Gene Editing in Plants: CRISPR-Cas and Its Applications

✍ Scribed by Ashwani Kumar (editor), Sudipti Arora (editor), Shinjiro Ogita (editor), Yuan-Yeu Yau (editor), Krishnendu Mukherjee (editor)

• Publisher: Springer
• Year: 2024
• Tongue: English
• Leaves: 871
• Category: Library

✦ Synopsis

This book is a collection of information about applying CRISPR-Cas systems for genome editing in plants. The main focus of this book is to address the recent advances and future prospects of CRISPR-Cas technology in crops.

Genome editing technology is important because it can be used to improve plant traits. The earlier genome-engineering tools, zinc finger nucleases (ZFNs), and TAL effector nucleases (TALENs) are complicated to design and not flexible. The novel genome editor, CRISPR-Cas systems, has advantages over ZFNs and TALENs. The advantages are simple and easy to design precision in targeting and efficiency. Due to its precision and simplicity, the CRISPR-Cas technology has rapidly become the most popular genome-editing platform in life-science fields. CRISPR-Cas technology has been used widely for human gene therapy to treat diseases and for plant breeding programs for crop improvement.

This book is of interest and useful to genome-editing professionals, plant breeders, horticulturists, field-level extension workers, nurserymen, planters, ecologists, and valuable source of reference to the relevant researchers.

✦ Table of Contents

Foreword
Preface
Acknowledgment
Contents
Editors and Contributors
1: CRISPR-Cas: A History of Discovery and Innovation
1.1 Introduction
1.1.1 Background
1.1.2 Discovery of CRISPR-Cas Technology
1.1.2.1 Discovery of CRISPR-Cas Systems
1.2 Classification of CRISPR-Cas Systems
1.3 Structure and Function of CRISPR-Cas9 Systems
1.4 CRISPR-Cas Technology for Engineering Virus-Resistant Plants
1.5 CRISPR-Cas for Epigenetic Editing: Activation and Repression of Gene Expression
1.5.1 Factors Influencing Epigenetic Memory and Plant Phenotype
1.5.2 Synthetic Epigenomes
1.5.3 Epigenetic Modification with CRISPR-Cas Systems
1.5.4 Challenges and Issues of CRISPR-dCas9 Technology
1.5.4.1 Transformation Techniques
1.6 CRISPR-Cas Technology for Base Editing and Prime Editing
1.6.1 Base Editing (BE)
1.6.2 Prime Editing (PE)
1.7 Final Remarks and Future Perspectives
References
2: Plant Recombinant Gene Technology for Pest Control in the Twenty-First Century: From Simple Transgenesis to CRISPR/Cas
2.1 Introduction
2.2 Bt Bacterial Toxins
2.2.1 Bt Rice
2.2.2 Bt Cotton
2.2.3 Bt Potato
2.2.4 Other Bt Crops
2.3 Using of Nonbacterial and Non-plant Toxins
2.4 Pest Gene Silencing with RNA Interference
2.5 Plant Gene Manipulation
2.6 CRISPR/Cas-Based Genome Editing in Plants for Pest Resistance
2.7 Perspectives
References
3: Different Classes of CRISPR-Cas Systems
3.1 Introduction
3.2 Classification of CRISPR-Cas Systems
3.2.1 Class I CRISPR-Cas System
3.2.1.1 Type I
3.2.1.2 Type III
3.2.1.3 Type IV
3.2.2 Class II Crispr-Cas System
3.2.2.1 Type II
3.2.2.2 Type V
3.2.2.3 Type VI
3.3 Significance of Various CRISPR-Cas Systems in Plant Gene Editing
3.4 Conclusion
References
4: Can CRISPR/CAS Help Fight Multidrug Resistance (MDR) Bacterial Infections?
