Foreword
Preface
Contents
Editors and Contributors
Part I: Introduction to Genome Editing and Crop Improvement
Chapter 1: Genome Editing Is Revolutionizing Crop Improvement
1.1 Introduction
1.2 Brief Overview of Genome Editing Technologies
1.2.1 Zinc-Finger Nucleases (ZFNs)
1.2.2 Transcriptional Activator-Like Effector Nucleases (TALENs)
1.2.3 CRISPR/Cas System: A Genome Editing Marvel
1.3 Application of CRISPR/Cas for Crop Improvements
1.3.1 Resistance to Biotic and Abiotic Stresses
1.3.2 Tolerance to Herbicides
1.3.3 Improvement of Crop Yield and Quality
1.3.4 Crop Domestication
1.4 Novel CRISPR/Cas-Based Breakthrough for Crop Improvement
1.4.1 Base-Editing Technology
1.4.2 Prime-Editing Technology
1.5 Perspectives and Future Challenges
References
Part II: Genome Editing Tools and Approaches
Chapter 2: Genome Editing Tools for Food Security
2.1 Introduction
2.2 Traditional Approaches for Crop Improvement
2.3 Trending Towards Genome Editing
2.4 Combining Genome Editing with Speed Breeding
2.5 Improving Crop Traits for Food Security
2.5.1 Yield Improvement
2.5.2 Biotic Stress Tolerance
2.5.3 Abiotic Stress Tolerance
2.5.4 Quality and Nutritional Improvement
2.6 Regulatory Concerns and Status of Genome-Edited Crops
2.7 Conclusion and Prospects
References
Chapter 3: CRISPR-Cas9/Cpf1-Based Multigene Editing in Crops
3.1 Introduction
3.2 The Mechanism of CRISPR/Cas9 System
3.3 CRISPR/Cas Produce Homozygous (Biallelic) Mutants at T0 and Multiple Knockouts
3.4 Rise of CRISPR 2.0: An Improved CRISPR/Cas9 Tool for Genome Editing in Plants
3.5 Cas9 and Cpf1: The Lead Players in the Game of Genome Editing
3.6 Assembly and Delivery of CRISPR/Cas9 Components into Living Cells
3.6.1 Physical and Chemical Delivery of CRISPR/Cas Components
3.6.2 Agrobacterium tumefaciens-Mediated Delivery of CRISPR/Cas Components
3.6.3 Delivery of CRISPR/Cas Components into Plant Cells Using Agrobacterium rhizogenes
3.6.4 Plant Virus-Mediated Delivery of CRISPR/Cas Components
3.6.5 Delivery of CRISPR/Cas Components by Biolistics
3.6.6 Delivery of CRISPR/Cas Components Via Protoplast Transformation
3.7 CRISPR/Cas9 and Cpf1 for Single-, Dual-Gene Multigene Editing in Crop Plants
3.7.1 Dual-Gene Editing
3.7.2 Multigene Editing
3.8 Application of CRISPR/Cas Technology in Crop Plants
3.9 Construction of Multigene Editing Vectors
3.10 Current Limitation of CRISPR/Cas Technology
3.10.1 Off-Target Effects
3.11 Future Prospects of Genome Editing in Plants
References
Chapter 4: CRISPR/Cas9 Tools for Multiplex Genome Editing in Crops
4.1 Introduction
4.2 CRISPR/Cas9-Mediated Plant Genome Editing
4.3 Multiplex Genome Editing Systems in Plants
4.4 Precise Deletions Induced by Multiplex Genome Editing
4.5 Conclusion
References
Chapter 5: Plant Genome Editing Mediated by CRISPR/Cas12a System
5.1 Introduction
5.2 Mechanism of CRISPR/Cas12a
5.3 Development of CRISPR/Cas12a
5.4 Establishment and Utilization of CRISPR/Cas12a System in Plants
5.5 Other Applications and Future Prospect by CRISPR/Cas12a
References
Chapter 6: Genome Editing in Crops Via Homology-Directed Repair Using a Geminivirus-Based CRISPR/Cas9 System
6.1 Introduction
6.2 Expression and Delivery of CRISPR Reagents
6.2.1 Microinjection
6.2.2 Electroporation
6.2.3 Agrobacterium-Mediated Transformation
6.2.4 Other Nonviral Vehicles
6.2.5 Viral-Based Approaches
6.3 Geminivirus as Delivery Vehicles
6.4 Geminivirus Replicons (GVRs) for Crop Improvements
6.5 Layout for Engineering CRISPR-GVRs Cassette
6.5.1 Deconstruction of Geminivirus for Designing the DNA Replicon
6.5.2 CRISPR/Cas Vector Construction
6.5.3 Transformation in Ex-Plants
6.6 Prospects and Conclusion
References
Chapter 7: Targeted Gene Replacement in Plants Using CRISPR-Cas Technology
