Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries

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
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