Advances in Animal Genomics

Advances in Animal Genomics
Copyright
Dedication
Contributors
Preface
Key features of the book
Organization of the book
Acknowledgments
1. Introduction
1.1 Introduction
1.2 Branches of animal genomics
1.2.1 Structural genomics
1.2.2 Functional genomics
1.2.3 Epigenomics
1.2.4 Metagenomics
1.2.5 Pharmacogenomics
1.3 Genetic markers used in animal genomics
1.3.1 Restriction fragment length polymorphism (RFLP)
1.3.2 Random amplified polymorphic DNA (RAPD)
1.3.3 Microsatellites
1.3.4 Single nucleotide polymorphism (SNP)
1.4 Techniques used in creating transgenic animals
1.4.1 Microinjection
1.4.2 Somatic cell nuclear transfer (SCNT)
1.4.3 Artificial chromosome transfer
1.4.4 Embryonic stem (ES) cell-based cloning and transgenesis
1.4.5 Viral vector-mediated DNA transfer
1.5 Application of animal genomics
1.5.1 Livestock breeding industry
1.5.2 Transgenic animal
1.5.3 Gene therapy
1.5.4 Superovulation
1.5.5 Improving hair and fiber
1.5.6 Disease resistant animals
1.5.7 Nutritious food
1.6 Conclusion
References
Further reading
2. From gene to genomics: tools for improvement of animals
2.1 Introduction
2.2 Genes
2.2.1 Chromosome structure and organization
2.2.2 Gene structure and organization
2.2.2.1 Eukaryotic gene
2.2.2.2 Prokaryotic gene
2.3 Genome
2.3.1 Anatomy of the eukaryotic genome
2.3.1.1 Gene and gene-related sequences
2.3.1.1.1 Exons (protein-coding regions)
2.3.1.1.2 Regulating sequences
2.3.1.1.3 Introns
2.3.1.1.4 Gene fragments
2.3.1.1.5 Pseudogenes
2.3.2 Sequencing genomes
2.3.2.1 Shotgun approach
2.3.2.2 Clone contig approach or clone by clone approach
2.3.3 The methodology for DNA sequencing
2.3.3.1 Chemical method (Maxam-Gilbert sequencing)
2.3.3.2 Chain termination method or dideoxy method (Sanger's method)
2.3.3.3 Next-generation sequencing (NGS) methods or high-throughput sequencing (HTS)
2.3.4 The Human Genome Projects
2.3.5 Genomic libraries
2.3.6 cDNA libraries
2.4 Genomics
2.4.1 Types of genomics
2.4.1.1 Structural
2.4.1.2 Functional
2.4.1.3 Comparative
2.4.1.3.1 Exon shuffling
2.4.1.3.2 Genome similarity
2.4.1.3.3 Gene order comparison
2.4.1.3.4 Horizontal gene transfer
2.4.1.3.5 Single nucleotide polymorphisms (SNPs)
2.4.1.3.6 Phylogenetic footprinting
2.5 Evolution of animal genomics
2.5.1 Mapping genomes
2.5.1.1 Genetic mapping
2.5.1.2 Physical mapping
2.5.2 Regulation of gene expression
2.5.2.1 Regulation of gene expression in eukaryotes
2.5.2.1.1 Chromatin structure
2.5.2.1.2 Initiation of transcription
2.5.2.1.3 Post-transcriptional processing
2.5.2.1.4 Initiation of translation
2.5.2.1.5 Post-translational processing
2.5.2.2 Regulation of gene expression in prokaryotes
2.5.2.2.1 Catabolite-regulation
2.5.2.2.2 Transcriptional attenuation
2.6 Role of genomics in animal improvement
2.7 Conclusions
References
3. Stem cells: a potential regenerative medicine for treatment of diseases
3.1 Introduction
3.1.1 Totipotent stem cells
3.1.2 Pluripotent stem cells
3.1.3 Multipotent stem cells
3.1.4 Oligopotent stem cells
3.1.5 Unipotent stem cells
3.2 History of stem cells
3.2.1 Types of stem cells
3.2.1.1 Embryonic stem cells
3.2.1.2 Adult stem cells
3.2.1.3 Induced pluripotent stem cells (iPSCs)
3.3 Materials and methods
3.3.1 Cryopreservation of mesenchymal stem cells for a long time for further use
3.3.2 Characterization of adipose tissue-derived mesenchymal stem cells
3.3.3 Confirmation for the presence of MSCs on wound areas of treated animals
3.3.4 Isolation of ovarian surface epithelium cells for generation of oocytes
