Cereal Crops: Genetic Resources and Breeding Techniques

Cover
Half Title
Title Page
Copyright Page
Dedication
Table of Contents
Editors
Contributors
Chapter 1 Farming Systems Improvements in Different Regions
1.1 Introduction
1.2 Cropping Systems in Semi-Arid Areas of Zimbabwe
1.3 Effects of Legumes on Cereal Productivity
1.4 Effects of Legumes on Soil Properties
1.5 Intercropping of Legumes and Cereals
1.6 Conclusion
References
Chapter 2 Stepwise Intensification Option for Enhancing Cereal-Based Cropping Systems
2.1 Introduction
2.2 Types of Intercropping Systems
2.3 Advantages and Disadvantages of Intercropping
2.4 Evaluation of the Efficiency of Intercropping Systems
2.5 Cropping Pattern in Egypt
2.5.1 Intercropping Cereals with Legumes
2.5.1.1 Intercropping Maize with Soybean
2.5.1.2 Intercropping Maize with Groundnut
2.5.1.3 Intercropping Maize with Cowpea
2.5.1.4 Intercropping Maize or Wheat with Tomato
2.5.2 Intercropping Cereals with Sugar Crops
2.5.2.1 Intercropping with Sugarcane
2.5.2.2 Intercropping with Sugar Beet
2.5.3 Relay Intercropping Cotton with Wheat
2.5.4 Intercropping Cereal Crops with Cassava
2.5.5 Intercropping Cassava with Maize
2.6 Conclusion
References
Chapter 3 Cereal Yield in Dry Environments: Adaptability of Barley vs. Wheat
3.1 Introduction
3.2 Physiological and Biochemical Reactions to Dry Environments
3.2.1 Photosynthesis
3.2.2 Water and Nutrient Relations
3.2.3 Oxidative Status
3.2.3.1 Reactive Oxygen Species (ROS)
3.2.3.2 Antioxidant System
3.2.4 Osmotic Balance and Hormonal Effect
3.3 Breeding for Dry Environment Tolerance
3.3.1 Genetics for Dry Environment Tolerance at Different Growth Stages
3.3.1.1 At the Germination Stage
3.3.1.2 At the Seedling Stage
3.3.1.3 At the Flowering and Grain-Filling Stages
3.3.2 Distinct Genotyping and Phenotyping for Improving Dry Environment Tolerance in Wheat and Barley
3.3.3 The Use of Nanotechnology to Improve Breeding and Dry Environment Tolerance
3.4 Genetics for Dry Environment Tolerance in Wheat and Barley
3.4.1 The Genetic Basis of Dry Environment Tolerance
3.4.2 Functional Validation of Dry Environment Tolerance QTLS and Candidate Genes
3.4.3 Genomics Analyses of Dry Environment Tolerance
3.4.4 Genetic Engineering of Dry Environment–Tolerant Genes in Wheat and Barley
3.5 Adaptation of Barley and Wheat to Dry Environments
3.5.1 Adaptation of Barley and Wheat to Dry Environments: Morphological Characters
3.5.2 Adaptation of Barley and Wheat to Dry Environments: Apical Development, Leaf, and Tiller Appearance
3.5.3 Adaptation of Barley and Wheat to Dry Environments: Plant Ideotype and Grain Yield
3.6 Conclusion
References
Chapter 4 Cereal Performance and Senescence
4.1 Introduction
4.2 Physiological Characteristics to Improve Yield Stability
4.3 Evaluating the Yield Stability of the Population under Changing Environment
4.3.1 Senescence is the Ultimate Evolving Phase of Plant Growth
4.3.2 Metabolism of Nitrogen and Re-translocation
4.3.3 Senescence-Related Gene Expression
4.3.4 Genetic Regulation of Aging Phenotype
4.4 The Senescence Process of Barley and Wheat
4.5 High Nutrient Mobilization Efficiency
4.6 Ideal Cereal Senescence Phenotype
4.7 How to Achieve This in Practice
4.8 Conclusion and Remarks
References
