Plant-microbe Interactions: Harnessing Next-generation Molecular Technologies for Sustainable Agriculture (Advances and Applications in Biotechnology)

Cover
Half Title
Series Page
Title Page
Copyright Page
Table of Contents
Preface
Editors
Contributors
1. Novel Approaches and Advanced Molecular Techniques for Crop Improvement
	1.1 Introduction
	1.2 Plant Tissue Culture in Crop Improvement
	1.3 Crop Improvement by Genetic Engineering
		1.3.1 Mutagenesis
		1.3.2 Genome Editing
		1.3.3 RNA Interference (RNAi)
		1.3.4 Metabolic Engineering
	1.4 Novel Genomics Technologies
		1.4.1 Application of Next- Generation Sequencing (NGS) Technologies to Crop Improvement
		1.4.2 Implications of Different “Omics” Approaches in Crop Improvement
			1.4.2.1 Genomics in Crop Improvement
			1.4.2.2 Transcriptomics in Crop Improvement
			1.4.2.3 Proteomics in Crop Improvement
			1.4.2.4 Metabolomics in Crop Improvement
	1.5 Role of Bioinformatics in Crop Improvement
	1.6 Nanotechnology in Crop Improvement
	1.7 Modern Breeding Techniques for Crop Improvement
		1.7.1 Allele Mining for Crop Improvement
			1.7.1.1 EcoTILLING-Based Allele Mining
			1.7.1.2 Sequencing-Based Allele Mining
			1.7.1.3 Haplotype-Based AM
		1.7.2 Gene Pyramiding for Crop Improvement
			1.7.2.1 Marker-Assisted Gene Pyramiding
			1.7.2.2 Marker-Assisted Backcrossing
		1.7.3 Implication of Marker-Assisted Recurrent Selection (MARS) in Crop Improvement
		1.7.4 Implication of Genome- Wide Selection or Genomic Selection (GWS or GS) in Crop Improvement
	1.8 Summary and Future Prospects
	Abbreviations
	References
2. The Chemical Dialogue during Plant–Microbe Interaction: Implications in Sustainable Agriculture
	2.1 Introduction
	2.2 Role of Plant Root Exudates in Microbial Colonization
	2.3 Chemotaxis Motility and Colonization by Rhizosphere Microbiota
	2.4 Role of Extracellular Polysaccharides in PMI
	2.5 Quorum Sensing and Biofilm Production during Microbial Colonization
	2.6 Modulation of the Plant Immune System by Microorganisms
	2.7 Conclusions
	References
3. Implication of Microbial Signals: Plant Communication
	3.1 Introduction
	3.2 Plants: Contribution to Microbes
	3.3 Chemical Signals in the Rhizosphere and Phyllosphere
	3.4 Characterized Chemical Compounds with Role in Plant–Microbe Interactions
		3.4.1 Microbial Phytohormones
		3.4.2 Cytokinins
		3.4.3 Indole-3-Acetic Acid
		3.4.4 Gibberellins
		3.4.5 Defense Hormones: Mediators of Plant–Microbe Interactions
		3.4.6 Stimulatory Compounds
			3.4.6.1 Siderophores
			3.4.6.2 Lipopeptides
		3.4.7 Toxins
			3.4.7.1 Polyketides
			3.4.7.2 NRPs
			3.4.7.3 Terpenes
			3.4.7.4 Indole Alkaloids
	3.5 Plant Flavonoid Signals
	3.6 Impact of Rhizosphere Community Structure on Flavonoid-Mediated Communications
		3.6.1 Modification of Patterns of Exudation
		3.6.2 Microbial Catabolism
	3.7 Role of Volatile Organic Compounds
	3.8 Molecular Mechanisms Underlying Volatile Perception
	3.9 Chemistry of Plant–Plant Signaling
	3.10 Microbial Signals Involved in Plant Growth and Development
	3.11 Conclusions and Future Aspects
	References
4. Molecular Aspects of Host–Pathogen Interaction
	4.1 Introduction
	4.2 Different Stages of Host–Pathogen Interaction
		4.2.1 Invasion of the Host by a Pathogen
