Translating Physiological Tools to Augment Crop Breeding

Preface
Contents
About the Editors
Chapter 1: Importance of Integrating Physiological Breeding to Augment Crop Breeding
1.1 Introduction
1.2 History of Physiological Breeding
1.3 Need and Importance of Physiological Breeding
1.4 Diverse Pipeline Used in Physiological Breeding for Crop Improvement
1.5 Future Prospects
References
Chapter 2: Stacking of Complex Traits Through Physiological Prebreeding
2.1 Introduction
2.2 Prebreeding: Historical Antecedents
2.3 Physiological Traits in Wheat and Breeding Conduits
2.4 Prerequisites of Prebreeding and Breeding for Physiological Traits
2.4.1 Genetic Variation
2.4.2 Trait Transfer Protocols from Wild Species
2.4.3 Marker-Assisted Selection (MAS)
2.4.4 Stacking of the Physiological Traits
References
Chapter 3: Strategies to Develop Heat and Drought-Tolerant Wheat Varieties Following Physiological Breeding
3.1 Introduction
3.2 Germplasm Utilization for Improving Heat Tolerance
3.3 Physiological Traits to Be Targeted to Improve Yield Under Heat and Drought Tolerance
3.3.1 Heat Stress
3.3.2 Drought Stress
3.4 Plant Adaptive Mechanisms to Heat Stress
3.4.1 Heat Stress Avoidance
3.4.1.1 Changing Leaf Orientation
3.4.1.2 Transpirational Cooling
3.4.1.3 Leaf Rolling
3.4.1.4 Alteration of Membrane Lipid Compositions
3.4.2 Heat Stress Escape
3.4.3 Heat Stress Tolerance
3.4.3.1 Osmoprotectants
3.4.3.2 Antioxidant Defence
3.4.3.3 Expression of Stress Protein
3.4.3.4 Signalling Cascade and Transport Control
3.5 Heat and Drought Stress Tolerance Screening Methods
3.5.1 Direct Screening for Yield in Stress Environments Under Natural Conditions
3.5.2 Artificial or Controlled Environments
3.6 Breeding Strategies and Methods
3.6.1 Breeding for Physiological Traits for Improving Heat Tolerance in Wheat
3.6.2 Conventional Approaches for Developing Heat and Drought-Tolerant Lines
3.6.2.1 Breeding for Heat and Drought Tolerance
3.6.3 Molecular Breeding Strategies
3.6.3.1 Applications of Biochemical Markers to Improve Drought Tolerance
3.6.3.2 Molecular Marker
3.6.3.2.1 Marker-Assisted Backcross Breeding
3.6.3.2.2 Marker-Assisted Recurrent Selection
3.6.3.2.3 Genome-Wide Association Studies (GWAS)
3.6.3.2.4 Genomic Selection
3.6.3.2.5 Genetic Engineering and Gene Editing
3.6.4 Difficulties in Breeding for Drought and Heat Tolerance
3.7 Conclusion
References
Chapter 4: Developing Crop Varieties by Physiological Breeding for Improving Plant Nutrition
4.1 Introduction
4.1.1 Traditional/Conventional Plant Breeding
4.1.1.1 Molecular Breeding
4.1.1.2 Physiological Breeding
4.1.2 Transgenic Approach
4.1.2.1 Genome Editing
4.1.3 Agronomic Approach
4.1.4 Genomic Approach
4.2 Mineral Nutrition Under Climate Change Conditions
4.2.1 Rise in CO2 Level and Mineral Nutrition
4.2.2 Effect of Elevated CO2 on Arbuscular Mycorrhiza (AM)
4.2.3 High Temperature and Mineral Nutrition
4.2.4 Interactive Effect of Atmospheric CO2 Rise and Temperature on Plant Growth
4.3 Breeding Nutrient Efficient Crops
4.3.1 Exploiting Genetic Diversity for Nutritional Traits
4.3.2 Approaches for Enhancing Nutritional Quality
4.3.3 Engineering Pathways and Nutrient Use Efficiency (NUE)
4.3.4 Targeting Traits for Breeding Nutrient Efficient Crop
4.3.4.1 Root Characteristics and NUE
4.3.4.2 Staygreen and NUE
4.3.4.3 Nutrient Harvest Index (NHI) and NUE
4.4 Biofortification: Overview
4.4.1 Micronutrient Absorption Mechanism
4.4.2 Fertilizer´s Impact on Nutrition Composition
4.4.3 Nutritional Content and Quality Improvement: Future Challenges