7.1 Introduction
7.2 The Homologous Recombination Pathways
7.3 The Approaches of Increasing GT Efficiency in Plants
7.3.1 The Application of CRISPR/Cas12a
7.3.2 The Application of Cas9-VirD2 Variant
7.3.3 Supply of Sufficient Repair Templates Via Geminivirus Replicon
7.3.4 The ssDNA Donor
7.3.5 The RNA Donor
7.3.6 The dsODN Donor
7.3.7 The Application of Germline-Specific Promoters to Drive Cas9
7.4 Applications of CRISPR-Cas System-Mediated GT in Crop Improvement
7.4.1 Herbicide Resistance
7.4.2 Drought Tolerance
7.4.3 Improvement of Crop Quality
7.4.4 Disease Resistance
7.5 Challenges and Future Implications
7.5.1 Inhibition of NHEJ
7.5.2 Promotion of HR
7.5.3 Control of Cell Cycle to Facilitate GT
7.5.4 Optimizing Length of Homologous Arms
7.6 Conclusions
References
Chapter 8: Expanding the Scope of Base Editing in Crops Using Cas9 Variants
8.1 Introduction
8.2 Base Editors: Overview
8.2.1 DNA Base Editors
8.2.2 Cytosine Base Editors
8.2.3 Adenine Base Editors
8.2.4 RNA Base Editors
8.3 Cas9 Variants
8.4 Increasing the Scope of Base Editing Towards Crop Improvement
8.5 Conclusion
References
Chapter 9: Plant Precise Genome Editing by Prime Editing
9.1 Introduction
9.2 Prime Editing for Plant Genome Editing
9.3 Optimization of Plant Prime Editing
9.4 Conclusions and Perspectives
References
Chapter 10: Off-Target Effects of Crop Genome Editing and Its Minimization
10.1 Introduction
10.2 Concept of Off-Targets
10.3 Factors Associated with Off-Target
10.4 Methods of Off-Target Detection
10.4.1 Predicted Off-Target Sites for Amplification and Sequencing
10.4.2 Whole-Genome Sequencing (WGS)
10.4.3 Whole-Exome Sequencing (WES)
10.4.4 Breaks Labeling, Enrichment on Streptavidin, and Next-Generation Sequencing (BLESS)
10.4.5 Genome-Wide, Unbiased Identification of DSBs Enabled by Sequencing (GUIDE-Seq)
10.4.6 Linear Amplification-Mediated High-Throughput Genome-Wide Translocation Sequencing (LAM-HTGTS)
10.4.7 Digested Genome Sequencing (Digenome-Seq)
10.4.8 Cas9 Binding Assays: ChIP-Seq and BRET
10.4.9 Integrase-Deficient Lentiviral Vector (IDLV) Capture
10.4.10 Circularization for In Vitro Reporting of Cleavage Effects by Sequencing (CIRCLE-Seq)
10.4.11 Selective Enrichment and Identification of Tagged Genomic DNA Ends by Sequencing (SITE-Seq)
10.4.12 Endonuclease V Sequencing (ENDOV-Seq)
10.4.13 Discovery of In Situ Cas Off-Targets and Verification by Sequencing (DISCOVER-Seq)
10.5 Strategies for Reducing Off-Target Mutations
10.5.1 Effects of Temperature on Off-Targets
10.5.2 Designing of gRNA
10.5.3 Selection of GE Endonuclease
10.5.4 Concentration of sgRNA/Cas9 Complex
10.5.5 Aptazyme Overwhelms CRISPR/Cas9 Restrictions
10.5.6 Delivery of GE Machinery
10.5.7 Approachability of Target Site in Plant Genome
10.5.8 Genomic Data Availability
10.6 Conclusion
References
Part III: Genome Editing Towards Crop Improvement
Chapter 11: Genome Editing Toward Rice Improvement
11.1 Introduction
11.2 Genome Editing Tools Employed for Rice Improvement
11.2.1 Zinc Finger Nucleases (ZFNs)
11.2.2 TAL Effector Nucleases (TALENs)
11.2.3 CRISPR/Cas Systems
11.3 Disease Resistance
11.4 Abiotic Stress Tolerance
11.5 Herbicide Tolerance
11.6 Rice Grain Quality
11.7 Grain Yield-Associated Traits
11.8 Other Agronomic Traits
11.9 Base Editors
11.10 Prime Editor
11.11 Challenges and Future Implications
11.11.1 Recalcitrant Nature in Tissue Culture
11.11.2 PAM Requirement for CRISPR/Cas-Based Genome Editing Systems
11.11.3 Low Efficiency in Gene Knock-In/Replacement Editing
11.11.4 Scarcity in Significant Genes or Elements/SNPs Suitable for Editing
11.11.5 Biosafety Regulation and Commercial Cultivation of Genome-Edited Rice in the FarmerΒ΄s Fields
References