4.1 Introduction
4.1.1 The Source of Antibiotic Resistance or Resistome
4.2 Background
4.3 Methodology
4.4 Relationships Between the CRISPR-Cas System and Antibiotic Resistance
4.4.1 Direct Killing of Bacteria
4.5 Eradication of Antibiotic Resistance in Bacteria
4.6 Overcoming These Challenges
4.6.1 Targeting AMR in Bacteria with CRISPR-Cas
4.7 Resistance to CRISPR-Cas Is Growing
4.8 Discussion
4.9 Future Perspectives of CRISPR
References
5: Redesigning Saccharomyces cerevisiae Meyen ex E.C. Hansen Using CRISPR to Combat Industrial Needs
5.1 Introduction
5.2 Saccharomyces cerevisiae
5.2.1 Genetic Makeup of Saccharomyces cerevisiae
5.2.2 Biochemical Pathways in Saccharomyces cerevisiae
5.2.3 A Prototype of Bio-Factory: Saccharomyces cerevisiae
5.3 CRISPR-Cas9: Structure and Function
5.3.1 Cas9
5.3.2 Guide RNA
5.3.3 CRISPR-Cas and Use of Saccharomyces cerevisiae as Cell Factory
5.3.4 CRISPR-Based Genetic Modifications in S. cerevisiae for the Manufacturing of Industrial Compounds
5.4 CRISPR-Cas 9-Mediated Microbial Chemical Production in S. cerevisiae
5.5 Future Perspectives
References
6: CRISPRi-Mediated Gene Silencing in Biofilm Cycle and Quorum Sensing
6.1 Introduction
6.1.1 Biofilms Are Around Us, on Us, and in Us
6.2 Bacterial Biofilms
6.2.1 Biofilm Cycle
6.2.1.1 Adhesion of Planktonic Cells and Formation of Extracellular Polymeric Substance (EPS) (Fig. 6.1a)
6.2.1.2 Development of Microcolonies (Fig. 6.1b)
6.2.1.3 Biofilm Maturation (Fig. 6.1c)
6.2.1.4 Detachment and Dispersal (Fig. 6.1d)
6.3 Quorum Sensing
6.3.1 Autoinducers (AIs)
6.4 Regulation of Bacterial Biofilms and Quorum Sensing
6.4.1 Regulation of Biofilm Formation
6.4.2 Regulation of Quorum Sensing System
6.4.2.1 Regulation of Quorum Sensing System in Gram-Positive Bacteria
6.4.2.2 Regulation of Quorum Sensing System in Gram-Negative Bacteria
6.5 CRISPR System in Bacteria and Archaea
6.5.1 CRISPR Loci
6.5.1.1 Leader Sequence
6.5.1.2 Repeats and Spacer
6.5.1.3 Cas Genes
6.5.2 Repurposed CRISPR-Cas9 System
6.5.2.1 Single Guide RNA (sgRNA)
6.5.2.2 Cas9
6.5.2.3 Protospacer Adjacent Motif (PAM) and Seed Region
6.5.3 CRISPRi
6.5.3.1 dCas9
6.5.3.1.1 dCas9: Activation and Repression
6.5.4 CRISPR-dCas9-Mediated Gene Silencing and Gene Knockdown in Biofilm Regulation and Quorum Sensing
6.6 Future Perspectives
References
7: A New Era of CRISPR Technology to Improve Climate Resilience in Rice
7.1 Introduction
7.2 Applications of CRISPR/Cas9 in Rice Abiotic Stress Tolerance
7.2.1 CRISPR/Cas9 for Salinity Tolerance in Rice
7.2.2 CRISPR/Cas9 for Drought Tolerance in Rice
7.2.3 CRISPR/Cas9 for Heat Tolerance in Rice
7.2.4 CRISPR/Cas9 for Cold Tolerance in Rice
7.3 Mobile CRISPR for Genome Editing in Plants
7.4 Tunable Gene Editing Through Anti-CRISPR Proteins in Plants
7.5 Conclusion and Future Prospects
References
8: Deciphering the Role of CRISPR/Cas9 in the Amelioration of Abiotic and Biotic Stress Conditions
8.1 Introduction
8.2 Crop Improvement for Biotic and Abiotic Stress Tolerance: A Rationale
8.3 Crop Improvement Strategies: An Overview
8.4 CRISPR/Cas-Based Genome Editing: Novel Tool to Rewrite Genomes with Precision
8.5 Plant Responses to Mitigate Abiotic and Biotic Stresses: Tracking Targets Genes/Proteins
8.6 CRISPR/Cas-Mediated Editing in Plants for Abiotic Stress Tolerance