4.5 Improvement of Plant Nutrient and Nutritional Quality Through Genome Editing
4.5.1 Nutrient
4.5.2 Improvement of Nutritional Quality
4.5.3 Antinutritional Factor
4.5.4 Biofortification
4.6 Conclusion
References
Chapter 5: Role of Transpiration in Regulating Leaf Temperature and its Application in Physiological Breeding
5.1 Introduction
5.2 Leaf Energy Balance
5.2.1 Re-radiation
5.2.2 Sensible Heat Loss
5.2.3 Latent Heat Loss Through Transpiration
5.3 Transpiration as a Heat Avoidance Strategy
5.3.1 Canopy Temperature Depression (CTD)
5.3.2 Complex Relationship of Transpiration and Leaf Temperature with Plant and Physical Factors
5.3.2.1 Transpiration and Leaf Temperature Affected by Plant Physiological Attributes
5.3.2.1.1 Stomatal Conductance (gs)/Stomatal Resistance (rs)
5.3.2.1.2 Leaf Boundary Layer Conductance (gb)/Resistance (rb)
5.3.2.1.3 Leaf Mesophyll Conductance (gm)/Resistance (rm)
5.3.2.1.4 Leaf Cuticular Resistance (rc)
5.3.2.1.5 Water Absorption and Transport Capacity of the Vascular System: Roots, Stems, and Leaves
5.3.2.1.5.1 Root Traits Associated with Improved Transpirational Cooling through Better Water Absorption
5.3.2.1.5.2 Efficiency of Root Water Absorption and Transport through the Vascular System
5.3.2.2 Transpiration and Leaf Temperature as Affected by Environmental Parameters
5.3.2.2.1 Air Temperature and Atmospheric VPD
5.3.2.2.2 Soil Water Availability
5.3.2.3 Transpiration and Leaf Temperature as Affected by Plant Anatomy and Morphology
5.3.2.3.1 Transpiration, Leaf Temperature, and Glaucousness
5.3.2.3.2 Transpiration, Leaf Temperature, and Pubescence
5.3.2.3.3 Transpiration Leaf Temperature and Leaf Rolling
5.3.2.3.4 Transpiration, Leaf Temperature, and Canopy Architecture
5.3.2.3.5 Transpiration, Leaf Temperature, and Leaf Thickness
5.3.2.3.6 Transpiration, Leaf Temperature, and Leaf Size
5.4 Transpirational Cooling Under Future Climate: Applications in Physiological Breeding
5.5 Conclusion
References
Chapter 6: Photosynthesis as a Trait for Improving Yield Potential in Crops
6.1 Introduction
6.2 Phenotyping for Photosynthesis/Photosynthetic Efficiency (PSE) under Controlled and Field Conditions
6.2.1 Precise Studying of Photosynthetic Efficiency (PSE)
6.2.1.1 Portable Photosynthesis System (PP)
6.2.2 Rapid Screening for Photosynthetic Efficiency
6.2.2.1 Chlorophyll Fluorescence (CFL)
6.2.3 Imaging Techniques for Rapid Screening of PSE
6.3 Approaches Followed for Improving PSE in Crops
6.3.1 Enhancing the Photosynthesis of Nonlaminar Organ
6.3.2 Introduction of C4-like Anatomy in C3 Plants
6.3.3 Introduction of C4 Pathway into C3 Crops Through Introducing C4 Enzymes
6.3.4 Introduction of Carbon Concentrating Mechanism
6.3.5 Modifying the Rubisco
6.3.6 Optimization of Calvin Cycle´s Enzymes
6.3.7 Redesigning Photorespiration and CO2 Fixation Pathways
6.3.8 Controlling the PSII Efficiency
6.3.9 Insertion of Inorganic Carbon Transporter B (ictb) Gene
6.3.10 Downregulation of Genes to Improve PSE
6.3.11 Agronomical Approaches
6.3.11.1 Increased Photosynthesis Through Application of Nitrogen (N)
6.3.11.2 Use of CO2 Fertilizers
6.3.12 Molecular Markers for Improving PSE
6.4 Effect of Climate Change on Photosynthesis
6.5 Future Prospect
References
Chapter 7: Cuticular Waxes and Its Application in Crop Improvement
7.1 Introduction
7.2 Cuticular Wax Biosynthesis in Plants
7.3 Transporters of Cuticle Precursors
7.4 Transcriptional Regulation in Biosynthesis of Cuticular Waxes
7.4.1 APETALA2/Ethylene Responsive Factor