Chapter 5 Cereal Responses to Nutrients and Avenues for Improving Nutrient Use Efficiency
5.1 Introduction
5.2 Cereal Production and Food Security
5.2.1 World Population, Food Security, and Cereals Demand in Developing Countries
5.2.2 The State of Cereals Production and Challenges in Developing Countries
5.3 Basics of Plant Nutrition for Food Security
5.3.1 Recent Trends of Global Nutrient Utilization and NUE in Cereals
5.3.2 Trends in Nutrient Utilization and Nutrient Use Efficiency in Cereals
5.3.3 Impact of Plant Nutrition on Food Quality and Human Health
5.3.4 Impact of Plant Nutrition on Food Quality
5.4 Impact of Plant Nutrition on Human Health
5.4.1 Removal, Loss Mechanism, and Environmental Consequences of Plant Nutrients
5.4.1.1 Removal and Loss of Nutrients
5.4.1.2 Consequences of Loss of Nutrients in Environment
5.5 Optimizing Plant Nutrition for Enhanced NUE and Cereal Production
5.5.1 Chemical Fertilizers and the Concept of 4R Nutrient Stewardship for Sustainable Cereals Productions
5.5.1.1 Right Source
5.5.1.2 Right Rate
5.5.1.3 Right Time
5.5.1.4 Right Place
5.6 Genetic Approaches to Improve Nutrient Use Efficiency in Cereal Crops
5.6.1 Genotypes with Improved NUE
5.6.2 Genes Involved in the NUE
5.6.2.1 Nitrogen Transporter Genes
5.6.2.2 Nitrogen Assimilation and Amino Acid Biosynthesis Genes
5.6.2.3 Signaling Molecule and Transcription Factor in NUE
5.6.3 Phosphate Transporter and Transcription Factors for NUE
5.6.4 Transporter Gene for the Uptake of Micronutrient
References
Chapter 6 Genetic Resources of Cereal Crops: Collection, Characterization, and Conservation
6.1 Introduction
6.2 Taxonomy
6.2.1 Rice
6.2.2 Maize
6.2.3 Barley
6.2.4 Sorghum
6.3 Botany of Major Cereals
6.3.1 Wheat
6.3.2 Maize
6.3.3 Rice
6.3.4 Sorghum
6.3.5 Barley
6.4 Origin, Domestication, Distribution, and Spread
6.4.1 Wheat
6.4.2 Barley
6.4.3 Rice
6.4.4 Maize
6.4.5 Sorghum
6.5 Germplasm Conservation
6.5.1 Wild Genetic Resources of Cereal Crops
6.5.2 Collections and Conservation Strategies
6.5.3 Conservation Strategies
6.6 Status of Cereal Crop Genetic Resources
6.6.1 Status of Wheat Genetic Resources
6.6.2 In Situ Conservation Status
6.6.3 Ex Situ Conservation Status
6.6.4 Gaps and Priorities
6.7 Status of Rice Genetic Resources
6.7.1 In Situ Conservation Status
6.7.2 Ex Situ Conservation Status
6.7.3 Gaps and Priorities
6.8 Status of Maize Genetic Resources
6.8.1 In Situ Conservation Status
6.8.2 Ex Situ Conservation Status
6.8.3 Gaps and Priorities
6.9 Status of Sorghum Genetic Resources
6.9.1 Ex Situ Conservation Status
6.9.2 Gaps and Priorities
6.10 Germplasm Use
6.10.1 Major Constraints on Cereal Crop Production
6.10.2 Traits Desired
6.10.3 Evaluation of Genetic Diversity
6.10.4 Sources of Desirable Traits
6.10.5 Breeding Options
6.10.6 Genomics-Assisted Breeding
6.10.7 Present Status of Use or Incorporation of Desired Traits
6.10.8 Research Needs
6.11 Future Perspective
6.12 Recent Trends in Supply and Demand for Cereals
6.13 Demand for Cereals
References
Chapter 7 Resistance Identification and Implementation: Genomics-Assisted Use of Genetic Resources for Breeding against Abiotic Stress
7.1 Introduction
7.2 Abiotic Stress and Plant Metabolism
7.2.1 Drought
7.2.2 Salinity
7.2.3 Temperature
7.2.4 UV Light
7.2.5 Flood
7.2.6 Heavy Metals
