Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries [1° ed.] 0128163526, 9780128163528

Table of contents :
Front Cover
Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries
Copyright Page
Contents
List of contributors
About the editors
Foreword
Preface
1 Introduction
1 Cattle genomics: genome projects, current status, and future applications
1.1 Introduction
1.2 Sequencing cattle genome
1.3 Bovine single nucleotide polymorphism arrays
1.4 Genome-wide association studies in dairy cattle
1.5 Marker-assisted selection and genomic selection
1.6 Status and attainments of cattle genome projects
1.6.1 Cattle genome projects in Canada
1.6.2 Achievements and status of cattle genome sequencing in European countries
1.7 INTERBULL concept for genetic evaluation of breeding bulls
1.8 Achievements and status of cattle genome sequencing in Australia
1.9 Achievements and status of cattle genome sequencing in Brazil
1.10 Status of genomic selection across the world in bovine
1.10.1 Genomic selection in dairy cattle
1.10.2 Global scenario of genomic selection in beef cattle
1.10.3 Genomic selection in multibreed cattle populations
1.11 Conclusion
References
Further reading
2 Metagenomics revealing new virus species in farm and pet animals and aquaculture
2.1 Introduction
2.2 Technical aspects of viral metagenomics
2.3 Virus enrichment and nucleic acid amplification
2.4 Sequencing technologies
2.4.1 First-generation sequencing
2.4.2 Second-generation sequencing
2.4.2.1 Pyrosequencing
2.4.2.2 Illumina/solexa sequencing
2.4.2.3 Sequencing by oligonucleotide ligation and detection
2.4.2.4 Semiconductor sequencing
2.4.3 Third-generation sequencing
2.4.3.1 Single molecule real-time sequencing
2.4.3.2 Nanopore sequencing
2.5 Bioinformatics
2.6 Practical aspects of viral metagenomics
2.7 Viral metagenomics and discovery of new viruses in livestock
2.7.1 New viruses in pigs
2.7.2 New viruses in cattle
2.7.3 New viruses in small ruminants
2.7.4 Novel viruses in chickens
2.7.5 Novel viruses in turkeys
2.7.6 Novel viruses in other birds
2.8 Viral metagenomics and discovery of new viruses in pets
2.8.1 Novel viruses in dogs
2.8.2 Novel viruses in cats
2.9 Metagenomics revealing new virus species in aquaculture
2.9.1 Virome characterization
2.9.2 Complete genome sequencing by next generation sequencing
2.9.3 Discovery of novel viruses
2.10 Conclusion
Acknowledgements
References
Further reading
3 Genome editing in animals: an overview
3.1 Introduction
3.2 Existing methods
3.2.1 Zinc finger nucleases
3.2.2 Transcriptional activator-like effector nucleases
3.2.3 RNA-guided endonucleases
3.3 Types of CRISPR/Cas system
3.3.1 Type II CRISPR/Cas9 system for genome editing
3.3.1.1 Cas9 activity
3.3.1.2 Multiple gene editing
3.4 Potential pitfalls
3.4.1 Off-target effects
3.4.1.1 SgRNAs design
3.4.1.2 Cas9 nickase
3.4.1.3 “Enhanced Specificity” SpCas9(eSpCas9)
3.4.1.4 Cpf1
3.4.1.5 Cas9-HF1
3.4.1.6 HypaCas9
3.4.2 Delivery methods
3.4.3 Incidence of HDR
3.5 Comparing the CRISPR/Cas9 system versus zinc finger nucleases and transcriptional activator-like effector nucleases
3.6 Applications of CRISPR/Cas9 genome editing technology in animal agriculture
3.6.1 Study of developmental biology
3.6.2 Better food production
3.6.3 Disease control
3.6.3.1 Producing disease-resistant animals
3.6.3.1.1 African swine fever