8.6.1 Salinity
8.6.2 Drought
8.6.3 Temperature
8.6.4 Heavy Metals
8.6.5 Herbicide Resistance
8.7 CRISPR/Cas-Based Editing in Plants for Biotic Stress Tolerance
8.7.1 Bacterial Resistance
8.7.2 Fungal Infection
8.7.3 Viral Diseases
8.8 Challenges with CRISPR/Cas-Mediated Genome Editing in Plants
8.9 Conclusion and Future Prospects
References
9: Detailed Insight into Various Classes of the CRISPR/Cas System to Develop Future Crops
9.1 Introduction
9.2 CRISPR/Cas System Based Immunity in Bacteria
9.3 Classification of the CRISPR/Cas System
9.3.1 Class 1
9.3.1.1 Type I
9.3.1.2 Type III
9.3.1.3 Type IV
9.3.2 Class 2
9.3.2.1 Type II
9.3.2.2 Type V
9.3.2.3 Type VI
9.4 Type II CRISPR/Cas System in Detail
9.5 CRISPRloci
9.6 Advancements in Gene Editing
9.6.1 Cas9-NG
9.6.2 CjCas9
9.6.3 xCas9
9.6.4 XNG-Cas9
9.6.5 Cas12a (Cpf1)
9.6.6 Cas13a
9.6.7 Cas14a
9.6.8 Cas9 Nickase
9.6.9 dcas9
9.6.10 Base Editing
9.6.11 Prime Editing
9.6.12 DNA Free Genome Editing
9.6.13 Multiplex Genome Editing
9.6.14 PAM Less Genome Editing
9.6.15 Dimeric RNA-guided FokI Nucleases (RFNs)
9.6.16 CRISPR and λ-red Recombinase-based MAGE Technology (CRMAGE)
9.7 Advantages of CRISPR/Cas9
9.8 Limitations
9.9 Conclusion and Future Prospects
References
10: Role of CRISPR-Cas and Its Application in Mitigating Plant Stress
10.1 Introduction
10.2 Types of Stress in Plants
10.2.1 Biotic Stress
10.2.2 Abiotic Stress
10.3 Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated Protein
10.4 Approaches to Design Disease-resistant Plants with CRISPR Technologies
10.4.1 Gene Disruption
10.4.1.1 Insertion/Deletion in Coding Sequence
10.4.1.2 Insertion/Deletion in Promoter Regions
10.4.2 Gene Deletion
10.4.3 Gene Insertion
10.4.4 Biomimicking
10.5 Molecular Mechanism of CRISPR/Cas as a Key for Plants´ Resistance to Abiotic Stress
10.5.1 Salinity Stress
10.5.2 Drought Stress
10.5.3 Temperature Stress
10.5.4 Herbicide Stress
10.6 Molecular Mechanism of CRISPR/Cas as a Tool for Generating Biotic Stress-resilient Plants
10.6.1 Weed Resistant
10.6.2 Insect Resistant
10.6.3 Microbe Resistant
10.7 Limitations and Challenges
10.8 Conclusion and Future Prospects
References
11: Application of CRISPR for Plant-Mediated Resistance
11.1 Introduction
11.1.1 Molecular Mechanisms of Plant-Mediated Resistance
11.1.2 Application of Plant-Mediated Resistance
11.1.3 Conventional Breeding Techniques for Developing Resistant Plant Varieties
11.1.3.1 Selection of Plants with Natural Resistance
11.1.3.2 Use of Hybridization
11.1.3.3 Mutation Breeding
11.1.4 CRISPR-Cas Technology and Its Potential for Improving Plant-Mediated Resistance
11.2 Basics of CRISPR-Cas Technology
11.2.1 CRISPR-Cas System and Its Mechanism
11.2.2 Comparison of CRISPR-Cas Technology with Other Gene-Editing Techniques
11.2.2.1 CRISPR-Cas Technology
11.2.2.2 Zinc Finger Nucleases (ZFNs)
11.2.2.3 Transcription Activator-Like Effector Nucleases (TALENs)
11.2.3 Overview of the Tools and Methods Used for CRISPR-Mediated Gene Editing in Plants
11.2.3.1 Tools for CRISPR-Mediated Gene Editing in Plants
11.2.3.2 Methods for CRISPR-Mediated Gene Editing in Plants
11.3 Applications of CRISPR for Plant-Mediated Resistance
11.3.1 Recent Application of CRISPR for Developing Plant-Mediated Resistance Against Diseases