		4.2.2 Evasion of the Host Defense System
		4.2.3 Replication of Pathogen Inside the Host
		4.2.4  Host-Inherent Capacity to Eradicate the Pathogen
	4.3 Genetic and Molecular Basis of  Host–Pathogen Interaction
		4.3.1 Disease Resistance in Plants through Innate Immunity
			4.3.1.1 Basal Defense
			4.3.1.2 R Gene-Mediated Defense
		4.3.2 Major Classes of R Gene
	4.4 Metabolomics in Studying  Host–Pathogen Interaction
		4.4.1 Concept of Metabolomics
		4.4.2 Role of Metabolomics in Plant Pathology
		4.4.3 Role in Studying  Host–Pathogen Interactions
	4.5 Online Repositories for  Host–Pathogen Interaction
	4.6 Conclusions
	4.7 Future Prospects
	References
5. Omics: A Potential Tool to Delineate the Mechanism of Biocontrol Agents against Plant Pathogens
	5.1 Introduction
	5.2 Genomics
		5.2.1 Trichoderma sp
		5.2.2 Pseudomonas sp
		5.2.3 Bacillus sp
	5.3 Proteomics
		5.3.1 Protein Identification
			5.3.1.1 Gel-Based Techniques
			5.3.1.2 Gel-Free Techniques
			5.3.1.3 Label-Free Techniques
		5.3.2 Fundamentals of Plant–Microbe (PM) Interactions
		5.3.3 Records of Plant, Pathogen, and PGPR Interactions through Proteomic Approaches
	5.4 Secretomics in Plant– Pathogen Interaction
		5.4.1 Apoplastic Protein Extraction
		5.4.2 Analysis of in planta Secreted Proteins
	5.5 Transcriptomics in Plant–Pathogen– Antagonist Interaction
		5.5.1 Application of Transcriptomics
	5.6. Culturomics
	5.7 Concluding Remarks
	Acknowledgment
	References
6. Bioinformatics Approaches to Improve and Enhance the Understanding of Plant–Microbe Interaction: A Review
	6.1 Introduction
	6.2 Genomics
	6.3 Gene expression Data
		6.3.1 Expressed Sequence Tags
		6.3.2 Microarrays
		6.3.3 RNA-Seq
		6.3.4 MicroRNAs
	6.4  Protein–Protein Interaction (PPI) Prediction
		6.4.1 Homology-Based Prediction
		6.4.2 Structure-Based Prediction
		6.4.3 Domain-Based Approaches
		6.4.4 Motif-and Integration-Based Approaches
		6.4.5 Motif–Domain and Motif–Motif Interaction-Based Approaches
		6.4.6 Surface Electrostatics and Epitope Prediction
		6.4.7 Analysis of Dynamic Character of PPI
	6.5 Machine Learning-Based Predictions
	6.6 Systems Biology Approach
	6.7 Conclusions
	References
7. Plant–Microbe Interactions in the Age of Sequencing
	7.1 Introduction
	7.2 Sequencing Technology
		7.2.1 First-Generation Sequencing
		7.2.2 Second-Generation Sequencing
		7.2.3 Third-Generation Sequencing
	7.3 Selection of NGS Technique
	7.4 Analysis of Sequencing Results
		7.4.1 Amplicon Analysis
		7.4.2 Metagenome Analysis
		7.4.3 De novo Microbial Genome Assembly
		7.4.4 Metatranscriptomic Analysis
	7.5 Conclusions
	References
8. Metaomics Technologies in Understanding Ethnomedicinal Plants and Endophyte Microbiome
	8.1 Introduction
	8.2 Metaomics
	8.3 Endophytic Metagenomics
	8.4 Approaches to Studying Metagenome
	8.5 Comparative Metagenomics
	8.6 Techniques Coupled with Metagenomics
	8.7 Software for Metagenomic Analysis
	8.8 Endophytic Metatranscriptomics
	8.9 Endophytic Metaproteomics
	8.10 Endophytic Metabolomics
	8.11 Methodological Challenges
	8.12 Conclusions
	References
9. Plant–Rhizomicrobiome Interactive Ecology through the Lenses of Multi-Omics and Relevant Bioinformatics Approaches
	9.1 Introduction
	9.2 Genomics and Metagenomics
	9.3 Transcriptomics and Metatranscriptomics
