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Sustainable Agriculture in the Era of the OMICs Revolution

✍ Scribed by Channa S. Prakash (editor), Sajid Fiaz (editor), Muhammad Azhar Nadeem (editor), Faheem Shehzad Baloch (editor), Abdul Qayyum (editor)


Publisher
Springer
Year
2023
Tongue
English
Leaves
511
Category
Library

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✦ Synopsis


Access to food with enough calories and nutrients is a fundamental right of every human. The global population has exceeded 7.8 billion and is expected to pass 10 billion by 2055. Such rapid population increase presents a great challenge for food supply. More grain production is needed to provide basic calories for humans. Thus, it is crucial to produce 60-110% more food to fill the gap between food production and the demand of future generations.

Meanwhile food nutritional values are of increasing interest to accommodate industrialized modern lives. The instability of food production caused by global climate change presents another great challenge. The global warming rate has become more rapid in recent decades, with more frequent extreme climate change including higher temperatures, drought, and floods. Our world faces various unprecedented scenarios such as rising temperatures, which causes melting glaciers and the resulting various biotic and abiotic stresses, ultimately leading to food scarcity. In these circumstances it is of utmost importance to examine the genetic basis and extensive utilization of germplasm to develop “climate resilient cultivars” through the application of plant breeding and biotechnological tools. Future crops must adapt to these new and unpredictable environments. Crop varieties resistant to biotic and abiotic stresses are also needed as plant disease, insects, drought, high- and low-temperature stresses are expected to be impacted by climate change. Thus, we need a food production system that can simultaneously satisfy societal demands and long-term development.

Since the Green Revolution in the 1960s, farming has been heavily dependent on high input of nitrogen and pesticides. This leads to environmental pollution which is not sustainable in the long run. Therefore, a new breeding scheme is urgently needed to enable sustainable agriculture; including new strategies to develop varieties and crops that have high yield potential, high yield stability, and superior grain quality and nutrition while also using less consumption of water, fertilizer, and chemicals in light of environmental protection.

While we face these challenges, we also have great opportunities, especially with flourishing developments in omics technologies. High-quality reference genomes are becoming available for a larger number of species, with some species having more than one reference genome. The genome-wide re-sequencing of diverse varieties enables the identification of core- and pan-genomes. An integration of omics data will enable a rapid and high-throughput identification of many genes simultaneously for a relevant trait. This will change our current research paradigm fundamentally from single gene analysis to pathway or network analysis. This will also expand our understanding of crop domestication and improvement. In addition, with the knowledge gained from omics data, in combination with new technologies like targeted gene editing, we can breed new varieties and crops for sustainable agriculture.