3.6.3.1.2 Porcine reproductive and respiratory syndrome
3.6.3.1.3 Tuberculosis
3.6.3.1.4 Pseudorabies
3.6.3.2 Cell therapeutics—next generation of cure
3.6.3.2.1 Cancer
3.6.3.2.1.1 Adoptive T-cell Transfer
3.6.3.2.1.2 Harnessing CAR T cells
3.6.3.2.1.3 Studying synthetic lethal interactions
3.6.3.2.1.4 Antichaperon therapy
3.6.3.2.1.5 Dysregulation of Notch signaling
3.6.3.2.2 Diabetes
3.6.4 Diagnostics development
3.6.5 Vector control
3.6.6 Fighting antimicrobial resistance
3.6.7 Producing disease models
3.7 Ethical issues
3.7.1 Ecosystem disequilibrium
3.7.2 Regulatory hurdles
3.7.3 Genetic enhancement
3.8 Future prospects
3.8.1 Deextinction
3.8.2 Customization of pets
3.8.3 Drug discovery
3.8.4 Future farming
3.9 Conclusion
References
Further reading
2 Biotechnology for farm and pet animals
4 Genetic markers for improving farm animals
4.1 Introduction
4.2 Genetic markers related to farm animal productivity
4.2.1 Genetic markers in large ruminants
4.2.1.1 Markers for dairy production traits
4.2.1.2 Genetic markers related to reproductive performance
4.2.1.3 Genes associated with meat production
4.2.1.4 Genes related to draught power
4.2.2 Genetic markers in small ruminants
4.2.2.1 Meat and milk production
4.2.2.2 Reproductive traits
4.2.2.3 Wool production
4.2.3 Genetic markers in swine
4.2.3.1 Meat quality traits
4.2.3.2 Reproductive traits
4.2.4 Genetic markers in equine
4.2.5 Genetic markers in poultry
4.2.5.1 Meat
4.2.5.2 Eggs
4.3 Conclusion
Acknowledgment
References
Further reading
5 Applications of genome editing in farm animals
5.1 Introduction
5.2 Development of CRISPR/Cas9 system
5.3 The molecular structure of CRISPR/Cas9
5.4 Delivery and expression system
5.5 Mechanism of action
5.6 Gene editing using CRISPR/Cas9 in farm Animals
5.7 Technical challenges of the CRISPR/Cas9 genome editing
5.8 Premises and promises of genome editing by CRISPR/Cas9
Acknowledgment
References
6 Applications of genome editing in pet world
6.1 Introduction
6.2 Overview of gene editing tools
6.2.1 Zinc finger nucleases
6.2.2 Transcription activator-like effector nucleases
6.2.3 Clustered regularly-interspaced short palindromic repeat/Cas9 system
6.3 Scope of genome editing
6.4 Companion animals and gene editing: scope and prospects
6.4.1 Super muscular dogs
6.4.2 Micro pigs
6.4.3 Pet animals as disease model
6.4.4 Other prospects of gene editing in pets
6.5 Conclusion
Conflict of interest
Acknowledgements
References
7 Modulation of animal health through reverse genetics applications
7.1 Introduction
7.2 In vitro mutagenesis
7.3 RNA interference
7.4 Targeted genome modification by homologous recombination
7.5 Nuclease-based reverse genetics tools
7.5.1 Zinc finger nuclease
7.5.2 Transcription activator-like effector endonucleases
7.5.3 Clustered regularly interspaced short palindromic repeats and its associated gene 9
7.6 Applications of nuclease-based gene editing tools in modulating animal health
7.7 Conclusion
References
8 Animal models: bridging cross-species variation through animal biotechnology
8.1 Introduction
8.2 Animal models of diseases
8.2.1 Induced models
8.2.1.1 Pharmacological or chemical-induced models
8.2.1.2 Lesion-induced models
8.2.1.3 Stress-induced models
8.2.1.4 Induction of disease through biological molecules
8.2.2 Spontaneous models
8.2.3 Negative models
8.2.4 Genetically-modified models
8.2.5 Orphan models