7.4.2 Homologous of WIN/SHN
7.4.3 Negative Regulators of WIN/SHN
7.4.4 WAX PRODUCTION1 (WXP1)
7.4.5 WRINKLED and CBF TFs
7.4.6 Myeloblastosis Family (MYB)
7.4.7 Homeodomain-Leucine Zipper Class IV Factors
7.4.8 Curly Flag Leaf1, a Negative Regulator of HD-Zip IV
7.5 Cuticular Wax, a Multifunctional Trait
7.6 Attempts to Manipulate Cuticular Trait
7.7 Conclusion
References
Chapter 8: Radiation Use Efficiency (RUE) as Target for Improving Yield Potential: Current Status and Future Prospect
8.1 Introduction
8.2 What Is RUE
8.3 Is It Possible to Improve RUE
8.4 Approaches to Improve RUE
8.4.1 Light Harvesting and Electron Transport
8.4.1.1 Canopy Architecture
8.4.1.2 Expanding the Absorption Spectra
8.4.1.3 Maximizing Light Harvesting by Reducing Chlorophyll Content
8.4.2 Improving Photosynthetic Efficiency
8.4.2.1 Reducing Energy Loss Via Nonphotochemical Quenching
8.4.2.2 Engineering Rubisco and Reducing Energy Loss Via Photorespiration
8.4.2.3 Increasing CO2 Uptake and Capture (CCM)
8.4.2.3.1 Expression of Algal or Photosynthetic Bacterial CO2 and Bicarbonate Transporters in Chloroplast Membranes of C3
8.4.2.3.2 Install the C4 Pathway in C3 Plants
8.4.2.3.3 Install Cyanobacterial or Algal CCM Characterized by Bicarbonate Transporters and Occurrence of Carboxysome or Pyren...
8.4.2.4 Modulating RuBP Regeneration
8.5 Future Prospect: Designing Smart Canopy
References
Chapter 9: Application of Stable Isotopes in Crop Improvement
9.1 Introduction
9.2 Stable Isotopes
9.3 Measuring Stable Isotopes
9.4 Utilization of Stable Isotopes in Different Field
9.5 Stable Isotopes for Physiological Traits
9.5.1 Water Use Efficiency: An Important Trait for Drought
9.5.1.1 Gravimetric Approach
9.5.1.2 Gas Exchange Studies
9.5.1.3 Carbon Isotope Discrimination
9.5.1.3.1 Range of δ13C Composition
9.5.1.3.2 Carbon Isotope Discrimination (Δ13C) at Different Steps During Photosynthesis
9.5.1.3.3 Δ13C as a Surrogate for WUE
9.5.1.3.3.1 Δ13C and WUE Relationship
9.5.1.3.3.2 Wheat
9.5.1.3.3.3 Rice
9.5.2 Mean Transpiration Rate (MTR)
9.5.3 Stable Isotopes of Oxygen
9.6 Conclusion or Future Prospects
References
Chapter 10: Root Phenotyping for Improved Resource Use Efficiency in Crops
10.1 Introduction
10.2 How Can Resource Use Efficiency Be Enhanced?
10.3 Root Responses to Resource Deficiency
10.4 Root Phenotyping Needs
10.5 Demonstrated Efforts and Success of Root Phenotyping
10.5.1 Perforated Basket Method
10.5.2 Soil Cylinder and Visual Scoring
10.5.3 Cylinder Containing Growth Medium
10.5.4 Soil-Filled Root Chambers
10.5.5 Buried Herbicide Method
10.5.6 Agar Gel Method
10.5.7 Grow Screen-Agar
10.5.8 NIR Image-Based Technique
10.5.9 RGB Image-Based Technique
10.5.10 Blotting Paper Method
10.5.11 Backhoe-Assisted Monolith Method
10.5.12 Rhizoslides: Paper-Based Method
10.5.13 Field Mini-Rhizotron Method
10.5.14 15N Tracer Method
10.5.15 X-Ray CT Method
10.5.16 RhizoTubes
10.5.17 MISIRoot: Minimally Invasive, in Situ Imaging System for Plant Root Phenotyping
10.5.18 ChronoRoot
10.6 Way Forward
References
Chapter 11: Root System Architecture and Phenotyping for Improved Resource Use Efficiency in Crops
11.1 Introduction
11.2 Components of Root Structure Architecture (RSA)
11.2.1 Root Morphological Phenes
11.2.2 Root Anatomical Phenes
11.3 Rhizospheric Components Defining Root Traits
11.4 Genetics of Root Phenes
11.5 High-Thoroughput Techniques for Root Phenotyping
11.5.1 Trenching
11.5.2 Shovelomics
11.5.3 Core Cutting
11.5.4 Rhizotron
11.6 Sensing Technologies in High-Throughput Root Phenotyping