7.3 Engineering Abiotic Stress-Tolerant Plants
7.3.1 Conventional Techniques
7.3.2 Transgenic Approaches
7.3.3 CRISPR/Cas 9-Mediated Genome Editing
7.4 Future Prospects
References
Chapter 8 Genomics-Assisted Use of Genetic Resources for Environmentally Adaptive Plant Breeding: Salinity Tolerance
8.1 Introduction
8.1.1 Soil Salinity: Serious Threats to Cereal Crops Production and Global Food Security
8.1.2 Assessing Salinity Tolerance in the Current Cereal Crops
8.1.3 Advances and Challenges in Developing Salt-Tolerant Cereal Crops
8.2 Genetic Resources for Cereals Improvements: Road toward Designing of Sophisticated and Environmentally Adaptive Plant Breeding
8.2.1 Conventional Breeding
8.2.2 Molecular Breeding
8.2.3 Basic Genome Screening Technologies
8.2.4 Advanced Genome Screening Technologies
8.3 Genomics-Assisted Use of Genetic Resources for Salinity-Resilience Genotypes Developing
8.3.1 Next-Generation Breeding of Salt-Resilient Cereal Germplasms
8.3.2 Mutational Approaches to Develop Salt-Resilient Genotypes
8.3.3 Genome/Gene Editing to Accelerate Cereal Crops’ Salt Tolerance
8.4 Concluding Remarks: Way Forward and Challenges Ahead
References
Chapter 9 Metabolomics-Assisted Breeding for Enhancing Yield and Quality of Cereals
9.1 Introduction to Plant Metabolomics
9.2 Analytical Techniques and Methodologies Exploited in Metabolomics
9.2.1 Nuclear Magnetic Resonance Spectroscopy
9.2.2 High-Resolution Mass Spectrometry (HRMS)
9.3 Separation Techniques Exploited in Metabolomics
9.3.1 Liquid Chromatography
9.3.2 HPLC
9.3.3 SPME MS
9.3.4 SFC MS
9.3.5 GC-MS and GC-GC MS
9.4 Metabolomics-Assisted Cereal Breeding
9.4.1 Metabolomics-Assisted Breeding to Improve Cereals Composition and Yield
9.4.2 Metabolomics-Assisted Breeding to Control Biotic Stress in Cereals
9.4.2.1 Metabolomics Response toward Necrotrophic Pestilential
9.4.2.2 Metabolomics Response toward Biotrophic Potential
9.4.2.3 Metabolomics Response toward Viral Pestilential
9.4.2.4 Metabolomics Response toward Insect Pestilential
9.4.3 Metabolomics-Assisted Breeding to Control Abiotic Stress in Cereals
9.4.4 Metabolomics-Assisted Breeding to Escalate Amino Acid Contents in Cereals
9.4.5 Targeted Metabolomics in Transgenic Cereals
9.4.6 Untargeted Metabolomics in Transgenic Cereals
9.5 Applications of Metabolomics-Assisted Crop Breeding
9.5.1 Biomarkers for Transgenic Crop Evaluation
9.5.2 Predictor of Heterosis
9.6 QTL Mapping for Refining Crop Metabolomics
9.7 Future Prospects and Limitations
9.8 Conclusion
References
Chapter 10 Metabolic Responses in Plants under Abiotic Stresses
10.1 Introduction
10.2 Plant Growth Responses under Abiotic Stresses
10.3 Regulation of Metabolic Processes: Osmolyte Accumulation
10.4 Plant Metabolomics Involves Plant Responses at Different Levels
10.4.1 Carbohydrate/Sugar, Amino Acid and Fatty Acid Metabolism
10.4.2 Role of Phytohormones
10.4.2.1 Crosstalk between Phytohormones under Abiotic Stresses
10.4.2.2 Metabolic Engineering of Phytohormones
10.4.2.3 Metabolic Responses in Plants Correlated with Circadian Rhythms
10.4.2.4 Regulation of Circadian Rhythms by Metabolites
10.5 Metabolic Alterations in Response to Different Abiotic Stresses
10.5.1 Drought Stress
10.5.1.1 Osmolyte Accumulation
10.5.2 Salinity Stress
10.5.3 Heat Stress
