Genomics in Aquaculture

 
 
Academic Press
  • 1. Auflage
  • |
  • erschienen am 29. Juli 2016
  • |
  • 304 Seiten
 
E-Book | ePUB mit Adobe DRM | Systemvoraussetzungen
E-Book | PDF mit Adobe DRM | Systemvoraussetzungen
978-0-12-801690-9 (ISBN)
 

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
  • Englisch
  • San Diego
  • |
  • USA
Elsevier Science
  • 8,42 MB
978-0-12-801690-9 (9780128016909)
0128016906 (0128016906)
weitere Ausgaben werden ermittelt
  • Cover
  • Title page
  • Copyright page
  • Contents
  • List of Contributors
  • 1 - The new era of genome sequencing using high-throughput sequencing technology: generation of the first version of th...
  • Introduction
  • The first version of the Atlantic cod genome
  • The sequencing of a wild-caught cod specimen
  • The challenges of assembling large, outbred genomes
  • Assembling the first version of the cod genome
  • Annotating the first version of the cod genome
  • Synteny with other teleost genomes
  • Ongoing efforts to improve the Atlantic cod genome assembly
  • The impact of combining different sequencing technologies
  • Software developments for de novo assembly
  • Goals for a new reference genome
  • Acknowledgments
  • Glossary
  • References
  • 2 - The rainbow trout genome, an important landmark for aquaculture and genome evolution
  • Rainbow trout
  • Rainbow trout and Salmonids commercial importance
  • Rainbow trout: a freshwater laboratory rat
  • Rainbow trout life cycle
  • Genomic aspects
  • The rainbow trout genome: diversity, structure, organization
  • Genomic resources preexisting before the first genome sequence in rainbow trout
  • Rainbow trout genome sequencing
  • Rainbow trout genome structure
  • A genome for genetic and functional investigations
  • Deciphering the genetic architecture of traits
  • Functional insights in Rainbow trout nutrition
  • Selected examples of nutritional regulation of transcript levels
  • Nutrition and flesh quality: molecular LC-PUFA biosynthesis pathway is functional
  • Functional but atypically regulated glucose metabolism
  • Linking nutrition to metabolism: hormonal and nutrient sensor roles
  • The 21st century or the "omics" boom in nutritional studies
  • Nutritional regulation of hepatic glucose-6-phosphatase genes expression in rainbow trout: how the trout genome sequencing ...
  • Trout genomics for health
  • The rainbow trout immunome: the added value of a full repertoire of fish immunity genes
  • Toward the definition of a trout immunome
  • The case of antigen specific receptors, Igs and TCRs
  • Interest of a genome assembly for linkage studies: gene clusters and linkage studies
  • Rainbow trout reproduction with a genome sequence
  • Future directions and concluding remarks: resources are still expending
  • References
  • 3 - An improved version of the Atlantic cod genome and advancements in functional genomics: implications for the future...
  • The Atlantic cod fisheries-and the rebirth of cod aquaculture
  • Immunogenomics-the unusual immune system of Atlantic cod
  • Atlantic cod functional genomics research
  • Immunity and/or stress
  • Reproduction and development
  • Nutrigenomics
  • Toxicogenomics
  • Generation of a new version of the Atlantic cod genome
  • Annotation using MAKER2
  • Tandem repeat content-assembly and biological implications
  • An improved Atlantic cod genome-a valuable resource for biological inferences, fisheries management and the future cod aqua...
  • References
  • 4 - Catfish genomic studies: progress and perspectives
  • Introduction
  • The genome: structure and organization
  • Development of molecular markers
  • Linkage mapping
  • Physical mapping
  • Whole genome sequencing
  • Genome evolution and comparative genomics
  • The transcriptome: expression and function
  • Early efforts of EST sequencing
  • RNA-Seq based transcriptome analysis
  • Protein-coding genes
  • Long noncoding RNAs
  • MicroRNAs
  • Analysis of gene expression under various stress conditions
  • Gene pathways, networks, and their regulation
  • The genome: single nucleotide polymorphisms and genomic variations
  • Single nucleotide polymorphisms
  • Strain and population level genomic variations
  • Historical application of molecular markers for the analysis of populations
  • Development of high-density SNP arrays
  • The genome: its relationship with phenome
  • QTL analysis
  • Genome-wide association studies
  • Sex determination and progress toward understanding of sex in catfish
  • Gene expression and regulation in control of phenotypes
  • Future directions
  • Functional analysis of genes
  • Gene knockout systems and their potential use in catfish
  • Concluding remarks
  • References
  • 5 - Tilapia genomic studies
  • Introduction
  • Life history
  • The genome: structure and organization
  • Development of molecular markers
  • Linkage mapping
  • Repetitive sequences in the tilapia genome
  • Physical mapping
  • Whole genome sequencing
  • Genome evolution and comparative genomics