11.6.1 Surface Scanning Systems: Optical and Spectra Imaging
11.6.2 Sub-surface Scanning Systems: X-Ray, MRI, Microwave, and GPR
11.7 Root Modeling
11.8 Future Prospects
References
Chapter 12: Harnessing Root Associated Traits and Rhizosphere Efficiency for Crop Improvement
12.1 Introduction
12.2 Root Exudation
12.3 Root Architecture
12.4 Rhizosphere Microbiome
12.5 Mechanisms of Adaptation for Root Traits
12.5.1 Mechanism of Exudation
12.5.2 Mechanisms of Root Architecture Modification
12.5.3 Mechanism Adopted by Microbiome Community
12.6 State-of-the Art Analytical Tools Available for Assessment of Root Traits
12.6.1 Root Exudate Analysis
12.6.2 Root Architecture Study
12.6.3 Rhizosphere Microbiome
12.7 Case Studies for Rhizosphere Management
12.8 Maximization of Rhizosphere Efficiency for Higher Crop Productivity
12.9 Challenges and Future Prospects
12.10 Conclusions
References
Chapter 13: High-Throughput Phenomics of Crops for Water and Nitrogen Stress
13.1 Introduction
13.2 HTP Sensors for Water and Nitrogen Stress/Use Efficiency
13.3 Phenotyping Based on Longitudinal Phenotypic Characteristics
13.3.1 3D Imaging (Three-Dimensional Imaging)
13.3.2 Near-Infrared Imaging
13.3.3 Digital Imaging
13.3.4 Reflectance Spectroscopy and Near-Infrared Spectroscopy
13.3.5 Modelling of Virtual Phenotypes
13.4 Recent Uses of HTP for Water and Nitrogen Stress Utilising the Sensors and Platforms
13.4.1 Spectral Signature and Stress Caused by a Water Deficiency
13.4.2 Multivariate Techniques for RWC Estimation
13.4.3 Differential Response of Rice Genotypes to Water Stress
13.4.4 Spectral Discrimination of Rice Genotypes
13.4.5 Field Phenotyping with Drone Platform
13.5 Challenges and Opportunities
13.6 Conclusion
References
Chapter 14: Metabolomics as a Selection Tool for Abiotic Stress Tolerance in Crops
14.1 Introduction
14.2 Approaches in Metabolomics
14.2.1 Targeted Metabolomics
14.2.2 Non-targeted Metabolomics
14.3 Metabolomic Approach Applications (Crop/Plant Research)
14.3.1 Phytochemical Diversity and Phenotyping
14.3.2 Functional Genomics
14.3.3 Environmental/Abiotic Stresses
14.3.4 Crop Improvement
14.4 Abiotic Stresses and Metabolomic Responses
14.4.1 Drought Stress
14.4.1.1 Osmolytes
14.4.1.2 Hormones
14.4.1.3 Gene-Metabolite Linkage
14.4.2 Heat Stress
14.4.2.1 Pollen Metabolites
14.4.2.2 Membrane Protection
14.4.2.3 Gene-Metabolite Linkage
14.4.3 Salinity Stress
14.4.3.1 Antioxidants
14.4.3.2 Osmoprotectants
14.4.3.3 Gene-Metabolite Linkage
14.5 Metabolomics-Assisted Crop Improvement
14.6 Conclusion
References
Chapter 15: Remote Sensing Algorithms and Their Applications in Plant Phenotyping
15.1 Introduction
15.2 Common Types of Remote-Sensing Tools Used in Plant Phenotyping
15.2.1 Visible Light Sensor
15.2.2 Infrared Sensor
15.2.3 Hyperspectral Sensor
15.3 Leaf Reflectance Relationship with Plant Phenotypes in Different Crops
15.3.1 Nitrogen and Pigments Associated Leaf Reflectance Spectra
15.3.2 Correlations of Mid-Day Leaf Water Potential with Spectral Indices
15.4 Advancement in the Analysis of Hyperspectral Reflectance Data
15.4.1 Leaf Reflectance for Early Season Disease Diagnosis
15.4.2 Crop Species Discrimination Using Hyperspectral Data
15.4.3 Leaf Reflectance and Soil Nutrients
15.5 Future Perspectives
References
Chapter 16: Endophyte-Mediated Crop Improvement: Manipulation of Abiotic Stress-Specific Traits
16.1 Introduction
16.2 Endophytes: An Ideal Tool for Manipulating Plant Traits
16.2.1 Defining Endophytes