11.3.2 CRISPR-Cas Technology Can Be Used for Modifying Genes Involved in Plant Defense Mechanisms
11.3.2.1 Pattern Recognition Receptors (PRRs)
11.3.2.2 Effector-triggered Immunity (ETI)
11.3.2.3 Systemic Acquired Resistance (SAR)
11.3.3 CRISPR-mediated Gene Editing for Developing Resistance Against Specific Pests and Diseases
11.3.3.1 Development of Wheat Resistant to Powdery Mildew
11.3.3.2 Development of Rice Resistant to Bacterial Blight
11.3.3.3 Development of Tomato Resistant to Tomato Yellow Leaf Curl Virus (TYLCV)
11.3.4 CRISPR-Cas in Crop Breeding and Upgrading
11.4 Advantages and Challenges of CRISPR-Mediated Plant Resistance
11.4.1 Advantages of Using CRISPR-Cas Technology for Plant-Mediated Resistance
11.4.1.1 Precision
11.4.1.2 Efficiency
11.4.1.3 Flexibility
11.4.2 Overview of the Challenges Associated with CRISPR-Mediated Plant Resistance
11.4.2.1 Challenges Associated with CRISPR-Mediated Plant Resistance
11.4.2.1.1 Off-Target Effects
11.4.2.1.2 Regulatory Issues
11.4.2.1.3 Potential for Gene Flow
11.4.3 Comparison of CRISPR-Mediated Plant Resistance with Conventional Breeding Techniques
11.4.3.1 CRISPR-Cas-Based Strategies Conferring Disease Resistance Plants
11.4.3.1.1 Viral Disease Resistance Through CRISPR-Cas
11.4.3.1.2 Bacterial Disease Resistance Through CRISPR-Cas
11.4.3.1.3 Fungal Disease Resistance Through CRISPR-Cas
11.5 Conclusion
References
12: Nutrient Biofortification in Crop Plants by the CRISPR/Cas9 Technology: A Potential Approach for Sustainable Food Security
12.1 Introduction
12.2 Overview of the CRISPR/Cas9 System
12.2.1 Structure and Mechanism of CRISPR/Cas9 System
12.2.2 Repair Mechanisms for Double-Strand Breaks of DNA
12.2.2.1 Nonhomologous End Joining (NHEJ)
12.2.2.2 Homology-Directed Repair (HDR)
12.3 Application of CRISPR/Cas Technology in Biofortification of Crops
12.3.1 Carotenoid-Enriched Crops
12.3.2 gamma-Aminobutyric Acid (GABA)-Enriched Crops
12.3.3 Improvement of Fatty Acid Content
12.3.4 Starch with Low Amylose
12.3.5 Micronutrient-Enriched Crops
12.3.6 Low-Gluten Wheat
12.3.7 Reduction in Phytic Acid Content
12.3.8 Improvement in Physical Appearance
12.4 Conclusion
References
13: CRISPR-Cas and Its Applications in Food Production
13.1 Introduction
13.2 Basic Aspects of CRISPR
13.2.1 Locus
13.2.2 Role
13.2.3 Classification
13.2.3.1 Class 1 CRISPR-Cas System
13.2.3.1.1 Type I System
13.2.3.1.2 Type III System
13.2.3.1.3 Type IV System
13.2.3.2 Class 2 CRISPR-Cas System
13.2.3.2.1 Type II System
13.2.3.2.2 Type V System
13.2.3.2.3 Type VI System
13.3 CRISPR: An Attractive Genome-Editing Tool
13.3.1 StGBSSI
13.3.2 OsGS3
13.3.3 TaCKX2-D1
13.4 CRISPR-CAS in Food Production
13.4.1 Improvement in Yield
13.4.2 Food Quality Improvement
13.4.3 Food Crop Protection
13.4.3.1 Resistance Against Viral Diseases
13.4.3.2 Resistance Against Fungal Diseases
13.4.3.3 Resistance Against Bacterial Diseases
13.4.4 Production of Food Bioactive Compounds
13.5 Safety Issues and Regulation
13.5.1 US Regulation
13.5.2 European Regulation
13.5.3 India
13.5.4 China
13.6 Conclusion
References
14: CRISPR/Cas: A Genome-Editing Tool for Crops Improvement
14.1 Introduction
14.2 CRISPR/Cas System and Gene Editing in Plants
14.3 CRISPR-Cas System in Crop Improvement
14.3.1 CRISPR-Cas-Based Genome Editing in Cucumber for Virus Resistance