3.3.5 Characterization of OSE-derived primordial germ cell-like structure
3.4 Applications of embryonic and adult stem cells
3.4.1 Study of diseases and how they develop
3.4.2 Stem cells: a model for screening, discovery, and development of drugs
3.4.3 Transgenic animal production
3.4.4 Therapeutic cloning
3.4.5 Regenerative medicine
3.5 Current clinical applications of adult mesenchymal stem cells in regenerative medicine
3.5.1 Treatment of massive wounds of animals
3.5.2 Mastitis treatment
3.5.3 Metritis and endometritis
3.5.4 Bone fracture and orthopedic defects
3.5.5 Spinal cord injury
3.5.6 Treatment of dogs
3.5.7 Blood stem cell transplantation
3.5.8 Burn therapy
3.5.9 Corneal regeneration
3.5.10 Immunomodulatory disease treatments
3.5.11 Neurodegenerative diseases
3.5.12 Liver diseases
3.5.13 Cardiac related diseases
3.5.14 Treatment of diabetes with MSCs
3.5.15 Treatment of cancer with MSCs
3.6 Challenges of stem cells
3.6.1 Stem cells in reproduction and infertility
3.6.2 Testis xenografting
3.6.3 Spermatogonial stem cell transplantation
3.6.4 Spermatogonial stem cells as a source for fertility restoration
3.6.5 Generation of oocytes from ovarian surface epithelium for regenerative medicine
3.7 Conclusion
References
4. Alternative transcriptome analysis to build the genome-phenome bridges in animals
4.1 Introduction
4.2 Modern sequencing platforms and transcriptome profiling strategies
4.2.1 High-throughput sequencing technologies
4.2.2 RNA sequencing
4.2.3 5′-end sequencing
4.2.4 3′-end sequencing
4.2.5 Isoform sequencing
4.2.6 Single-cell RNA sequencing
4.3 Genome-wide profiling of ATS and APA sites
4.3.1 WTSS-seq and WTTS-seq design
4.3.2 Characterization of ATS and APA sites
4.3.3 WTSS-seq and WTTS-seq: mutual validation
4.3.4 Advantages of WTTS-seq over RNA-seq
4.4 Genome to phenome via alternative transcriptome
4.4.1 Alternative transcriptome: bridges between genome and phenome
4.4.2 Alternative transcriptome: interactions with gene biotypes
4.4.3 Alternative transcriptome: alteration under gene knockouts
4.4.4 Alternative transcriptome: responses to a high-fat diet
4.4.5 Alternative transcriptome: the future of genome biology
Acknowledgments
References
5. RNA sequencing: a revolutionary tool for transcriptomics
5.1 Introduction
5.2 Transcriptional landscape: regulatory RNAs
5.3 Transcriptome sequencing
5.3.1 RNA isolation, reverse transcription and library preparation
5.3.2 Sequencing platforms
5.3.3 Analysis of the transcriptional landscape
5.3.3.1 Raw reads
5.3.3.2 Read alignment
5.3.3.3 Transcript assembly
5.3.4 Differential gene expression analysis
5.3.5 Alternatively-spliced transcript analysis
5.3.6 Allele specific expression
5.3.7 Fused gene analysis
5.3.8 Small RNA analysis
5.3.9 Expression quantitative trait loci analysis
5.4 Future perspectives
References
6. Targeted genome editing: a new era in molecular biology
6.1 Introduction
6.2 Homologous recombination
6.2.1 Scientific/clinical significance
6.3 Endonucleases/zinc-finger nucleases
6.3.1 Scientific/clinical significance
6.4 Transcription activator-like effector nucleases (TALENS)
6.4.1 Scientific/clinical significance
6.5 CRISPR-Cas9
6.5.1 Origin of CRISPR-Cas9
6.5.2 Underlying mechanism
6.6 Scientific advantage/applications
6.7 Clinical aspect
6.7.1 Limitations
6.8 Ethical concerns
6.9 Conclusion
References
7. RNAi for livestock improvement
7.1 Introduction
7.2 History behind RNAi
7.3 Versatility of RNA molecule
7.4 Mechanism of RNAi
7.5 Pathways of RNA silencing