16.2.2 Endophyte-Host Plant Association and Benefits
16.2.3 Host Fitness by Holobiont Regulation
16.2.4 Transmission of Endophytes
16.2.5 Endophytes as Potential Tools for Manipulating Stress Tolerance Traits
16.3 Endophytes Improve Stress Tolerance Traits in Crop Plants
16.3.1 Activation of Drought Traits
16.3.2 Activation of Salt Stress Tolerance Traits
16.3.3 Activation of Heat Stress Tolerance Traits
16.4 Endophyte-Mediated Manipulation of Traits in Plants: Options and Challenges
16.5 Conclusions
References
Chapter 17: Influence of High Temperature Stress on Grain Crops
17.1 Introduction
17.2 Sensitive Stages to HT Stress in Grain Crops
17.2.1 Impact of HT Stress on Wheat
17.2.2 Impact of HT Stress on Sorghum
17.2.3 Impact of HT Stress on Pearl Millet
17.2.4 Impact of HT Stress in Finger Millet
17.2.5 Impact of HT Stress on Soybean
17.2.6 Impact of HT Stress on Peanut/Groundnut
17.3 Conclusions and Future Prospects
References
Chapter 18: Morpho-physiological Basis of Finger Millet to Withstand Climatic Extremes: A Special Reference to Drought
18.1 Introduction
18.2 Physiological Basis of Drought Stress Adaptation
18.2.1 Morpho-physiological Traits of Drought Escape
18.2.1.1 Seed Germination
18.2.1.2 Tillering
18.2.1.3 Root Traits
18.2.1.4 Flowering
18.2.2 Morpho-physiological Traits of Drought Avoidance
18.2.2.1 Root Traits
18.2.2.2 Leaf Characters
18.2.3 Morpho-physiological Traits of Drought Tolerance
18.2.3.1 Water Relations
18.2.3.2 Photosynthesis Pigments and Gas Exchange Traits
18.2.3.3 Osmolyte Accumulation and Antioxidant Enzymes
18.2.3.4 Partitioning of Photo-assimilates to the Grain
18.3 Approaches for Improving Yield Under Stress Conditions
18.4 Conclusions and Future Prospects
References
Chapter 19: Comprehending the Physiological Efficiency of Millets Under Abiotic Stress
19.1 Introduction
19.2 Understanding the Physiology of Millets
19.3 Millets as Model Crops for Stress Tolerance, their Traits Contributing for Climate Resilience
19.4 Photosynthetic Variation and Leaf Anatomy of Minor Millets
19.5 Adaptation Mechanisms Underlying Climate Resilience of Millets
19.5.1 Escape Mechanism
19.5.2 Avoidance by Way of Phenotypic Adjustments
19.5.3 Tolerance
19.5.4 Stress Recovery
19.6 Millet Germplasm Resources Available for Abiotic Stress Tolerance Research
19.7 Conclusion
References
Chapter 20: Role of Next Generation Sequencing in Trait Identification, Genetic Mapping, and Crop Improvement
20.1 Introduction
20.2 Principle of Genetic Mapping
20.2.1 Mapping Then and Now
20.3 Application of NGS in Plant Research
20.4 Case Studies
20.4.1 Rice
20.4.1.1 WGS, RNA-Seq, Rad-Seq, Etc.
20.5 Tools for Mapping
20.5.1 SHOREmap
20.5.2 NGM
20.5.3 MutMap
20.5.4 Easymap
20.5.5 SNPTrack
20.5.6 SIMPLE
20.5.7 MMAPPR
20.6 Future Prospects
References
Chapter 21: Application of Artificial Intelligence and Machine Learning in Agriculture
21.1 Introduction
21.2 Artificial Intelligence, Machine Learning, and Deep Learning
21.3 Major Applications of AI and ML Techniques in Agriculture
21.3.1 Soil and Irrigation Management
21.3.1.1 Soil Management
21.3.1.2 Irrigation Management
21.3.2 Crop Health Management
21.3.2.1 Disease Identification
21.3.2.2 Pest Identification
21.3.3 Plant Phenotyping
21.3.4 Recommender Systems
21.3.5 Semantic Web, Knowledge Base, and Natural Language Processing
21.3.6 GIS and Remote Sensing Coupled with AI
21.4 Framework for Phenology Study Using Artificial Intelligence
21.4.1 Data Layer
21.4.2 Processing Layer
21.4.3 Application Layer
21.5 Conclusion
References