14.3.2 CRISPR-Cas-Based Genome Editing in Potato for Amylose- Free Starch Tubers
14.3.3 CRISPR-Cas-Based Genome Editing in Tomato
14.3.3.1 CRISPR-Cas-Based Genome Editing in Tomato for Virus Resistance
14.3.3.2 CRISPR-Cas-Based Genome Editing in Tomato with Enhanced Lycopene
14.3.4 CRISPR-Cas-Based Genome Editing in Rice
14.3.4.1 CRISPR-Cas-Based Genome Editing in Rice for Improving Quality and Quantity of Grains
14.3.4.2 CRISPR-Cas-Based Genome Editing in Rice for Carotenoid-Rich Grains
14.3.5 CRISPR-Cas-Based Genome Editing in Wheat
14.3.5.1 CRISPR-Cas-Based Genome Editing in Wheat to Reduce Gliadins
14.3.5.2 CRISPR-Cas-Based Genome Editing in Wheat for Enhanced Yield with Good-Quality Grains
14.4 Safety Concerns and Future Prospects
References
15: Development of a CRISPR-Cas9-Based Multiplex Genome-Editing Vector and Stay-Green Lettuce
15.1 Introduction
15.2 Plasmid Concept and Construction
15.3 Experimental Procedure
15.4 Construction of Plasmid for Genome Editing of LsBCM and LsSGR
15.5 Lettuce Transformation
15.6 Screening of Transformants and Phenotypic Analysis
15.7 Application of Multiplex Genome-Editing Vector
References
16: Potato Genome Editing: Recent Challenges and a Practical Procedure
16.1 Introduction
16.2 Crop Trait Engineering by Potato Genome Editing
16.3 Modification of Tuber Starch Composition
16.4 Cold-Induced Sweetening and Acrylamide Generation
16.5 Secondary Metabolites in Potato
16.6 Herbicide Resistance-Related Genes
16.7 Disease Resistance Genes
16.8 Self-Incompatibility Genes
16.9 Overview of Technical Progress in Potato Genome-Editing Technology
16.10 Approach by Protoplast Transfection of the CRISPR/Cas9 Ribonucleoprotein Complex
16.11 PEG-Mediated DNA Transfection
16.12 Application Toward High-Fidelity Genome Editing
16.13 Genome Editing by Transient Agrobacterium Infection
16.14 Improvement in the Conventional Genome-Editing System and Increasing Crossing Efficiency
16.15 A Procedure for the Creation of Potato Mutants Using the CRISPR/dMac3-Cas9 System
16.16 Conclusion and Future Aspects
References
17: Crispr Gene Editing for Secondary Metabolite Production: A Review
17.1 Introduction to the CRISPR/Cas9 System
17.2 Most Recent Uses of CRISPR/Cas9-Mediated Genome Editing
17.2.1 In Plants
17.2.1.1 Abiotic Stress
17.2.1.2 Biotic Stress
17.2.1.3 Crop Nutrient Quality
17.2.1.4 Pathogen Prevention
17.2.2 In Bacteria
17.2.3 In Gene Function
17.3 Examples of CRISPRa in Improving Secondary Metabolite Contents
17.4 Challenges and Constraints Associated with the Implementation of Genome Editing Using CRISPR/Cas9 Technology
17.5 Prospective Uses of the CRISPR/Cas9 Technique in Medicinal Plants and Filamentous Fungi
References
18: CRISPR/Cas Systems for Enhancing Photosynthesis: Climate Resilience and Food Production
18.1 Introduction
18.2 Clustered Regularly Interspaced Short Palindromic Repeats(CRISPR) and CRISPR-associated Protein (Cas): CRISPR/Cas for Gen...
18.2.1 Background: Photosynthesis and Climate Change
18.2.2 Innovative CRISPR-Cas Technology
18.3 CRISPR/Cas System in Way to Improve Photosynthesis: CRISPR -Based Targeted Gene Editing
18.3.1 CRISPR/Cas and Mode of CO2 Fixation to Abide Optimum Photosynthesis
18.3.2 Focus on Photosynthesis Components: Where CRISPR/Cas System Can Nick and Link Genes Directly Modify Photosynthetic Perf...