7.5.1 Posttranscriptional gene silencing (PTGS)
7.5.2 Transcriptional gene silencing (TGS)
7.6 The miRNA pathway
7.7 piRNA
7.8 Transgenesis in livestock improvement
7.9 RNAi in livestock
7.10 Transgenic expression of RNAi-inducing molecules
7.11 Applications of RNAi in livestock
7.12 RNAi in functional genomics
7.12.1 RNA therapeutics
7.12.2 Molecular insights into stem cell biology and genetic engineering
7.12.3 Toward environmentally friendly farm animals
7.13 Challenges
7.14 Conclusions
References
Further reading
8. Microbial metagenomics: potential and challenges
8.1 Introduction
8.2 Metagenome and metagenomics
8.2.1 Habitat selection
8.2.2 Sampling
8.2.3 Macromolecule recovery
8.3 Next-generation sequencing (NGS) to explore microbial communities
8.3.1 Pyrosequencing
8.3.1.1 Ion Torrent sequencing
8.3.1.2 Illumina technology
8.3.1.3 PacBio RS and Oxford Nanopore
8.3.2 Reconstructing the genomic content of the microbial community from NGS data
8.3.3 Amplicon sequencing analyses
8.3.4 Shotgun metagenomics
8.3.4.1 Assessment of taxonomy based on markers
8.3.4.2 The binning strategy
8.4 Bioprospecting of metagenomes
8.4.1 Sequence-based analyses
8.4.2 Function-based analyses
8.4.2.1 Metagenomic DNA extraction
8.4.2.1.1 Direct DNA extraction
8.4.2.1.2 Freeze/thaw
8.4.2.1.3 Indirect DNA extraction
8.4.2.2 Library preparation
8.4.2.3 Screening
8.5 Applications of metagenomics
8.5.1 Biocatalysts and metagenomics
8.5.1.1 Xylanases
8.5.1.2 Proteases
8.5.1.3 Lipases
8.5.1.4 Amylases
8.5.1.5 Cellulases
8.5.2 Metagenomics and pharmaceuticals
8.5.3 Metagenomics and biosurfactants
8.5.4 Metagenomics and biodegradation
8.6 Conclusions and future perspectives
References
9. Molecular markers and its application in animal breeding
9.1 Introduction
9.2 Quantitative and molecular genetics
9.3 Molecular markers
9.3.1 Restriction fragment length polymorphism (RFLP)
9.3.1.1 Principle of RFLP
9.3.1.2 RFLP technique
9.3.1.3 Applications of RFLP
9.3.1.4 Limitations of RFLP
9.3.2 Random amplified polymorphic DNA (RAPD)
9.3.2.1 Principle of RAPD
9.3.2.2 RAPD technique
9.3.2.3 Applications of RAPD
9.3.2.4 Limitations of RAPD
9.3.3 Amplified fragment length polymorphism (AFLP)
9.3.3.1 Principle of AFLP
9.3.3.2 AFLP technique
9.3.3.3 Applications of AFLP
9.3.3.4 Limitations of AFLP
9.3.4 Microsatellites
9.3.4.1 Applications of microsatellites
9.3.4.2 Limitations of microsatellites
9.3.5 Minisatellites
9.3.6 Single nucleotide polymorphisms (SNPs)
9.3.6.1 Methods of SNP
9.3.6.2 Applications of SNP
9.3.7 Allozyme markers
9.3.7.1 Applications
9.3.8 Mitochondrial DNA (mtDNA)
9.3.8.1 Functions and uses of mtDNA
9.3.8.2 Maternal transmission
9.3.8.3 Heteroplasmy
9.3.8.4 Recombination
9.3.8.5 Applications of mtDNA markers
9.3.9 DNA barcoding markers
9.3.9.1 Animal identification by DNA barcoding
9.4 Marker assisted selection (MAS)
9.4.1 Applications of MAS
9.5 Conclusion
References
Further reading
10. Genomic selection: a molecular tool for genetic improvement in livestock
10.1 Introduction
10.2 Conventional selection
10.3 Selection - the major tool for genetic improvement
10.4 Principles of selection
10.5 Natural selection
10.6 Artificial selection
10.7 Selection for additive gene action
10.8 Selection for multiple alleles
10.9 Selection for epistasis
10.10 Selection intensity
10.11 Generation interval
10.12 Selection accuracy
10.13 Phenotypic value
10.14 Breeding value
10.15 Population mean
10.16 Average effect
10.17 Dominance deviation
10.18 Genetic control on production traits