Chapter 12: Genome Editing Toward Wheat Improvement
12.1 Introduction
12.2 Progress of Wheat Genetic Transformation as the Basis of Genome Editing
12.2.1 Biolistic Particle-Mediated Genetic Transformation
12.2.1.1 Grain Quality Improvement
12.2.1.2 Agronomic and Physiologic Trait Improvement
12.2.1.3 Abiotic Stress Tolerance Enhancement
12.2.1.4 Biotic Stress Resistance Enhancement
12.2.2 Agrobacterium-Mediated Genetic Transformation
12.2.2.1 General Description
12.2.2.2 Combining of PureWheat Technique and Plant Regeneration-Related Gene
12.2.2.3 Agronomic and Botanic Trait Improvement
12.2.2.4 Growth and Development Trait Improvement
12.2.2.5 Processing and Nutrition Trait Improvement
12.2.2.6 Improvement on Abiotic Stress Tolerance
12.2.2.7 Improvement on Biotic Stress Resistance
12.3 Development of Genome Editing Technologies in Wheat
12.3.1 Different Genome Editing Technologies
12.3.2 Base Editing and Its Applications in Wheat
12.3.3 Prime Editing and Its Applications in Wheat
12.3.4 Identification of Cas9 Variants
12.3.5 Optimization of CRISPR/Cas9 System in Wheat
12.3.6 Editing Wheat Genes Mediated by Maize Pollens
12.4 Modifying Wheat Traits Using Genome Editing Technology
12.4.1 Improvement of Powdery Mildew Resistance
12.4.2 Development of Haploid Induction Lines
12.4.3 Improvement of Grain Size and Weight
12.4.4 Modifications of Grain Compositions
12.4.5 Induction of Male Sterility
12.4.6 Prohibition of Pre-harvest Sprouting
12.4.7 Modification of Plant Architecture
References
Chapter 13: The Use of CRISPR Technologies for Crop Improvement in Maize
13.1 Introduction
13.2 Maize Transformation
13.3 Examples of Maize Genome Editing
13.3.1 Waxy Corn
13.3.2 Complex Trait Loci
13.4 Gene Activation as a Tool for Maize Genome Engineering
13.5 New CRISPR Tools and Applications
References
Chapter 14: Genome Editing Towards Sorghum Improvement
14.1 Introduction
14.1.1 Origin and Distribution
14.1.2 Taxonomy and Botany
14.1.3 Abiotic and Biotic Interactions
14.1.3.1 Nutrient Use
14.1.3.2 Soil Salinity
14.1.3.3 Heat Tolerance
14.1.3.4 Drought Tolerance
14.1.3.5 Pests
14.1.3.6 Diseases
14.2 Food and Non-food Uses of Sorghum
14.2.1 Nutritional Composition of Sorghum Grain
14.2.2 Nutritional Importance/Health Benefits of Sorghum
14.2.2.1 Gluten-Free Grain
14.2.2.2 Low Glycemic Index (GI)
14.2.2.3 Low Lipid Content
14.2.2.4 Rich in Dietary Fibre, Starch and Protein
14.2.2.5 Rich Source of Phytochemicals (Including Tannins, Phenolic Acids, Anthocyanins)
14.3 Current and Future Uses of Sorghum
14.4 Sorghum Genome Editing Techniques and Transformation
14.5 Hurdles Associated with Sorghum Genome Editing and Sorghum Transformation
14.6 Sorghum Transformation Techniques
14.6.1 Electroporation and Pollen-Mediated Transformation
14.6.2 Particle and Microprojectile-Mediated Transformation
14.6.3 Agrobacterium-Mediated Transformation
14.7 Current Progress in Genetic Editing
14.7.1 Exploration of Genes Through Non-targeted Mutagenesis
14.7.2 Targeted Mutagenesis for Crop Improvement
14.8 The Future of Sorghum Improvement and Gene Editing
14.8.1 Potential Targets for Genetic Improvement in Sorghum
14.8.2 Waxy (Wx) Loci
14.8.3 Dwarfing (Dw) Loci
14.8.4 Maturity (Ma) Loci
14.9 Extrachromosomal Genome Engineering
14.9.1 Organellar and Plastid Genome Engineering: Potentials and Challenges
14.10 Potential Targets for Genetic Improvement in Sorghum Via Plastid Genome Engineering
14.10.1 Polyhydroxybutyric (PHB) Acid Production
14.10.2 Synthesis of Biopharmaceutical Compounds
References
Chapter 15: Accelerating Cereal Breeding for Disease Resistance Through Genome Editing
15.1 Introduction
15.2 Biotic Challenges for Cereal Production
15.3 Emerging Trends in Global Cereal Pathogen Outbreaks