	9.4 Proteomics and Metaproteomics
	9.5 Metabolomics
	9.6 Genome Editing Tools
	9.7 Bioinformatics Tools and Online Databases
	9.8 Conclusive Remarks
	9.9 Future Directions
	References
10. Future Prospects of Next-Generation Sequencing
	10.1 Introduction
	10.2 First-Generation Sequencing Techniques (FGSTs)
	10.3 Second-Generation Sequencing Techniques (SGSTs)
	10.4 Third-Generation Sequencing Techniques (TGSTs)
	10.5 Single-Molecule DNA Sequencing (SMDS)
	10.6 Single-Molecule Real-Time Sequencing (SMRT)
	10.7 Nanopore Sequencing
	10.8 Potential TGSTs
	10.9 NGS Data Analysis
	10.10 Use of NGS Techniques in Molecular Plant Biology and Crop Improvement
	10.11 Transcriptome Investigation
	10.12 Gene Expression Profiling
	10.13 Small Noncoding RNA Profiling
	10.14 Gene Annotation Using Transcriptome Sequence Data
	10.15 Phylogenetic and Ecological Studies
	10.16 Allele Mining
	10.17 Genetical Genomics
	10.18 Epigenetics Studies
	10.19 Regulatory Protein Binding Domain Prediction
	10.20 Metagenomic Analysis
	10.21 Single-Cell Genomics
	10.22 Exome Sequencing
	10.23 Multiple Genome Sequencing and Resequencing
	10.24 Accelerating Genetic Gain in Breeding Populations
	10.25 Development of Pan-Genome and Super- Pan-Genome
	10.26 Pan-Genome size
	10.27 Type of Accessions
	10.28 Accelerating the Use of Gene-Based Markers in Breeding
	10.29 Capturing Exome Variation
	10.30 Future Prospects
	10.31 Concluding Remarks
	References
11. Revisiting Molecular Techniques for Enhancing Sustainable Agriculture
	11.1 Introduction
	11.2 Molecular Techniques for Deciphering Plant–Microbiome Interactions
	11.3 Why are Plant–Microbe Interactions Important for Crop Improvement?
	11.4  Next-Generation Techniques in Studying Plant–Microbe Interactions
		11.4.1  Next-Generation Sequencing Analysis of Plant–Microbe Interactions
		11.4.2 Transcriptome Scan of Plant–Microbe Interactions
		11.4.3 Proteome Analyses of Plant–Microbe Interactions
		11.4.4 Metabolomics Analyses of Plant–Microbe Interactions
		11.4.5 Simultaneous Perusal of Interaction between Plants and Related Microorganisms
		11.4.6 Use of Transcriptomics of Multiple Species in Understanding Plant–Microbe Interactions
		11.4.7 Phenomics
		11.4.8 Challenges and Future Perspectives
	11.5 Conclusions
	References
12. Nanotechnology in Plant Pathology: An Overview
	12.1 Introduction
	12.2 Need for Nanotechnology in Agriculture
	12.3 Nanoformulations of Agrochemicals for Crop Improvement
	12.4 Synthesis of Metal NPs from Plant Extract
	12.5 Synthesis of Silver NPs from Plant Extract
	12.6 Synthesis of Gold NPs from Plant Extract
	12.7 Synthesis of Copper NPs from Plant Extract
	12.8 Synthesis of Iron and Zinc Oxide NPs from Plant Extract
	12.9 Application of Nanotechnology in Plant Pathology
	12.10 Silver NPs
	12.11 Copper NPs
	12.12 Zinc NPs
	12.13 Silicon NPs
	12.14 Magnesium NPs
	12.15 Sulfur NPs
	12.16 Gold NPs
	12.17 Carbon NPs
	12.18 Titanium Dioxide (TiO[sub(2)]) NPs
	12.19 Molybdenum NPs
	12.20 Liposomes
	12.21 Dendrimers
	12.22 Conclusions
	References
13. An Overview of CRISPR and Gene Chip Technology to Study Plant–Microbe Interaction
	13.1 Introduction
	13.2  Holo-Omics for Plant Biology: Advantages and Challenges
	13.3 Recent Advancements in Plant–Microbe Crosstalk Studies