10.19 Genetic control on reproductive traits
10.20 Genetic control on embryonic mortality in dairy cows
10.21 Marker assisted selection
10.22 MAS versus conventional selection
10.23 Whole-genome selection
10.24 Principle of genomic selection
10.25 Estimation of genomic breeding value
10.26 Factors influencing genomic selection
10.27 Present status of genomic selection in livestock breeding schemes
10.28 Prospects of genomic selection in cattle and buffaloes in India
10.29 Genetic gain by genomic selection
10.30 Methods of genomic selection
10.31 Advantage of genomic selection over conventional breeding
10.32 Reabilities (r2v) of EBV and regression coefficient (REG) of corrected phenotypic values
10.33 Genomic evaluations in developing versus developed countries
10.34 Genomic selection in developed countries
10.35 Genome-wide signatures for selection using molecular genomic tools
10.35.1 SNP Chip
10.36 Functional genomics in fertility traits
10.37 Approaches for developing disease tolerant livestock
10.38 Candidate genes for disease resistance for milk production
10.39 Production of disease-resistant genetically modified livestock
10.39.1 Dominant negative proteins
10.39.2 Ribonucleic acid interference (RNAi)
10.39.3 Ribonucleic acid decoys
10.39.4 Animal pharming
10.39.5 Antibodies
10.40 CRISPR
10.41 RNA editing
10.42 Disease treatment
10.43 Conclusion
References
11. Gene therapy
11.1 Genes
11.2 Gene therapy
11.3 Use of gene therapy
11.4 Types of gene therapy: somatic and germline
11.5 Types of vectors
11.6 Techniques of gene therapy
11.7 History of human gene therapy
11.8 CRISPR gene editing
11.9 Gene therapy in animals
11.9.1 Large animal disease models
11.9.2 Strategies, methods, and vectors for gene transfer
11.9.3 Gene therapy for the treatment of AIDS in animals
11.9.4 Brain cancer
11.9.5 The plastic bubble disease
11.9.6 Cure for blindness
11.10 Some other potential uses of gene therapy
11.11 Safety issues of gene therapy
11.11.1 Ethical and moral concerns surrounding gene therapy
11.12 Conclusion
References
12. Nanobiotechnology in animal production and health
12.1 Introduction
12.2 Quantum dot nanoparticles
12.3 Carbon-based nanoparticles
12.4 Dendrimers nanoparticles
12.5 Liposomes nanoparticles
12.6 Metal and metal oxides nanoparticles
12.7 Polymeric nanoparticles
12.8 Conclusions
Acknowledgment
References
Further reading
13. Cell signaling and apoptosis in animals
13.1 Introduction
13.2 Cell signaling in animals
13.3 Classification of cell signaling in animal cells
13.3.1 Autocrine
13.3.2 Paracrine
13.3.3 Endocrine
13.3.4 Signaling through direct contact
13.4 Signaling receptors
13.4.1 Intracellular signaling receptors
13.4.2 Cell- surface signaling receptors
13.4.2.1 G-protein-coupled signaling receptor (GPCR)
13.4.2.2 Ligand-gated ion channels
13.4.2.3 Enzyme-linked receptors
13.4.2.4 Receptor tyrosine kinases (RTKs)
13.5 Second messengers in animal cell signaling
13.6 Pathways of cell signaling
13.7 Computational mapping of animal cell signaling
13.8 Apoptosis
13.9 Classification of cell death in animal cells
13.9.1 Autophagy
13.9.2 Necrosis
13.10 Cellular and biochemical feature of apoptotic cells
13.11 Apoptosis: proteins and signaling pathways
13.12 Regulatory mechanism of apoptosis in animal cells
13.13 Apoptosis deregulation and diseases
13.14 Methods of apoptosis detection
13.15 Conclusion
References
14. Molecular Network for Management of Neurodegenerative Diseases and their Translational Importance using Animal Biotechnolog ...