15.4 Recent Changes in Plant Pathogen Populations
15.5 Fast-Forwarding Crop Breeding Using CRISPR/Cas-Mediated Genome Editing
15.6 Supplementing Natural Germplasm Diversity
15.7 Power of CRISPR/Cas System in Diagnostics
15.8 Application of Genome Editing Toward Improved Disease Resistance
15.8.1 Fungal Disease Resistance Through Targeting Host Susceptibility Factors/Genes
15.8.2 Bacterial Disease Resistance Through CRISPR/Cas9 By Targeting Host Genes
15.8.3 Viral Disease Resistance Through CRISPR/Cas9-Mediated Genome Editing
15.8.4 Multiple Disease Resistance Through CRISPR/Cas9-mediated Targeting Of Host Genes
15.9 Challenges of Genome Editing for Disease Resistance
15.9.1 Technical Issues
15.9.2 Ethical Issues in Deployment of Gene Editing in Improving Cereal Crop Resistance
15.10 Future Prospects
References
Chapter 16: Genome Editing Technologies Contribute for Precision Breeding in Soybean
16.1 Introduction
16.2 Successful Application of CRISPR/Cas9 in Hairy Roots of Soybean
16.3 CRISPR-Mediated Functional Study and Agronomic Trait Improvement in Soybean
16.3.1 CRISPR Broadens the Latitude Adaptability of Soybean
16.3.2 CRISPR Contributes for Altering the Plant Architecture in Soybean
16.3.3 CRISPR Contributes for Improving the Quality of Soybean Seeds
16.3.4 CRISPR Contributes for Studies in the Resistance to Biotic and Abiotic Stresses
16.4 Current Challenges of CRISPR Technologies in Soybean and Perspectives for Future Agriculture
16.4.1 Improved Delivery Systems of CRISPR Technologies
16.4.2 Increased Efficiency of HDR-Mediated Accurate Genome Editing
16.4.3 Expansion of the Range of Optional Target Sites
16.4.4 Development of High-Throughput Genetic Mutations
16.4.5 Improved Accuracy in Genome Editing Techniques
References
Chapter 17: Genome Editing for the Improvement of Oilseed Crops
17.1 Introduction
17.2 Historical Development of Genome Editing in Plants
17.2.1 ZFNs and TALENs
17.2.2 CRISPR-Cas Genome Editing System
17.3 Genome Editing of Oilseed Crops
17.3.1 Herbicide Resistance
17.3.2 Oil Content and Quality
17.3.3 Plant Architecture
17.3.4 Flowering Time
17.3.5 Nodulation
17.3.6 Abiotic Stress
17.3.7 Biotic Stress
17.4 Conclusion
References
Chapter 18: Genome Editing Tools for Potato Improvement
18.1 Introduction
18.2 The CRISPR Toolbox for Genome Editing in Potato
18.2.1 The Canonical CRISPR-Cas9 System for Potato Gene Knockout
18.2.1.1 Expression Systems
18.2.1.2 Spacer Sequence Selection
18.2.2 The CRISPR-Cas9 System for Allele Replacement in Potato
18.2.2.1 Nucleotide Conversion Using CRISPR-Mediated Base Editing
18.2.2.2 Allele Replacement Using Donor Templates
18.2.3 Prime Editing
18.3 Making a Genome-Edited Potato Plant
18.3.1 Methods for Delivery of Genome Editing Components
18.3.1.1 Stable Transformation
18.4 Transgene-Free Editing Approaches
18.4.1 Transient Expression
18.4.2 Ribonucleoprotein (RNP) Complexes
18.4.3 Methods for Plant Regeneration
18.4.3.1 Indirect Organogenesis
18.4.3.2 Direct Organogenesis
18.4.4 Genotyping an Edited Potato Plant
18.5 Applications of Genome Editing in Potato
18.6 Engineering Potato Virus y (pvy) Resistance by Editing eif4e Factors
18.7 Future Directions for Next-Generation Potatoes
18.8 Regulation of Genome-Edited Crops
18.9 Conclusions
References
Chapter 19: Genome Editing for Tomato Improvement
19.1 Introduction
19.2 Improvement of Tomato Fruit Quality Using Genome Editing
19.3 Improvement of Tomato Fruit Texture
19.4 Parthenocarpic Fruit Development Using Genome Editing
19.5 Improvement of Biotic Stress Tolerance in Tomato Using Crispr/Cas9 Editing
19.6 Improvement of Abiotic Stress Tolerance in Tomato
19.7 Genome Editing and Tomato Domestication
19.8 Conclusion and Future Perspectives
References