8.3 Mimicking clinical conditions in animals
8.4 Engineering of animal models
8.5 Specific pathogen-free animals
8.5.1 Production methodology
8.5.2 Importance of specific pathogen-free animals in research
8.6 Gnotobiotic animals
8.7 Biotechnological approaches for generating animal models
8.7.1 Nuclease editors
8.7.1.1 Clustered regularly interspaced short palindromic repeats/Cas9
8.7.1.2 Zinc finger nucleases
8.7.2 Somatic cell nuclear transfer
8.7.3 Pronuclear microinjection
8.7.4 RNA interference
8.8 Translational significance of animal models
8.9 Pathological and pharmacological considerations
8.9.1 Physiological considerations
8.9.2 Pharmacological considerations
8.10 Ethical and regulatory issues
8.11 Conclusion
References
Further reading
3 Biotechnology for poultry and fishery
9 Transgenic chicken/poultry birds: serving us for survival
9.1 Introduction
9.2 Transgenesis usage for the poultry industry and environment protection
9.3 Poultry transgenesis and human nutrition
9.4 Poultry transgenesis and medicine
9.5 Conclusion
References
Further reading
10 Transgenesis and genome editing in chickens
10.1 Introduction
10.2 History of chicken genome manipulation
10.3 Embryo culture
10.4 Delivery of transgenes
10.5 Primordial germ culture
10.6 Precise genome editing
10.6.1 Zinc finger nucleases
10.6.2 Transcription activator-like effectors
10.6.3 Clustered regularly interspaced short palindromic repeats
10.6.4 Cre/LoxP
10.7 Conclusion
References
11 Concepts and potential applications of gene editing in aquaculture
11.1 Introduction
11.2 Genome editing
11.3 Zinc finger nucleases
11.4 Transcriptional activator-like effector nucleases
11.5 Clustered regularly-interspaced short palindromic repeats/CRISPR-associated protein 9
11.6 Comparison of three genome editing platforms
11.6.1 Efficiency
11.6.2 Specificity
11.7 Delivery system
11.8 Ease of designing
11.9 Multiplexing
11.10 Applications of genome editing
11.10.1 Research and development
11.10.2 Treatment of diseases
11.10.3 Functional genomics
11.10.4 Fishery science
11.10.5 Production of the mono-sex population
11.10.6 Production of fast-growing fishes
11.10.7 Sterility
11.10.8 Development of pollution markers
11.10.9 Production of ornamental fishes
11.10.10 Functional characterization of genes
11.11 Conclusion
References
Further reading
12 Marine biotechnology for food
12.1 Introduction
12.2 Food from marine sources
12.2.1 Marine fish
12.2.2 Molluscs, echinoderms, and crustaceans
12.2.3 Marine algae
12.3 Mariculture technologies for food
12.4 Biotechnology in mariculture
12.4.1 Genetic manipulation
12.4.1.1 Selective breeding
12.4.1.2 Polyploidy
12.4.1.3 Transgenics
12.4.2 Health management
12.4.3 Environment management
12.5 Bioprospecting for food
12.5.1 Functional foods and nutraceuticals from marine organisms
12.5.2 Marine sources of bioactive molecules
12.5.3 Bioactive compounds of importance in farming
12.5.3.1 Carotenoids
12.6 Conclusion
References
4 Biotechnology for Animal Disease Diagnosis and Prevention
13 Biotechnological innovations in farm and pet animal disease diagnosis
13.1 Introduction
13.2 Infectious diseases’ impact
13.3 Diagnosis of pathogens
13.3.1 Serological diagnostic assays
13.3.2 Nucleic acid-based diagnostic assays
13.3.2.1 Hybridization-based methods
13.3.2.2 Amplification-based methods
13.3.2.2.1 Polymerase chain reaction and its variants