18.3.2.1 Chloroplast and Thylakoid Membrane
18.3.2.2 Chlorophyll and Other Pigments
18.3.2.3 Light-harvesting Complex System (LHC-I and LHC-II)
18.3.2.4 Rubisco Enzyme-Slower than Demands: First Target to Engineer
18.3.2.4.1 Rubisco Activase
18.3.2.4.2 RbcL (Rubisco Large Subunit) Genes
18.3.2.4.3 RbcS (Rubisco Small Subunit) Genes
18.3.2.5 Regulatory Genes
18.3.2.5.1 CAB (Chlorophyll a/b-Binding) Genes
18.3.2.5.2 Transcription Factors
18.3.2.6 PEPCase (Phosphoenolpyruvate Carboxylase) Genes
18.3.2.7 MicroRNA Level
18.3.2.8 Phytochrome
18.3.2.9 Calvin-Benson-Bassham (CBB) Cycle
18.3.2.10 Phosphoglycerate Kinase (PGK)
18.3.2.11 CP12-(Chloroplast Protein 12) Master Regulator of Calvin Cycle
18.3.2.12 Photosynthetic Electron Transfer Chain (PETC) Genes
18.3.2.13 Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) and Phosphoribulokinase (PRK)
18.3.2.14 Glucose-6-Phosphate Dehydrogenase (G6PDH)
18.3.2.15 Base Editing
18.4 CRISPR/Cas in Agriculture: In Way from Lab to Field
18.4.1 Wheat
18.4.2 Rice
18.4.3 Maize
18.4.4 Soybean
18.4.5 Potato
18.4.6 Tomato
18.4.7 Fruit Crops
18.5 Indirect Enhancement of Photosynthesis or Crop Productivity by CRISPR Mutagenesis
18.5.1 Crop Yield
18.5.2 Disease Resistance
18.5.3 Environmental Stress Tolerance
18.5.4 Altering Genes Involved in Stomata Regulation
18.5.5 Leaf Angle
18.6 Food Value Addition by Harnessing the CRISPR Power
18.6.1 Rubisco as a New Protein Source
18.6.2 Gluten-Free Wheat
18.7 Limitations and Challenges: CRISPRCas System
18.7.1 Technical Challenges
18.8 Conclusion
References
19: Combined Use of Unidirectional Site-Specific Recombination System and CRISPR-Cas Systems for Plant Genome Editing
19.1 Introduction
19.2 The Bxb1-att SSR System
19.2.1 Discovery of Bxb1-att SSR System and Its Genomic Structure
19.2.2 Using the Bxb1-att System in Mammalian Cells
19.2.3 Application of the Bxb1-att System for Genome Manipulation in Plants
19.3 Future Applications of SSRs and Genome Editing in Plants
19.3.1 Next-Generation Precise Gene Integration and Gene Stacking
19.3.2 Combination Use of Bxb1-att and Genome-Editing Tools for Versatile Genome Manipulation
19.3.2.1 Use Genome-Editing Tools to Launch a SSR Landing Pad to a Specific Locus
19.3.2.2 Simplify the Generation of `Conditional´´ Gene Knockout Mediated by SSR 19.3.2.3 dCas9 Can Be Used to Repress a Specific Recombination Site for Site-Specific Recombination 19.3.2.4 Engineer dCas9-SSR (Site-Specific Recombinase) Fusion Protein for More Conserved and Precise Programmable DNA Sequenc... 19.3.3 Codon-Optimized Bxb1 Recombinase to Improve Site-Specific Recombination Efficiency in Plants 19.4 Conclusion References 20: Advances in Delivery of CRISPR-Cas Reagents for Precise Genome Editing in Plants 20.1 Introduction 20.2 Application of CRISPR-Cas System for Eukaryotic Genome Manipulation 20.3 Methods to Deliver CRISPR-Cas Reagents 20.3.1 Formats of CRISPR-Cas Reagents 20.3.1.1 Plasmid Vectors 20.3.1.2 Cas Protein and gRNA 20.3.1.3 Cas-gRNA Ribonucleoprotein Complex (RNP) 20.4 Delivery Systems for CRISPR-Cas Reagents 20.4.1 Agrobacterium-Mediated Delivery System 20.4.2 Particle Bombardment for Genetic Engineering 20.4.3 PEG-Mediated Protoplast Delivery 20.4.4 Viral Vector-Based Delivery System 20.4.5 Nanoparticle-Based Delivery System 20.4.6 By Lipofection 20.4.7 Alternative Strategy for Delivering CRISPR-Cas Reagents 20.5 Concluding Remarks References 21: Perspectives and Overview of CRISPR/Cas Technology in Plant Pathogenesis 21.1 Introduction 21.2 Mechanism of Plant Defense 21.3 Gene Disruption by Coding Sequence Indels 21.4 Multiplex sgRNA-Mediated Gene Deletion 21.5 Editing of Genome for Plant Disease Resistance Against Various Pathogens 21.6 Limitations in Developing Resistance in Plants 21.7 Conclusion and Future Perspective References 22: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Associated Proteins (Cas) [CRISPR-Cas]: An Emerging Tec... 22.1 Introduction 22.2 History of CRISPR (Cas) 22.3 Structural Features of CRISPR (Cas9) 22.4 Types of CRISPR (Cas) System 22.4.1 The Natural Mechanism of the Immune System by CRISPR (Cas9) in Prokaryotes 22.4.2 Cas9 Activation, Target DNA Detection and Breakage 22.4.3 Gene Regulation Through CRISPR Activation (CRISPRa) or CRISPR (dCas) and CRISPRi (Interference) and Craspase (CRISPR-Gu... 22.4.4 Some Major Steps for Gene Editing by CRISPR (Cas) Tool in Plant System and Fungi 22.4.5 Delivery Systems for CRISPR Components in Plant and Fungal Cells or Vectors Used in CRISPR (Cas9) System for Gene Editi... 