Molecular and Biotechnological Tools for Plant Disease Management

Preface
Contents
Recent Strategies in the Management of Bacterial Diseases for Cereals
	1 Introduction
	2 Bacterial Diseases of Cereal Crops
		2.1 Corn (Zea mays L.)
		2.2 Rice (Oryza sativa)
		2.3 Wheat (Triticum aestivum)
	3 Detection and Diagnosis of Pathogenic Bacteria for Cereals
		3.1 High-Throughput Sequencing and Molecular Approaches
		3.2 Nanodiagnostic Approaches
	4 Genome Editing Techniques
		4.1 CRISPR/Cas9
		4.2 Genome-Wide Association Studies (GWAS)
		4.3 Transcription Activator-Like Effector Nucleases (TALEN)
	5 The Use of PGPR
		5.1 Direct PGPR Mechanisms to Promote Cereal Crops
		5.2 Indirect Mechanisms
	6 Conclusion
	References
Diagnostics and Detection Tools for Pathogens in Food Crops
	1 Introduction
	2 Principal Diseases and Impact on Crops Worldwide
		2.1 Viral Diseases
		2.2 Bacterial Diseases
		2.3 Plant Parasitic Nematodes
		2.4 Fungal Diseases
		2.5 Diseases Caused by Parasitic Plants
	3 Detection and Diagnosis of Plant Pathogens
		3.1 Conventional Characterization for Plant Pathogens
		3.2 Accurate Diagnostic Tools for Plant Pathogens
		3.3 In-Field Detection of Plant Pathogens
		3.4 Biosensor Technologies for Plant Pathogen Detection
		3.5 Information Technology in Plant Pathology
	4 Database Programs for Plant Pathogens
		4.1 CABI/Plantwise
	5 Conclusion and Perspectives
	References
Molecular Diagnostics and Management of Phyto-Parasitic Nematodes
	1 Introduction
	2 Molecular Diagnostic Tools for PPNs
		2.1 PCR-Based Techniques
		2.2 DNA Sequencing
		2.3 DNA Barcoding
		2.4 Isothermal Amplification Techniques
	3 Molecular Techniques for PPN Management
		3.1 Gene Silencing
		3.2 Genome Editing
		3.3 Advantages and Limitations
	4 Challenges and Future Directions
	5 Conclusion
	References
Advances in the Management of Bacterial Diseases of Vegetable Crops
	1 Introduction
	2 Managing Vegetable Crop Bacterial Diseases
		2.1 Utilization of Copper and Antibiotics for Managing Bacterial Diseases and the Subsequent Development of Resistance
		2.2 Exploring Substitutes for Copper-Based Bactericides and Antibiotics in the Regulation of Bacterial Diseases
		2.3 Managing Vegetable Crop Fungal Diseases
		2.4 Bio-Management of Diseases Affecting Vegetables
	3 Exploring the Potential of Innovation in the Management of Bacterial Diseases and Its Prospects
		3.1 Nanoparticles
		3.2 Targeting the T3SS
		3.3 Targeting Quorum Sensing
		3.4 Targeting Bacterial Biofilms
		3.5 Genome Editing Techniques to Develop Sustainable Resistance Mechanisms
	4 Conclusion
	References
Emerging Approaches Based on Genome-Wide Association Studies (GWAS) for Crop Disease Tolerance
	1 Introduction
	2 GWAS: The Technique
	3 Post GWAS Steps
	4 Application of GWAS in Plant Diseases
	5 Greater Opportunities to Explore GWAS for Plant Pathogens
	6 Integrated GWAS for Plant Pathogen: Co-GWAS
	7 Perspectives and Future Prospects
	8 Conclusion
	References
Recent Diagnostics, Detection, and Monitoring Tools: Implications for Plant Pathogens and Their Management
	1 Introduction
	2 Traditional Diagnostics Tools
		2.1 Visual Inspection
		2.2 Microscopic Examination
		2.3 Culture-Based Methods
	3 Molecular Diagnostics Tools
		3.1 Lateral Flow Immunoassays (LFIA)
		3.2 Enzyme-Linked Immunosorbent Assay (ELISA)
		3.3 Polymerase Chain Reaction (PCR)
		3.4 Loop-Mediated Isothermal Amplification (LAMP) Assay
		3.5 Fluorescence In-Situ Hybridization (FISH)
	4 Multiplexed Detection
	5 Emerging Diagnostics Tools
		5.1 “Chemical-Nose”—Sensor-Based Detection of Plant Pathogens
		5.2 Electrochemical Sensors for Plant Pathogens
		5.3 Electronic Nose
		5.4 Gas Chromatography-Mass Spectrometry (GC–MS)
	6 Plant Wearable Devices
	7 Information and Communication Technology (ICT) for Phytopathological Management
	8 Conclusion and Looking Forward
	References
Molecular Diagnostics of Plant Viruses, Viroids, and Phytoplasma: An Updated Overview
	1 Introduction
	2 Biotic Stress Impact on the Growth of Plants
	3 Conventional Techniques for Identifying and Diagnosing Plant Diseases
	4 Molecular Diagnostics
	5 Types of Plant Molecular Diagnostics
		5.1 DNA-Based Approaches