13.3.2.2.2 Isothermal amplification methods
13.3.3 Novel and high throughput assays
13.3.3.1 Microarray
13.3.3.2 Peptide nucleic acids and aptamers
13.3.3.3 Biosensors
13.3.3.4 Next-generation sequencing
13.3.3.5 Point-of-care diagnostics
13.3.3.6 Patented diagnostic technologies
13.4 Applications of biotechnology in farm and companion animal’s disease diagnosis
13.4.1 Biotechnological tools in farm animal’s disease diagnosis
13.4.2 Biotechnological tools in companion animals’ disease diagnosis
13.5 Conclusion
Conflict of interest
Acknowledgments
References
14 Biotechnological tools in diagnosis and control of emerging fish and shellfish diseases
14.1 Introduction
14.2 Disease problems in fish culture
14.2.1 Fish diseases
14.2.2 Crustacean diseases
14.3 Diseases in shrimp (shellfish)
14.3.1 Diagnostic methods
14.3.1.1 Immunoassays
14.3.1.2 Molecular diagnostics for fish diseases
14.3.1.2.1 Polymerase chain reaction
14.3.1.2.1.1 Reverse transcriptase polymerase chain reaction
14.3.1.2.1.2 Nested polymerase chain reaction
14.3.1.2.1.3 Multiplex polymerase chain reaction
14.3.1.2.2 Real-time polymerase chain reaction
14.3.1.2.3 Hybridization techniques
14.3.1.2.4 Loop-mediated isothermal amplification
14.3.1.2.5 Microarrays
14.3.1.3 Matrix-assisted laser desorption/ionization-time of flight mass spectrometry
14.3.1.4 Nanotechnology and nanosensors
14.3.1.5 Genotyping techniques in characterization of pathogens
14.3.1.5.1 Pulse field gel electrophoresis
14.3.1.5.2 Polymerase chain reaction -based strain typing techniques
14.3.1.5.2.1 Arbitrarily primed - polymerase chain reaction and random amplified polymorphic DNA
14.3.1.5.2.2 Amplified fragment length polymorphism assays
14.3.1.5.2.3 Enterobacterial repetitive intergenic consensus - polymerase chain reaction, repetitive element - polymerase c...
14.3.1.5.2.4 Ribotyping
14.3.1.5.2.5 Amplified ribosomal DNA restriction analysis
14.4 DNA sequence analysis
14.5 Multilocus sequence typing analysis
14.6 Preventive and control measures
14.6.1 Vaccines for fish diseases
14.7 Immunostimulants
14.8 Probiotics
14.9 Therapeutics in fish diseases
14.10 Conclusion
References
Further reading
15 Advances and applications of vectored vaccines in animal diseases
15.1 Introduction
15.1.1 Vectors used for vaccine delivery
15.1.1.1 Poxvirus vectors
15.1.1.2 Adenovirus vectors
15.1.1.3 Retrovirus vectors
15.1.1.4 Lentivirus vectors
15.1.1.5 Cytomegalovirus vectors
15.1.1.6 Sendai virus vectors
15.2 Vectors for poultry vaccines
15.2.1 Herpesvirus of turkey
15.3 Vectored veterinary vaccines
15.4 Challenges in vectored veterinary vaccine
15.5 Conclusion
Conflict of interest
Acknowledgments
References
16 Bioinformatics for animal diseases: focused to major diseases and cancer
16.1 Introduction
16.1.1 Genomics
16.1.2 Transcriptomics
16.1.3 Proteomics
16.2 The investigation of the canine cancers using the omics data and bioinformatics methods: comparative aspects to human
16.2.1 Various types of the canine cancers
16.2.2 Genomics studies in the canine cancers
16.2.3 Transcriptomics studies in the canine cancers
16.2.4 Proteomics studies in the canine cancers
16.3 Bioinformatics and omics data in the cancers of other domestic animals
16.4 Genomics, transcriptomics, proteomics, and bioinformatics approaches to investigating the other animal diseases: a bri...