22.4.6 CRISPR (Cas) for Pathogen Detection and Disease Diagnosis 22.4.7 CRISPR (Cas) System for Pathogen or Disease Management 22.4.7.1 Production of Resistant Plants Against Virus by CRISPR (Cas) System 22.4.7.2 Production of Resistant Plants Against Bacterial Pathogens by CRISPR (Cas) System 22.4.7.3 Production of Resistant Plants Against Fungal Pathogens by CRISPR (Cas) System 22.5 Conclusion References 23: Application of Genome Editing for Improving Nematode Resistance in Plants: How far we have progressed? 23.1 An Introduction to Plant Nematodes and Their Role in Plant Yield Reduction 23.2 Limitations of Existing Nematode Management Strategies 23.3 R Genes vs S Genes 23.4 Different Types of Plant Genome Editing Systems 23.5 Susceptibility Factors as a Target for Plant Genome Editing Towards Achieving Nematode Resistance 23.6 Application of CRISPR-Cas9 Strategy in Understanding the Molecular Basis of Plant-Nematode Interrelationship 23.7 A Typical Genome Editing Workflow to Analyse S Gene Function Using CRISPR-Cas9 23.8 Conclusion and Future Directions References 24: CRISPR-Based Genetic Control Strategies for Insect Pests to Mitigate Classical Insecticidal Approaches 24.1 Introduction 24.2 Historical Overview of Plant Insect Pest Management 24.3 Genetic Engineering: Tools and Techniques 24.3.1 Diversification of CRISPR-Cas System 24.3.2 Efficacy of CRISPR-Based Genome Engineering 24.4 CRISPR Based Genome Editing in Crops for Insect Pest Management 24.4.1 CRISPR-Based Strategies to Disease Resistance Plant Development 24.5 CRISPR-Based Genome Editing in Insects for Insect Pest Management 24.6 CRISPR-Cas9-Based Techniques for Genetic Regulation in Insects 24.6.1 Gene Drive Based on CRISPR-Cas9 24.6.2 Sex-Ratio Distortion Due to CRISPR-Cas9 (CRISPRSRD) 24.6.3 Genetic-Sexing Strains Engineered with CRISPR-Cas9 (CRISPR-Engineered GSS) 24.6.4 Precision-Guided SIT (pgSIT) 24.7 Impediments and Future Prospects for Insect Management with CRISPR-Cas9-Based Genome Editing 24.8 Conclusion References 25: CRISPR-Based Approach: A Way Forward to Sustainable Development Goals (SDGs) 25.1 Introduction 25.1.1 CRISPR Path to Sustainability 25.1.2 Role of CRISPR to Achieve SDG 1: No Poverty 25.1.3 Role of CRISPR to Achieve SDG 2: Zero Hunger 25.1.4 Role of CRISPR to Achieve SDG 3: Good Health and Well-Being 25.1.5 Role of CRISPR to Achieve SDG 4: Quality Education 25.1.6 Role of CRISPR to Achieve SDG 6: Clean Water and Sanitation 25.1.7 Role of CRISPR to Achieve SDG 8 and SDG 9: Decent Work and Economic Growth and Industry, Innovation, and Infrastructure 25.1.8 Role of CRISPR to Achieve SDG 12: Responsible Consumption and Production 25.1.9 Role of CRISPR to Achieve SDG 13: Climate Action 25.1.10 Role of CRISPR to Achieve SDG 14: Life Below Water 25.1.11 CRISPR-Cas9 to Achieve SDG 15: Life on Land 25.1.11.1 Role of CRISPR for Resource Management and Conservation 25.1.11.2 Regaining Degraded Ecosystems 25.1.11.3 Conservation of Biodiversity 25.2 Conclusion References 26: CRISPR/Cas Technology: A Climate Saviour or a Genetic Pandora´s Box? 26.1 Introduction 26.2 What Is CRISPR/Cas Technology? 26.3 How It Can Help Mitigate Climate Change (A Global Issue)? 26.3.1 Creation of Climate-Resilient Crops 26.3.1.1 Development of Salinity and Drought-Tolerant Crops 26.3.1.2 Engineering of Disease-Resistant Crops 26.3.2 Engineering Microbes for Carbon Sequestration 26.3.3 Engineering Plants to Enhance Carbon Sequestering 26.3.4 Reducing the Carbon Footprint of Livestock Farming 26.3.5 Developing NovelCarbon-Neutral´ or Climate-Friendly Technologies