		13.3.1 CRISPR/Cas9 Manipulation
		13.3.2 Role of Microarrays and Gene Chip Technologies
	13.4 Conclusions
	Acknowledgment
	Conflict of Interest
	References
14. Functional Genomic Approaches to Improve Rice Productivity through Leaf Architecture
	14.1 Introduction
	14.2 Review of Literature
		14.2.1 Rice Taxonomy and Origin
		14.2.2 Rice Genetic Resources
		14.2.3 Improving Rice Productivity
		14.2.4 C[sub(4)] Leaf Anatomy
		14.2.5 Leaf Development
		14.2.6 Rice Genome Functional Analysis
		14.2.7 Semi- Quantitative PCR
		14.2.8 Gas Exchange Measurements
	14.3 Conclusions
	References
15. Tapping the Role of Plant Volatiles Inducing Multi- Trophic Interactions for Sustainable Agricultural Production
	15.1 Introduction
	15.2 Volatile Organic Compounds (VOCs): Classification and Biosynthesis
		15.2.1 Terpenoids
		15.2.2 Phenylpropanoid/ Benzenoid Compounds
		15.2.3 Fatty Acid Derivatives
		15.2.4 Amino Acid Derivatives
	15.3 Role of Volatile Organic Compounds (VOCs) in Plant Growth
	15.4 Role of Plant Volatiles in Stress Management
		15.4.1 VOCs Repelling Insect Herbivores
		15.4.2 VOCs Suppressing Phytopathogens
		15.4.3 VOCs Evading Abiotic Stress
	15.5 Application in Crop Improvement
	15.6 Conclusions and Future Prospects
	Acknowledgments
	References
16. Desiccation Tolerance in Orthodox and Recalcitrant Seeds
	16.1 Introduction
		16.1.1 Desiccation Tolerance as the Basis of Long-Term Seed Viability
	16.2 Mechanisms of Desiccation Tolerance in Developing Seeds
	16.3 Master Transcription Factors and Regulatory Mechanisms of Desiccation Tolerance
	16.4 The Role of Various Factors and Signaling in Developing Seeds
		16.4.1 The Role of ABA Signaling in DT
		16.4.2 The Role of LEA Protein and HSP Signaling in Seed DT
		16.4.3 The Role of Carbohydrate Signaling in Seed DT
			16.4.3.1 The Role of Sugars, Especially Sucrose, in DT
			16.4.3.2 The Role of RFO in Seed DT
	16.5 Antioxidants, Both Enzymatic and Non-Enzymatic, Play a Role in Seed Desiccation Tolerance
	16.6 Tolerance to Desiccation in Germinated Seeds
	16.7 Experimental Approaches to DT
	16.8 Modification in Desiccation: Removal of Cytoplasmic Water
	16.9 Contradictory Results
	16.10 Conclusions
	Abbreviations
	References
17. Chemical Ecology in Belowground Plant Communication
	17.1 Introduction
		17.1.1 Microbiome and Arbuscular Mycorrhizal Fungi
		17.1.2 Agricultural Practices and Plant Microbiome
			17.1.2.1 Glomalin and Microbiome
			17.1.2.2 Soil and Microbiome
	17.2 Conclusions
	References
18. Possible Bioremediation Strategies for Arsenic Detoxification by Consortium of Beneficial Bacteria
	18.1 Introduction
	18.2 Strategies Adopted by Bacteria to Alleviate Arsenic Toxicity
		18.2.1 Arsenic Uptake and Efflux Systems
		18.2.2 Bacterial Redox Reaction
			18.2.2.1 Oxidation of Arsenite to Arsenate
			18.2.2.2 Reduction of Arsenate to Arsenite
			18.2.2.3 Biovolatilization of Arsenic
	18.3 Molecular Mechanisms of Bacterial Tolerance to Arsenic Species
	18.4 Role of Bacteria in Arsenic Toxicity Amelioration in Plants
	18.5 A Genomic Perspective of Arsenic Bioremediation
	18.6 How a Bacterial Consortium Plays a Better Role Than Individual Strains
	18.7 Conclusions and Future Prospects
	Acknowledgments
	References
Index