		5.2 RNA-Based Approaches
		5.3 Protein-Based Approaches
	6 Molecular Diagnosis of Plant Virus
	7 Molecular Diagnosis of Plant Viroid
	8 Molecular Diagnosis of Plant Phytoplasma
	9 Conclusion
	References
Detection and Identification of Plant Viruses, Viroids, and Phytoplasma Based on High-Throughput Molecular Approaches
	1 Introduction
	2 Amplification Techniques
		2.1 Loop-Mediated Isothermal Amplification (LAMP)
		2.2 Rolling Circle Amplification (RCA)
		2.3 Helicase-Dependent Amplification (HDA)
		2.4 Recombinase Polymerase Amplification (RPA)
		2.5 Polymerase Chain Reaction (PCR)
	3 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)
		3.1 Combined Application of Different Techniques
	4 Molecular Hybridization Techniques
		4.1 Dot-Blot Hybridization
		4.2 DNA Microarray
	5 Sequencing Techniques
		5.1 NGS (Next Generation Sequencing)
		5.2 Short-Read Sequencing (Second Generation) Technology
		5.3 Long-Read Sequencing (Third Generation) Technology
	6 Conclusion
	References
Advances in Contemporary Tools for Detecting and Diagnosing Plant Pathogens
	1 Introduction
	2 Progress in Plant Pathogen Detection Methods
		2.1 Non-Invasive Optical and Spectral Detection Methods
		2.2 Cultivation-Based Methods
		2.3 Immunological Detection Methods
		2.4 Nucleic Acid-Based Assays for Detection
		2.5 Nucleic Acid Sequencing Methods
		2.6 Biosensor-Based Methods
	3 The Role of Nanotechnology in Pest Management
		3.1 Applications in Pest Management
		3.2 Nano-Pesticides
		3.3 Examples and Effects
	4 Conclusion
	References
Advanced Molecular Techniques in the Identification of Phytopathogenic Fungi
	1 Introduction
		1.1 A Brief Introduction
		1.2 Enzymes Degrading Plant Cell Wall
		1.3 Interaction Representing Molecular Mechanism Between the Plants and Phytopathogenic Fungi
		1.4 Signal Recognition of the Pathogenic Fungi an Infection Process
	2 Molecular Methods to Detect Phytopathogenic Fungi
		2.1 Identification of Phytopathogenic Fungi
		2.2 Molecular Approaches Developed for Identifying Phytopathogenic Fungi
	3 Conclusion and Future Prospectus
	References
Plant MicroRNAs: Identification and Their Application in Disease Management
	1 Introduction
	2 Plant MicroRNA Biosynthesis
	3 Mode of Action
	4 Plant MicroRNAs Against Phytopathogens
		4.1 Bacteria
		4.2 Fungi
		4.3 Viruses
		4.4 Nematodes
	5 Conclusion
	References
RNAi as a Potential Tool for Control and Management of Plant Disease: An Updated Overview
	1 Introduction
	2 Inception of RNA Interference Concept
	3 Mechanism of RNAi Action
	4 Induction of RNAi in Plants
		4.1 Spraying
		4.2 Agroinfiltation
		4.3 Micro-Bombardment
		4.4 Virus-Induced Gene Silencing (VIGS)
		4.5 Nanotechnology-Mediated Delivery of RNA
	5 RNA Interference Approach in Controlling and Managing Plant Diseases
		5.1 RNAi-Based Approaches to Control Plant Diseases Against Biotic Factors
		5.2 RNAi Against Plant Pathogenic Virus
		5.3 RNAi Against Plant Pathogenic Nematode
		5.4 RNAi Against Plant Insects
		5.5 RNAi Against Plant Pathogenic Bacteria
	6 RNAi-Based Approaches to Control Plant Diseases Against Abiotic Factors
		6.1 Drought Stress Tolerance
		6.2 Salt Stress Tolerance
		6.3 Commercialization of RNAi-Based Products
	7 Conclusion
	References
RNA Interference for Plant Disease Management: Updated Methods, Current Applications and Future Directions
	1 Mechanism of RNA Interference
	2 RNAi Techniques in Plant Disease Management
		2.1 Antisense RNA Interference
		2.2 VIGS (Virus Induced Gene Silencing)
		2.3 HIGS (Host Induced Gene Silencing)
		2.4 Spray Induced Gene Silencing (SIGS)
		2.5 Artificial Small RNA (Art-SRNA)
	3 Conclusion
	4 Future Perspectives of Rna Interference in Plant Pathology
	References
Emerging Molecular Tools and Breeding Strategies for Plant Bacterial Disease Management
	1 Introduction
	2 Molecular Tools and Breeding Techniques: Definition and Scope
		2.1 Omics Approaches
		2.2 Molecular Breeding
		2.3 Synthetic Biology
		2.4 Phage Therapy
		2.5 Precision Agriculture Technologies
		2.6 Big Data and Machine Learning
	3 Conclusion and Prospects
	References
Disease-Resistant Genes and Signal Transduction Pathways and Their Applications in Disease Management