26.3.6 Enhancing the Resilience of Environmental Stresses
26.3.7 Bioenergy Production
26.3.8 Sustainable Biofuel Production
26.3.9 Improving Soil Health
26.3.10 Enhancing Soil Carbon Storage
26.3.11 Biodegradable Plastics
26.3.12 Improving the Efficiency of Renewable Energy Technologies
26.4 Can This Be a Risk to Environment in the Long Run?
26.4.1 Risk of Gene Flow
26.4.2 Off-Target Effects
26.4.3 Unintended Consequences
26.4.4 Disruption of Ecosystems
26.4.5 Loss of Biodiversity
26.4.6 Regulatory Challenges
26.4.7 Social and Ethical Concerns
26.4.8 Amplification of Existing Inequalities
26.5 How Can We Achieve a Balanced Approach?
26.6 Conclusions: Future of Earth in the Era of CRISPR/Cas
References
27: An Analysis of Global Policies and Regulation on Genome Editing in Plants
27.1 Introduction
27.2 Challenges for GM and GE Crop Production
27.3 Biosafety Concerns of Genome-Edited Plants
27.4 Policies of Different Countries on Genome-Edited Plants
27.4.1 Policies of the United States of America
27.4.2 Policies of Canada
27.4.3 Policies of Argentina
27.4.3.1 Wheat
27.4.3.2 Soybean
27.4.3.3 Corn
27.4.3.4 Policies of Chile
27.4.3.5 Policies of Israel
27.4.3.6 Policies of Japan
27.4.3.7 Policies of Australia
27.4.3.7.1 Biotech Canola
27.4.3.7.2 Biotech Safflower
27.4.4 Policies of India
27.4.4.1 Salt-Tolerant Rice Through CRISPR Cas
27.5 Conclusions
References
28: CRISPR/Cas-Mediated Multiplex Gene Editing in Tomato (Solanum Lycopersicum L.)
28.1 Introduction
28.2 CRISPR/Cas9 Genome-Editing Technology
28.3 Applications of CRISPR/Cas9 in Tomato Improvement
28.3.1 Increasing the Production and Quality of Tomato Fruit
28.3.2 Taste and Nutritional Value
28.3.3 Parthenocarpy
28.3.4 Fruit Size and Ripening
28.3.5 Disease Resistance
28.3.6 Biotic and Abiotic Stress Resistance/Tolerance Traits
28.4 Discussion
28.5 Conclusions
References
29: CRISPR-Cas System and its Role in Quorum-Sensing Processes of Bacteria and Fungi
29.1 Introduction
29.2 CRISPR-Cas System in Understanding the Mechanisms of Quorum Sensing and Virulence
29.3 Bacterial QS Genes Regulation by CRISPR-Cas
29.4 CRISPR-Cas Systems´ Association with Virulence Regulation in Bacteria
29.5 CRISPR-Cas and Antibiotic Resistance
29.6 QS- Fungi and a less Known Mode of Communication
29.7 Mechanisms of QS in Yeast and Other Fungi
29.8 CCS-Mediated Genetic Editing of Fungi
29.9 Conclusions
References
30: Genome Editing Tool CRISPR-Cas: Legal and Ethical Considerations for Life Science
30.1 CRISPR-Cas Technology
30.2 Repurposed CRISPR-Cas Systems
30.2.1 Dead-Cas9 System
30.2.2 Base Editing System
30.2.3 Cas9 Variant System
30.2.4 RNA Editing System
30.2.5 Prime Editing System
30.3 Applications of CRISPR-Cas Technology
30.3.1 CRISPR-Cas-Mediated Genome Editing in Microbes
30.3.2 CRISPR-Cas-Mediated Genome Editing in Plants
30.3.3 CRISPR-Cas-Mediated Genome Editing in Animals
30.3.3.1 Nonhuman Primates and Mosaicism
30.3.3.2 Intentional Genomic Alterations (IGAs) in Animals and Public Health
30.3.4 CRISPR-Cas-Mediated Genome Editing in Humans
30.3.5 CRISPR-Cas, Human Embryo, and Germline
30.4 Ethical Issues
30.4.1 Off-Target Effects
30.4.2 Genetic Mosaicism
30.4.3 Incidence of HDR
30.5 Bioethical Issues, Scientific Temper, Debates, and Legislation
30.6 Future Prospects
30.7 Conclusion
References