✦ Table of Contents


Contents
Chapter 1: The Utilization of Speed Breeding and Genome Editing to Achieve Zero Hunger
Introduction
Evolution of SB and Genome Editing
Time-Saving Tools for Achieving Zero Hunger
Plant Breeding Acceleration Through SB
Genome Editing Strategies: A Progressive Way Toward Zero Hunger Goal
Enhancing Resistance via Genome Editing
Increasing Abiotic Tolerance via Genome Editing
Improving Herbicide Tolerance Through Genome Editing
Improvement of Crop Yield Through Genome Editing
Optimization of Nutrient Use Efficiency Through Genome Editing
Integration of SB and Genome Editing Technologies for Achievement of Zero Hunger
Shortcomings of SB and Genome Editing
Conclusion
References
Chapter 2: Multiomics Approach for Crop Improvement Under Climate Change
Introduction
Climate Change Scenario and Its Impact on Crop Yield
Application of Advanced Omics Approaches
Transcriptomics
Proteomics
Metabolomics
Ionomics
Phenomics
Emerging Molecular Techniques
Zinc Finger Nuclease (ZFN)
Oligonucleotide-Directed Mutagenesis (ODM)
RNA-Dependent DNA Methylation (RdDM)
Reverse Breeding
Agro-Infiltration
Synthetic Genomics
Widely Studied Crop
Conclusion and Future Prospects
References
Chapter 3: The Intervention of Multi-Omics Approaches for Developing Abiotic Stress Resistance in Cotton Crop Under Climate Change
Introduction
Impact of Abiotic Stresses on Cotton
Physiological Responses of Cotton Toward Abiotic Stresses
Molecular Changes Due to Abiotic Stresses
Regulation of miRNAs During Abiotic Stresses
Hormonal Regulation During Abiotic Stress
Calcium Signaling During Abiotic Stress
Type of Abiotic Stress-Induced Genes
Role of Heat Shock Proteins During Abiotic Stress
Role of Transcription Factors Under Abiotic Stress
Mitogen-Activated Protein Kinase (MAPK) Signaling Pathway During Abiotic Stress
Role of Multi-Omics Approaches in Developing Tolerance to Abiotic Stresses
Genomics
Mutagenomics
Epigenomics
Phylogenomics
Pangenomics
Transcriptomics
Proteomics
Metabolomics
Ionomics
Lipidomics
Cytogenomics
Phenomics
Panomics
Role of Bioinformatics in Multi-omics Strategies
Conclusion
References
Chapter 4: Big Data Revolution and Machine Learning to Solve Genetic Mysteries in Crop Breeding
Introduction
ML and Big Data in Agriculture
ML and Its Impact in the Field of Genetics
ML Approaches in Plant Breeding
ML for Genetic Selections
ML in Plant Disease Studies
Conclusion and Future Outlook
References
Chapter 5: Applications of Multi-omics Approaches for Food and Nutritional Security
Introduction
Agriculture, Crop Breeding, and Microbiome
Improving Nutritional Status
High-Quality Plant-Based Food
Nutritional Crops for Food Security
Traditional Medicinal Plants for Food and Health Security
Improvement of Food Crops Towards Food Security
Feedomics
Food Safety and Environmental Effects on Food Safety
Health Status Versus Food Intake
The Challenges for Maintaining Adequate Nutrition
Nutrition, Diet, and Its Associated Diseases
A Multi-omics Strategy to Study the Role of Nutrition
Conclusion and Future Perspective
References
Chapter 6: Applications of High-Throughput Phenotypic Phenomics
Introduction of Phenomics
High-Throughput Phenomics (HTP)
Phenotypic Technologies
HTP Methods
RGB Imaging
Near-Infrared Imaging
Hyperspectral Imaging
Fluorescence Imaging
Applications of High-Throughput (HTP) Phenotypic (Phenomics)
Phenotypic Technologies
High-Throughput Phenomic Methods
Quantitative Plant Morphology Detection Through Phenomics
Quantitative Plant Morphology Detection Through Phenomics
Phenotyping of Roots in Plants Through Phenomics
References
Chapter 7: Basil (Ocimum basilicum L.): Botany, Genetic Resource, Cultivation, Conservation, and Stress Factors
Introduction
Botany and Distribution
Origin, Domestication, and Spread
Plant Genetic Resources
Collections and Conservation
Characterization and Evaluation
Use of Basil Genetic Resource
Ecology and Cultivation of Basil
Agricultural Systems
Agronomic Studies on Basil
Use of Organic Manure and Inorganic Fertilizers in Basil
Influence of Some Abiotic Factors on Basil Growth and Secondary Metabolite Production
Salinity Stress
Drought and Low-Temperature Stress
Looking Forward or Future Perspective
References
Chapter 8: Multi-Omics Approaches for Breeding in Medicinal Plants
Introduction
Multi-Omics in Technologies
Omics in Medicinal Plants
Genomics
Transcriptomics
Proteomics
Metabolomics
Multi-Omics and System Biology for Plant Improvement
Panomics for Crop Breeding Science