	1 Introduction
		1.1 The Emergence of a Complex, Multicomponent System for Plant Disease Resistance
		1.2 Detection and Reaction Are Key Elements in Plant Defence
		1.3 Virulence of the Pathogen Depends on Attack and Evasion
	2 Detection of Pathogens
		2.1 WAKs and PRRs Track Down PAMPs and DAMPs
		2.2 NLRs Find Effectors of Pathogens
	3 Transduction of Signals
		3.1 Numerous Signaling Pathways Mediate Resistance.
		3.2 Resistance is Systematically Initiated and Repressed by Plant Hormones
		3.3 Transcription Factors Are Important for Transcriptional Reprogramming
		3.4 PDR and Epigenetic Regulation Offer Additional Regulatory Mechanisms.
	4 Defense Reaction
		4.1 Pathogen Infection is Inhibited by Cell Wall, HR, and ROS Modification
		4.2 The Enzymes and Inhibitors of Enzymes Prevent Harmful Effects and Help in the diagnosis
		4.3 Defensins and Proteins that Resemble Thaumatins Actively Prevent Infections Caused by Pathogenic Bacteria
		4.4 Chemical and Biological Plant Weapons Include Phytoalexins and Beneficial Symbionts
	5 Conclusions and Future Directions
	References
Genome Editing Technologies for Resistance Against Phytopathogens
	1 Introduction
	2 Molecular Targets for Phytopathogen Resistance
		2.1 Identification and Characterization of Susceptibility Genes
		2.2 Understanding Plant-Pathogen Interactions
		2.3 Targeting Key Genes Involved in Plant Defense Mechanisms
	3 Strategies for Genome Editing in Plants
		3.1 Gene Knockout and Knockdown Strategies
		3.2 Gene Insertion and Gene Replacement Approaches
		3.3 Multiplex Genome Editing for Enhanced Resistance
	4 Challenges and Considerations in Using Genome Editing for Resistance Against Phytopathogens
		4.1 Off-Target Effects and Unintended Consequences
		4.2 Regulatory Issues and Public Acceptance
		4.3 Delivery Methods and Transformation Efficiency
		4.4 Intellectual Property Rights and Access to Technology
	5 Future Prospects and Emerging Trends
		5.1 Advances in Precision and Efficiency of Genome Editing Techniques
		5.2 Integration of Genome Editing with Other Plant Breeding Methods
		5.3 Potential Applications in Non-Model Plant Species
		5.4 Ethical Considerations and Responsible Use of Genome Editing
	6 Conclusion
	References
CRISPR/Cas9 System of Crop Improvement: Understanding the Underlying Machinery
	1 Introduction
	2 Genetic Strategies in Crop Improvement
	3 Components of CRISPR/Cas9
	4 Advantages of CRISPR/Cas9 System
	5 CRISPR-CAS Applications in Plant Breeding
		5.1 Male Sterility Induction
		5.2 Fixation of Hybrid Vigor
	6 Induction of Haploid
	7 Manipulating Self-Incompatibility
	8 Scope and Prospect
	References
CRISPR-Edited Plants for Plant-Disease Management
	1 Introduction
	2 Host–Pathogen Interaction Mechanisms
	3 An Overview of CRISPR-Based Tools
	4 Genome Editing in Plant Pathogens
		4.1 Genome Editing of Viral Pathogens Through CRISPR/Cas9
		4.2 Resistance Against Fungal Pathogens Using CRISPR/Cas9-Mediated Tools
		4.3 Genome Editing in Bacteria and Nematodes Using CRISPR/Cas9–mediated Tools
	5 CRISPR Plants
		5.1 Rice
		5.2 Citrus Plants
		5.3 Tomato
		5.4 Watermelon
		5.5 Soybean
		5.6 Wheat
		5.7 Barley
		5.8 Banana
	6 Advantages and Challenges of CRISPR in Genome Editing
	7 Challenges of CRISPR in Genome Editing for Plant Disease Management
	8 Conclusions and Future Aspects
	References