14.1 Introduction
14.2 Pathogenesis and Molecular Mapping of Neurodegenerative Diseases
14.2.1 Alzheimer's Disease (AD)
14.2.2 Parkinson's Disease (PD)
14.2.3 Huntington's Disease (HD)
14.2.4 Amylotrophic Lateral Sclerosis (ALS)
14.3 Drug Targets of Protein Aggregates in Neurodegenerative Diseases with Translational Impacts
14.4 Conclusion and Future Direction of Research
Acknowledgment
References
15. Issues and policies in animal genomics
15.1 Introduction
15.1.1 Genomic technologies in animal husbandry
15.2 Global (transcontinental) scenario in transgenic animal research: issues and policies
15.2.1 North America
15.2.2 South America
15.2.3 Australia/Oceania
15.2.4 Europe
15.2.5 Asia
15.2.6 Africa
15.2.7 Antarctica
15.3 Genomics vis-a-vis Indian policy and regulations: current deliberations
15.3.1 Scope of guidelines
15.3.2 Classification of pathogenic microorganisms
15.3.3 Containment
15.4 Mechanism of implementation of biosafety guidelines in India
15.4.1 Recombinant DNA Advisory Committee (RDAC)
15.4.2 Institutional Biosafety Committee (IBSC)
15.4.3 Review Committee on Genetic Manipulation (RCGM)
15.4.4 Genetic Engineering Approval Committee (GEAC)
15.4.5 State Biotechnology Coordination Committee (SBCC)
15.4.6 District Level Committee (DLC)
15.5 Assessment of environmental risk
15.5.1 Mechanisms by which the environment may be exposed to GMO hazards
15.6 Capacity to survive, establish and disseminate
15.7 Hazards associated with the inserted gene/element
15.8 Transfer of harmful sequences between organisms
15.9 Phenotypic and genetic stability
15.10 Risk assessment for human health
15.11 Mechanisms by which the GMO could be a risk to human health
15.12 Control measures to protect human health
15.12.1 Biosafety Level (BSL) facilities
15.12.2 Different Bio Safety Level nomenclatures
15.13 Animal Bio Safety Level (ABSL) facilities
15.13.1 Operational guide for ABSL facilities
15.13.2 Types of Animal Biosafety Level facilities
15.13.2.1 Animal Bio Safety Level 1 (ABSL-1)
15.13.2.2 Animal Bio Safety Level 2 (ABSL-2)
15.13.2.3 Animal Bi Safety Level 3 (ABSL-3)
15.13.2.4 Animal Bio Safety Level 4 (ABSL-4)
15.14 Approvals and prohibitions
15.15 Conclusion
Disclaimer
Conflict of Interests
Acknowledgments
References
Further reading
16. Silkworm genomics: current status and limitations
16.1 Introduction
16.2 Genomic basis of the demographic history of the domesticated silkworm, Bombyx mori
16.3 Cytogenetics of the silkworm, Bombyx mori
16.4 Silkworm genomics
16.5 Silkworm genome programs
16.6 Silkworm genome sequence
16.6.1 Phase I: draft genome sequence
16.6.1.1 Japanese 3 × - genome assembly
16.6.1.1.1 Genome sequence and assembly methods
16.6.1.2 Genome sequence assembly
16.6.1.3 Detecting genes in the WGS
16.6.1.4 Chinese 6 × -genome assembly
16.6.1.4.1 Genome sequence and assembly methods
16.6.1.5 Genome sequence assembly and Gene Ontology
16.6.1.6 BAC-end sequencing
16.6.1.7 Limitations between two sequencing methods
16.7 Phase II: integrated genome sequence (http://silkworm.genomics.org.cn/)
16.8 Integration method
16.8.1 Integrated genome assembly and its characteristics
16.8.2 De novo analysis for genome organization and gene count
16.8.3 Limitations in the integrated genome assembly
16.8.4 Phase III: high-quality new genome sequence and assembly