Potential Applications Translational Genomics to Breeding Design
Conclusion
References
Chapter 9: Applications of Some Nanoparticles and Responses of Medicinal and Aromatic Plants Under Stress Conditions
Introduction
Biotic Stress Factors
Abiotic Stress Factors
Salinity Stress
Higher Levels of Salinity Stress Alter the Responses of Plants Concerned with Their Physiology and Morphologies
Conflicts in Essential Oil Production as Responses Against High Levels of Salinity
Alterations in Phenolics as Responses Against High Levels of Salinity
Attempts to Diminish the Effects of Salinity Stress
Drought Stress
Drought Stress Alters the Responses of Plants Concerned with Their Physiology and Morphologies
Alterations in Essential Oil Yield and Composition as Response Against Drought Stress
Changes in Phenolics Under Drought Stress
Extreme Temperature Stress (Heat, Cold, and Frost Stress)
Heavy Metal Stress
Out of the Attempts Available: Uses, Efficiency, and Safety of Nanoparticles Against Stress Factors
An Overview on Nanomaterial Studies Using a Powerful Tool: VOSviewer Visualizing Scientific Landscapes
What Should Be the Priority Concerned with the Synthesis of Nanoparticles?
The Same Nanoparticles But Different Stress Factors: Compatible or Not?
A Hallmarked Indicator for Growth and Crop Productivity: But What Has Been Reported Regarding Metabolite Commodities Corresponding to the Agronomic Improvement Under Stress Conditions?
Conclusion
References
Chapter 10: Sustainable Agriculture Through Technological Innovations
Introduction
Role of Technology in Sustainable Agriculture
Digital Transformation for Sustainable Agriculture
Artificial Intelligence (AI) and the Internet of Things (IoT)
Monitoring Crops and Climate
Smart Farm Machinery
Radical Irrigation Systems and Fertilizer Applications
Pest and Weed Control
Robotics and Drone Technologies
OMICs and Genome Editing Technologies
Conclusion
References
Chapter 11: Sustainable Rice Production Under Biotic and Abiotic Stress Challenges
Introduction
Biotic Stress in Rice
Bacterial Leaf Blight
Rice Blast
Bakanae Disease
Weed
Control
Abiotic
Drought
High Temperature
Flood
Conclusion
References
Chapter 12: Emerging Techniques to Develop Biotic Stress Resistance in Fruits and Vegetables
Introduction
Biotic-Responsive Genes
Plant Defense Mechanisms to Biotic Stress
Basic/Molecular Mechanism of Host-Pathogen/Insect Interactions
Endophytes’ Sustainable Plant Protection for Stress Management
Nanotechnology: An Emerging Technology for Biotic Stress in Fruits and Vegetables
Disease Detection and Management
Insect Pest Management
Host Resistance Strengthening by Gene Cloning
Recombinant DNA Technologies
RNA Biology
Gene-Editing Technologies
CRISPR-Cas9
Eco-Sustainable Approaches to Improve Vegetables Resilience and Quality
Conclusion and Future Prospect
References
Chapter 13: Genome Editing in Crops to Control Insect Pests
Introduction
Genome-Editing Techniques
CRISPR/Cas9-Mediated Genome Editing
Variants of Cas9 for Genome Editing
CRISPR-Based Gene Editing Emerges over RNA Interference
Genome Editing in Plants
Genome Editing in Plants to Improve Resistance Against Insect Pests
Genome-Editing Targets
Specificity, Efficiency, and Off-Targeting
Delivery Techniques and Efficiency
Applications in Plant-Insect Resistance
Assessment of Plants Developed Through Genome-Editing Technologies
Challenges and Future Prospects
References
Chapter 14: CRISPR Revolution in Gene Editing: Targeting Plant Stress Tolerance and Physiology
Introduction
Evolution in CRISPR Systems
CRISPR Targeting Plant Stress Tolerance
CRISPR Targeting Plant Physiology
Challenges and Their Solutions
References
Chapter 15: Genomics for Abiotic Stress Resistance in Legumes
Abiotic Stresses and Importance of Legumes
Gene Discovery through Sequencing in Legumes
Stress-Inducible Genes
Alternative Approach to Identify Genes
Transcriptomic Changes
Heat Shock Factors and Stress Tolerance in Legumes
Transcription Factors
MicroRNA
Genome Editing for Stress Tolerance
Breeding Approaches
Chickpea and Common Beans
Cowpea, Lentils, and Soybean
Peas
Forage Legumes
References
Chapter 16: Genetic and Molecular Factors Modulating Phosphorus Use Efficiency in Plants
Introduction
Phosphorus Uptake and Transport
Phosphorus Use Efficiency
Plant Physiological Response to Phosphorus
Molecular and Genetic Responses to Phosphorus Deficiency
Role of Phosphorus in Plant Metabolism
Photosynthesis
Plant Energy Reactions
Genetic Transfer
