaculture provides the most up to date reviews of next generation sequencing technologies, their applications in aquaculture, and principles and methodologies for the analysis of genomic and transcriptomic large datasets using bioinformatic methods, algorithm, and databases. The book is unique in providing guidance for the best software packages suitable for various analysis, providing detailed examples of using bioinformatic software and command lines in the context of real world experiments. This book is a vital tool for all those working in genomics, molecular biology, biochemistry and genetics related to aquaculture, and computational and biological sciences.

From a global perspective aquaculture is an activity related to food production with large potential for growth. Considering a continuously growing population, the efficiency and sustainability of this activity will be crucial to meet the needs of protein for human consumption in the near future. However, for continuous enhancement of the culture of both fish and shellfish there are still challenges to overcome, mostly related to the biology of the cultured species and their interaction with (increasingly changing) environmental factors. Examples of these challenges include early sexual maturation, feed meal replacement, immune response to infectious diseases and parasites, and temperature and salinity tolerance. Moreover, it is estimated that less than 10% of the total aquaculture production in the world is based on populations genetically improved by means of artificial selection. Thus, there is considerable room for implementing breeding schemes aimed at improving productive traits having significant economic impact. By far the most economically relevant trait is growth rate, which can be efficiently improved by conventional genetic selection (i.e. based on breeding values of selection candidates). However, there are other important traits that cannot be measured directly on selection candidates, such as resistance against infectious and parasitic agents and carcass quality traits (e.g. fillet yield and meat color). However, these traits can be more efficiently improved using molecular tools to assist breeding programs by means of marker-assisted selection, using a few markers explaining a high proportion of the trait variation, or genomic selection, using thousands of markers to estimate genomic breeding values. The development and implementation of new technologies applied to molecular biology and genomics, such as next-generation sequencing methods and high-throughput genotyping platforms, are allowing the rapid increase of availability of genomic resources in aquaculture species. These resources will provide powerful tools to the research community and will aid in the determination of the genetic factors involved in several biological aspects of aquaculture species. In this regard, it is important to establish discussion in terms of which strategies will be more efficient to solve the primary challenges that are affecting aquaculture systems around the world. The main objective of this Research Topic is to provide a forum to communicate recent research and implementation strategies in the use of genomics in aquaculture species with emphasis on (1) a better understanding of fish and shellfish biological processes having considerable impact on aquaculture systems; and (2) the efficient incorporation of molecular information into breeding programs to accelerate genetic progress of economically relevant traits.

The global human population will reach nine billion by 2050, and seafood is projected to be the primary food source to sustain such a large population. According to a recent World Bank report, aquaculture will be the prime source of seafood by 2030. Tilapia is one of the promising species for commercial aquaculture and one of the second most farmed fish worldwide. Given the issues raised by Antibiotic misuse in intensive aquaculture, such as the occurrence of resistant bacteria, it is necessary to develop environment-friendly strategies that could be used to improve production in a sustainable manner. Also, there is a need to establish the best aquaculture practice (BAP) approaches to avoid significant disruption to the ecosystem, the loss of biodiversity, and substantial pollution impact on the environment. The book covers the recent findings regarding sustainable tilapia farming through environment-friendly approaches. This book contains chapters that cover the current status of world tilapia farming and the concept of sustainability of tilapia culture (Chap. 1). Chap. 2 discusses the health management of tilapia with a particular focus on various diseases and treatments. Chap. 3 provides an updated view of the possible effects of feed additives on tilapia reproductive performance. Chap. 4, 5, and 6 cover the recent findings on the gut microbiota of tilapia with a particular focus on structure and modulation. Chap. 7 focuses on the use of medicinal plants for sustainable tilapia farming. Chap. 8 provides insights into the application of alternative protein sources to decrease fish meal consumption. Chap. 9 highlights the importance of culture systems for the development of sustainable tilapia aquaculture. We believe the current book will be very helpful to academics, researchers, and policy-makers in aquaculture.

The foundation of quantitative genetics theory was developed during the last century and facilitated many successful breeding programs for cultivated plants and t- restrial livestock. The results have been almost universally impressive, and today nearly all agricultural production utilises genetically improved seed and animals. The aquaculture industry can learn a great deal from these experiences, because the basic theory behind selective breeding is the same for all species. The ?rst published selection experiments in aquaculture started in 1920 s to improve disease resistance in ?sh, but it was not before the 1970 s that the ?rst family based breeding program was initiated for Atlantic salmon in Norway by AKVAFORSK. Unfortunately, the subsequent implementation of selective breeding on a wider scale in aquaculture has been slow, and despite the dramatic gains that have been demonstrated in a number of species, less than 10% of world aquaculture production is currently based on improved stocks. For the long-term sustainability of aquaculture production, there is an urgent need to develop and implement e- cient breeding programs for all species under commercial production. The ability for aquaculture to successfully meet the demands of an ever increasing human p- ulation, will rely on genetically improved stocks that utilise feed, water and land resources in an ef?cient way. Technological advances like genome sequences of aquaculture species, and advanced molecular methods means that there are new and exciting prospects for building on these well-established methods into the future.