16.8.4.1 Genome sequence and assembly methods
16.8.4.2 Bombyx genome new assembly and its characteristics
16.8.4.3 New gene models and gene families
16.8.4.4 Genome-wide analysis of genes
16.9 Genome sequence of domesticated and wild silkworm strains
16.10 Repetitive/transposable elements in the silkworm genome
16.11 Mapping silkworm genome
16.11.1 The linkage map
16.12 Genetic and molecular linkage maps
16.13 Limitations
16.13.1 Physical map by bacterial artificial chromosome (BAC), and fluorescence in-situ hybridization (FISH)
16.13.1.1 Protein-gene mapping on the chromosome
16.13.2 Strategies for construction of a physical map
16.13.3 Limitations in the silkworm genome mapping
16.14 Silkworm genome resources
16.14.1 Complimentary DNA libraries (cDNA)
16.14.2 Expressed sequence tags (EST)
16.14.3 Single nucleotide polymorphisms (SNP)
16.14.4 Sequence-tagged sites (STS)
16.15 Microsatellites
16.16 Silkworm genome database and characteristics
16.16.1 KAIKObase (http://sgp.dna.affrc.go.jp/KAIKObase/)
16.16.2 SilkDB (http://www.silkdb.org)
16.17 Limitations in the application of genome data for the improvement of silkworm strains
References
Web references
17. Deciphering the animal genomics using bioinformatics approaches
17.1 Introduction
17.1.1 Need for bioinformatics in animal genomics
17.1.2 Application of animal genomics
17.2 Genomic-bioinformatics processes
17.2.1 DNA sequencing
17.2.1.1 First-generation sequencing
17.2.1.2 Second-generation sequencing
17.2.1.3 Third-generation sequencing
17.2.1.4 Fourth- generation sequencing
17.2.2 Alignment
17.2.3 Genome assembly
17.2.4 Annotation
17.3 Technologies to assess gene expression
17.3.1 Differential display
17.3.2 Microarrays
17.3.3 Transcriptome and RNA sequencing
17.3.4 Serial analysis of gene expression (SAGE)
17.4 Tools for genomic data manipulation
17.4.1 Database for annotation, visualization, and integrated discovery (DAVID)
17.4.2 UCSC genome bioinformatics site
17.4.3 R language and bioconductor
17.5 Animal genomes available in NCBI
17.5.1 Major genomes in aquaculture
17.5.1.1 Aqua-genomics
17.6 Databases/major genomes available in animal genomics
17.7 Popular genomes of domestic animals
17.7.1 Buffalo
17.7.2 Goat
17.7.3 Sheep
17.7.4 Cow
17.8 India on world genomes map in animal genomics
17.9 Future prospects
Acknowledgment
References
18. DNA barcoding: nucleotide signature for identification and authentication of livestock
18.1 Introduction
18.2 DNA barcoding as a technique to generate nucleotide signature
18.3 DNA barcoding in livestock management
18.4 The advent of DNA barcoding
18.5 Nucleotide signature and barcode
18.6 Types of DNA barcoding
18.6.1 Meta-barcoding
18.6.2 Mini-barcoding
18.7 Methods involved in DNA barcoding
18.7.1 Extraction and purification of DNA from the samples
18.7.2 The genetic markers to barcode
18.7.3 Barcode and Polymerase Chain Reaction
18.7.4 Nucleotide/molecular signature
18.7.5 Reference libraries and databases
18.7.6 Barcoding sequence analysis
18.8 Applications of DNA barcode
18.8.1 Identification of new species
18.8.2 Advantage of DNA barcoding in livestock management
18.8.3 Cryptic species demarcation
18.8.4 Barcode-based diet analysis in animals
18.9 DNA barcode and intellectual property right (IPR)
Acknowledgments
References
Index
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z