Nutrient Transport
Transgenic Approaches to Improve Phosphorus Use Efficiency
Future Prospects
References
Chapter 17: Recent Trends in Genome Editing Technologies for Agricultural Crop Improvement
Introduction
Mechanism and Framework of the CRISPR/Cas9 System in Plants
Recent Advances in Genome Editing Technologies
Multiplex Genome Editing
Modulation of Metabolite Production
Biofortification of Crops
Off-Target Effects of CRISPR
Production of Transgene Free Genome-Edited Crops
Discovery of New Cas Proteins in Addition to Cas9
Base Editing
Chromosomal Engineering
Role of Gene Editing for Crop Improvements
Conclusion and Outcomes
References
Chapter 18: Recent Trends and Applications of Omics-Based Knowledge to End Global Food Hunger
Introduction
Current Statistics of Major Food Crops and Their Future Demands to Increasing Population
Major Stresses Induced Due to Global Climate Change in Achieving Food Security Globally
Drought and Temperature
Omics Introduction
Agricultural Limitations and Their Alleviation via Omics Technologies
Omics Role in the Present Agriculture
Omics Intervention to Improve Quality of Crops
Applications of Omics
Challenges to Food Security
Conclusion
References
Chapter 19: Nutritional Enhancement in Horticultural Crops by CRISPR/Cas9: Status and Future Prospects
Introduction
CRISPR: A Brief Summary
CRISPR/Cas9 Mechanism of Action
Targeted Mutagenesis Using CRISPR/Cas9
CRISPR/Cas9 for Improving Vegetable Crops
Potato
Tomato
Lettuce
Kale
Carrot
Brassica
Eggplant
CRISPR-Cas9 in Fruit Crop Improvement
CRISPR-Cas9 in Grape and Grapevine
Banana
CRISPR/Cas9 for Non-transgenic Horticultural Crops
The Regulatory Status of CRISPR/Cas9 Horticulture Crops
CRISPR-Cas9-Mediated Genome Editing Limitations and Future Prospects
References
Chapter 20: Physiological Interventions of Antioxidants in Crop Plants Under Multiple Abiotic Stresses
Introduction
Strategies of Plants to Cope with Stress
Abiotic Stresses and Plants
Antioxidants Combat Plant Abiotic Stresses
Mode of Exogenous Applications of Antioxidants
Folair Applications of Antioxidants
Applications of Antioxidants Through Rooting Media
Applications of Antioxidants by Seed Soaking
Nonenzymatic Antioxidants
Ellagic Acid
Ascorbic Acid
Salicylic Acid
Tocopherols
Anthocyanins
Brassinosteroids
Carotenoids
Enzymatic Antioxidants
Catalases (CAT)
Peroxidases
Superoxide Dismutase (SOD)
Conclusion
References
Chapter 21: Proteomics and Its Scope to Study Salt Stress Tolerance in Quinoa
Introduction
Proteomics Approach
Protein Digestion and Solubilization
Protein Separation
Image Analysis
Protein Identification and Characterization
Chenopodium quinoa and Scope of Proteomics Analysis
Advantage of Proteomics over Other Techniques
Limitations/Disadvantages
Conclusion
References
Chapter 22: Sustainable Cotton Production in Punjab: Failure and Its Mitigating Strategies
Introduction
Obsolete Technology
Climate Change
Temperature
Excessive Rains
Availability of Quality Seed
Insect Pest Problem
Pesticide Quality, Efficacy, and Chemistry
Lack of Awareness About Crop Production Technology
Cotton Leaf Curl Virus Disease Losses
Weed Infestation
Low Plant Population
Cotton Competing Crops
Low Profitability
Socioeconomic Constraints
Water Shortage
Strategies for Sustainable Cotton Production
Approval and Adoption of Advanced Technology
Climate-Resilient Varieties
Seed Quality Issues
Launching Comprehensive IPM for Insect Pest Problem
Quality, Efficacy, and Chemistry of Pesticide
Improvements to the Seed Industry Through Private Sector
Farmers’ Capacity Building
Zoning of Crop
Laser Leveling
Farm Mechanization
Socioeconomic Constraint Barriers
References
Chapter 23: Biosafety and Biosecurity in Genetically Modified Crops
Introduction
Biosafety Objectives
Safeguarding Life from Dangerous Biological Factors
Plant Health Protection
Environmental Protection
Protection Against Theft, Loss, or Misuse
Biosafety Levels for GM Crops
First Level
Second Level
Third Level
Issues Associated with Biosafety and Biosecurity
Solutions
Improvement of Biosafety and Biosecurity Capability Worldwide
Improvement and Establishment of Biosafety and Biosecurity Network Worldwide
Improvement of Alert Mechanism to Deal Disease Outbreak
Improvement of Identification Level and Control of Pathogens
Improvement of Biotechnology Applications and Administration System
Improvement of Controlling Setup for Invasive Alien Species
References
Index


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