10.5.4 Flooding Stress
10.5.5 Ozone
10.5.6 Effect on Plant Biochemical Processes
10.5.7 Ozone Effects on Primary and Secondary Metabolism
10.5.8 Ozone Triggers Oxidative Stress
10.5.9 Oxidative Stress
10.6 Conclusion
References
Chapter 11 Climate Change and Cereal Modeling: Impacts and Adaptability
11.1 Introduction
11.2 Climate Change Influence
11.2.1 Climate Change Influence on Crop Production
11.2.2 Climate Change Influence on Soil Properties
11.2.3 Climate Change Impact on Insect Pests
11.2.4 Climate Change Impact on Plant Pathogens
11.2.5 Climate Change Impact on Yield and Food Security
11.3 Growing Conditions Required for Different Cereal Crops
11.3.1 Internal Factors Affecting Crop Production
11.3.2 External Factors Affecting Crop Production
11.3.2.1 Paddy (Rice)
11.3.2.2 Pearl Millet
11.3.2.3 Maize
11.3.2.4 Wheat
11.3.2.5 Sorghum
11.3.2.6 Oat
11.4 Cereal Modeling: Potential Approaches to Enhance Cereal Crops Production
11.4.1 Breeding
11.4.2 Recombinant Technology
11.4.3 Gene Editing
11.4.4 Zinc-Finger Nucleases (ZFNs)
11.4.5 Transcription Activator-Like Effector Nucleases (TALENs)
11.4.6 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)
11.5 Conclusion and Future Directions
References
Chapter 12 Genetic Transformation Methods in Cereal Crops
12.1 Introduction
12.2 Genetic Improvement of Cereals through Breeding and Classical Cytogenetics
12.2.1 Hybridization within the Primary Gene Pool
12.2.2 Distant Hybridization and Chromosomal Manipulation
12.2.3 Methods of Direct Gene Transfer in Cereals
12.2.3.1 Biolistic Transformation
12.2.3.2 Protoplast Transformation
12.2.3.3 Liposome Fusion Method
12.2.3.4 Genetic Manipulation via Electroporation
12.2.3.5 Silicon Carbide-mediated Transformation
12.2.3.6 Transformation through Pollination
12.2.4 Indirect Method of Gene Transfer
12.2.4.1 Agrobacterium Gene Transformation in Cereals
12.3 Combinations of Genetic Transformation Technologies
12.3.1 Combination of A. tumefaciens-mediated Transformation with Pollination
12.3.2 Combination of A. tumefaciens-mediated Transformation with Ballistic Transfection
12.3.3 Combination of A. tumefaciens-mediated Transformation by Using Silicon Carbide Fibers
12.4 Gene Transfer Using CRISPR–Cas
12.5 Traits Introduced in Cereals
12.5.1 Disease Resistance
12.5.2 Herbicide Resistance
12.5.3 Pest Resistance
12.5.4 Improvement of Cereal Grain Quality
12.6 Conclusion
References
Chapter 13 Genome-Edited Cereal Characterization Using Metabolomics
13.1 Introduction
13.2 Genome Editing
13.2.1 CRISPR–Cas9 System
13.2.2 CRISPR–Cpf1/Cas12a
13.2.3 Base Editing
13.3 Genome Editing in Cereals
13.3.1 Metabolomics
13.3.1.1 Role of Metabolomics in Improving Cereal Crops Traits
13.3.1.2 Metabolomic Analysis of Gene-Edited Cereal Crops
13.4 Concluding Remarks
References
Chapter 14 Multiplexed Genome Editing in Cereals: Trait Improvement Using CRISPR/Cas9
14.1 Introduction
14.2 Multiplex Genome Editing: An Overview
14.3 Development of Vectors for Multiplexing
14.4 CRISPR/Cas9-mediated Multiplex Genome Editing in Cereals
14.5 Gene Editing and Improvement of Cereals: CRISPR/Cas9 Perspective
14.6 Improvement of Yield and Related Traits
14.7 Improvement of Cereal Defense Responses
14.8 Challenges and Outlook of Multiplexing
References
Index