  • Transcriptome: expression and function
  • Expressed sequence tags (ESTs)
  • RNA-seq
  • microRNAs
  • Gene expression under different conditions
  • Liver transcriptome response to variation in dietary fat level
  • Response to pathogen infection
  • Functional and applied aspects
  • Reproduction-sex determination and differentiation
  • Salinity
  • Future direction and aspects
  • Whole genome sequence
  • Genetic improvement based on genomics
  • Conclusions
  • Acknowledgments
  • References
  • 6 - Turbot (Scophthalmus maximus) genomic resources: application for boosting aquaculture production
  • Biology and aquaculture
  • Turbot biology
  • Turbot production: aquaculture
  • Main problems of turbot production
  • Breeding programs
  • Impact of turbot aquaculture on wild populations
  • Genomic resources
  • Introduction
  • Transcriptome
  • Genetic map
  • Whole genome sequencing
  • Genetic architecture and function of productive traits
  • Growth-related traits
  • Molecular genomics of growth
  • QTL screening: growth-related QTL
  • QTL methodology
  • Growth-related QTL
  • Identification of candidate genes through comparative mapping
  • Genomics of the resistance of turbot to the main industrial diseases
  • Main diseases in turbot farms
  • High-throughput gene expression: microarrays and RNAseq
  • Functional genomics of the response to the main turbot diseases
  • Furunculosis versus scuticociliatosis
  • VHSV
  • Enteromyxosis
  • QTL screening: disease resistance related QTL
  • Crossing information from functional and association studies
  • Reproduction and sex control: general revision, QTL, functional genomics, and ongoing research
  • Sex differentiation in fish
  • Genetic architecture of sex determination in turbot
  • Gonad development and differentiation in turbot
  • Concluding remarks and perspectives
  • References
  • 7 - Zebrafish offer aquaculture research their services
  • Introduction
  • The Genome: diversity, structure and organization
  • The Genome and the corresponding transcriptome
  • Comparative perspectives
  • DNA and genome sequencing
  • Expressing the genome-the transcriptome defines all transcripts produced
  • Epigenetics-three levels of non-Mendelian heritage
  • Level 1: DNA methylation and hydroxymethylation
  • Level 2: histone protein modifications are dynamic
  • Level 3: Noncoding RNAs dominate the transcriptomes
  • Levels 1, 2, and 3 cross-talk in epigenetic landscapes
  • The toolbox: a set of advanced methods
  • Genome and epigenome editing
  • High-throughput imaging-screening
  • Functional and applied aspects of systems biology
  • Breeding model and reproduction control
  • What can we learn from history?
  • Reproduction control
  • Fish health
  • Bacterial infections and vaccine development
  • Viral infection genomics
  • Husbandry and nutrition
  • Husbandry guidelines
  • Nutritional omics
  • Effects of stressors
  • Zebrafish embryo toxicity test
  • High-throughput screening and transgenic reporter fish
  • Transgenerational effects
  • Future directions future perspectives
  • Acknowledgments
  • References
  • 8 - Current status in other finfish species
  • Introduction
  • Transcriptome resources and their main characteristics in gilthead seabream and soles
  • Current genetic maps and genome drafts in gilthead seabream and soles
  • Genetic maps and QTLs
  • Toward the first draft of Senegalese sole genome
  • Superscaffolds as putative chromosomes of Senegalese sole
  • Databases for genomic resources in gilthead seabream and soles
  • Functional and applied aspects using genomic approaches
  • Transcriptomic studies in larval stages and metamorphosis
  • Transcriptomic studies in nutrition
  • Transcriptomic studies in health and welfare
  • Future directions
  • Concluding remarks
  • Acknowledgments
  • References
  • 9 - Molluscs
  • Life history and biology
  • Genomes: diversity, structure, and organization
  • Functional and applied aspects
  • Growth
  • Immune function
  • Reproduction
  • Future directions
  • References
  • 10 - Genomics in the common carp
  • Common carp biology and aquaculture
  • The genome: diversity, structure, organization, and evolution
  • BAC-based genomics
  • Tetraploidized genome: genome structure, organization, and whole genome duplication
  • Genetic diversity studies
  • Genome evolution and gene fate of tetraploidization
  • Functional genomics research and applications in the common carp
  • Skin color
  • Immunity and disease resistance
  • Response to environmental stress
  • Toxicology
  • Genetic tool development
  • Future directions
  • Toward the perfect genome: updating the genome and annotation
  • Construction of comprehensive genome databases
  • Further develop genome resources from diverse populations
  • Unveiling the genetic basis of important traits for breeding applications
  • Concluding remarks
  • Acknowledgments
  • References
  • 11 - Future perspective
  • Index
  • Back cover

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