16.5 The future role of the bioinformatics and omics data in studying animal diseases (especially the cancers)
References
17 Biotechnological approaches to fish vaccine
17.1 Introduction
17.2 Biotechnology in developing new generation vaccines
17.2.1 Recombinant vaccines
17.2.2 Vector technology
17.2.3 Genetically attenuated pathogens
17.2.4 Vaccines based on naked DNA (DNA vaccines)
17.2.5 Reverse vaccinology
17.3 Conclusion
References
18 Contemporary vaccine approaches and role of next-generation vaccine adjuvants in managing viral diseases
18.1 Introduction
18.2 Structural vaccinology
18.3 Synthetic vaccines
18.4 Reverse vaccinology
18.5 Next-generation vaccine adjuvants
18.5.1 Aluminum salts (Alum)
18.5.2 Oil-in-water emulsions
18.5.3 Virosomes
18.5.4 Monophosphoryl lipid and adjuvant System 04
18.5.5 Carbohydrate adjuvants
18.5.6 Cytokines adjuvants
18.5.7 Nucleic acid-based mucosal adjuvants
18.5.8 Nanomaterial as adjuvants
18.6 Vaccine delivery technologies
18.7 Conclusion
18.8 Future perspectives
Acknowledgments
References
Further reading
19 Advances in structure-assisted antiviral discovery for animal viral diseases
19.1 Introduction
19.1.1 General strategies for identifying viral drug and vaccine targets
19.1.2 Structure determination techniques
19.1.2.1 X-ray crystallography
19.1.2.2 Nuclear magnetic resonance
19.1.2.3 Cryo-electron microscopy
19.1.3 Computational structure prediction and drug design
19.2 Animal viruses and viral diseases
19.2.1 Foot and mouth disease virus
19.2.1.1 Clinical signs of foot and mouth disease virus
19.2.1.2 Serotypes of foot and mouth disease virus
19.2.1.3 Structure and genome of foot and mouth disease virus
19.2.1.4 Foot and mouth disease virus nonstructural proteins
19.2.1.5 Vaccination
19.2.1.6 Structure-based drug development against foot and mouth disease virus
19.2.2 Herpesviruses
19.2.2.1 Structure of herpesvirus
19.2.2.2 Herpesviruses lytic and latent cycle
19.2.2.3 Antivirals against herpesviruses
19.2.3 Coronavirus (severe acute respiratory syndrome)
19.2.3.1 Replication of coronavirus
19.2.3.2 Structure-based antivirals against coronavirus
19.2.4 Alphaviruses
19.2.4.1 Functions of nonstructural proteins
19.2.4.2 Viral target proteins for drug development
19.2.5 Paramyxovirus
19.2.5.1 Antivirals against paramyxovirus
19.2.6 Avian influenza virus
19.2.7 Pestivirus
19.2.7.1 Vaccine and structure-based drug design
19.3 Conclusion
References
20 Vaccines the tugboat for prevention-based animal production
20.1 Introduction
20.2 Vaccines and one health
20.3 Types of vaccines
20.3.1 Conventional vaccines
20.3.1.1 Live-attenuated vaccines
20.3.1.2 Inactivated vaccines
20.3.1.3 Toxoids
20.3.2 Genetically-engineered vaccine
20.3.2.1 Subunit vaccine
20.3.2.2 Virus-like particle vaccines
20.3.2.3 Vectored vaccines
20.3.2.4 DNA vaccine
20.4 Developments in veterinary vaccinology
20.5 Diversity of vaccine
20.5.1 Bacterial diseases
20.5.1.1 Hemorrhagic septicemia
20.5.1.2 Brucellosis
20.5.1.3 Anthrax
20.5.1.4 Black quarter
20.5.1.5 Leptospirosis
20.5.1.6 Mycobacterium infection in cattle
20.5.1.7 Salmonellosis
20.5.1.8 Escherichia coli infection
20.5.2 Viral diseases
20.5.2.1 Foot and mouth disease
20.5.2.2 Rabies
20.5.2.3 Peste-des-petits ruminants
20.5.2.4 Bluetongue
20.5.2.5 Sheep pox and goat pox
20.5.2.6 Classical swine fever
20.5.2.7 Japanese encephalitis virus
20.5.2.8 Bovine viral diarrhea
20.5.2.9 Infectious bovine rhinotracheitis
20.5.2.10 Influenza (flu)
20.5.2.11 Winter dysentery
20.5.2.12 Rotavirus gastroenteritis
20.5.2.13 Parasitic vaccines
20.5.2.14 Theileriosis
20.5.2.15 Coccidiosis
20.5.2.16 Parasitic bronchitis
20.6 Combined vaccination
20.7 Poultry vaccines
20.8 Adverse effect of vaccines
References
Further reading
Index
Back Cover

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