Improving Crop Productivity in Sustainable Agriculture Book

Foreword XIX

Preface XXI

List of Contributors XXV

PART I Climate Change and Abiotic Stress Factors 1

1 Climate Change and Food Security 3
R.B. Singh

1.1 Background and Introduction 3

1.2 State of Food Security 6

1.3 Climate Change Impact and Vulnerability 9

1.4 Natural Resources Management 13

1.5 Adaptation and Mitigation 17

1.6 Climate Resilient Agriculture – The Way Forward 18

References 22

2 Improving Crop Productivity under Changing Environment 23
Navjot K. Dhillon, Satbir S. Gosal, and Manjit S. Kang

2.1 Introduction 23

2.1.1 Global Environmental Change Alters Crop Targets 28

2.1.2 Crop Productivity 28

2.1.3 Climatic Factors Affecting Crop Production 29

2.1.3.1 Precipitation 29

2.1.3.2 Temperature 29

2.1.3.3 Atmospheric Humidity 30

2.1.3.4 Solar Radiation 30

2.1.3.5 Wind Velocity 30

2.1.4 Plant Genetic Engineering 31

2.1.4.1 Engineering for Herbicide Resistance 32

2.1.4.2 Engineering for Insect Resistance 32

2.1.4.3 Engineering for Disease Resistance 33

2.1.4.4 Engineering for Improving Nutritional Quality 36

2.1.4.5 Engineering for Male Sterility 36

2.1.4.6 Engineering for Molecular Farming/Pharming 37

2.1.4.7 Engineering for Improving Postharvest Traits 37

2.1.4.8 Engineering for Abiotic Stress Tolerance 38

2.1.5 Molecular Breeding 39

2.2 Conclusions 40

References 40

3 Genetic Engineering for Acid Soil Tolerance in Plants 49
Sagarika Mishra, Lingaraj Sahoo, and Sanjib K. Panda

3.1 Introduction 49

3.2 Phytotoxic Effect of Aluminum on Plant System 50

3.2.1 Al-Induced Morphophysiological Changes in Roots 50

3.2.2 Negative Influence of Al on Cytoskeletal Network of Plant Cells 51

3.2.3 Interaction of Al3þ Ions with Cell Wall and Plasma Membrane 52

3.2.4 Oxidative Stress Response upon Al Stress 52

3.3 Aluminum Tolerance Mechanisms in Plants 53

3.3.1 Preventing the Entry of Al into Plant Cell 53

3.3.2 Role of Organic Acids in External and Internal Detoxification of Al 54

3.4 Aluminum Signal Transduction in Plants 55

3.5 Genetic Approach for Development of Al-Tolerant Plants 56

3.6 Transcriptomics and Proteomics as Tools for Unraveling Al Responsive Genes 59

3.7 Future Perspectives 60

References 61

4 Evaluation of Tropospheric O3 Effects on Global Agriculture: A New Insight 69
Richa Rai, Abhijit Sarkar, S.B. Agrawal, and Madhoolika Agrawal

4.1 Introduction 69

4.2 Tropospheric O3 Formation and Its Recent Trend 71

4.2.1 Projected Trends of Ozone Concentrations 74

4.3 Mechanism of O3 Uptake 75

4.3.1 Mode of Action 76

4.3.2 O3 Sensing and Signal Transduction 76

4.3.3 ROS Detoxification Mechanisms: From Apoplast to Symplast 77

4.3.4 Physiological Responses 80

4.3.4.1 Photosynthesis 80

4.3.5 Cultivar Sensitivity in Relation to Growth and Yield 84

4.4 Looking Through the “-Omics” at Post-Genomics Era 87

4.4.1 Evolution of Multi-Parallel “-Omics” Approaches in Modern Biology 87

4.4.2 “-Omics” Response in Ozone-Affected Crop Plants: An In Vivo Assessment 87

4.4.2.1 Case Studies in Major Crop Plants 88

4.5 Different Approaches to Assess Impacts of Ozone on Agricultural Crops 92

4.6 Tropospheric O3 and Its Interaction with Other Components of Global Climate Change and Abiotic Stresses 94

4.6.1 Elevated CO2 and O3 Interaction 94

4.6.2 O3 and Drought Interaction 95

4.6.3 O3 and UV-B Interaction 95

4.7 Conclusions 96

References 97

PART II Methods to Improve Crop Productivity 107

5 Mitogen-Activated Protein Kinases in Abiotic Stress Tolerance in Crop Plants: “-Omics” Approaches 109
Monika Jaggi, Meetu Gupta, Narendra Tuteja, and Alok Krishna Sinha

5.1 Introduction 109

5.2 MAPK Pathway and Its Components 112

5.2.1 MAP3Ks 112

5.2.2 MAP2Ks 114

5.2.3 MAPKs 114

5.3 Plant MAPK Signaling Cascade in Abiotic Stress 115

5.3.1 MAPK Cascades under Salt Stress 117

5.3.2 Drought Stress-Induced MAPKs 117

5.3.3 Temperature Stress Response and MAPK Cascades 119

5.3.4 Activation of MAPKs by Oxidative Stress 120

5.3.5 Ozone-Induced MAPKs 121

5.3.6 Wounding-Induced MAPKs 121

5.3.7 MAPKs in Heavy Metal Signaling 122

5.4 Crosstalk between Plant MAP Kinases in Abiotic Stress Signaling 122

5.5 “-Omics” Analyses of Plants under Abiotic Stress 123

5.6 Conclusions and Future Perspectives 127

Acknowledgments 128

References 128

6 Plant Growth Promoting Rhizobacteria-Mediated Amelioration of Abiotic and Biotic Stresses for Increasing Crop Productivity 133
Vasvi Chaudhry, Suchi Srivastava, Puneet Singh Chauhan, Poonam C. Singh, Aradhana Mishra, and Chandra Shekhar Nautiyal

6.1 Introduction 133

6.2 Factors Affecting Plant Growth 134

6.2.1 Biotic Stress 135

6.2.2 Abiotic Stress 135

6.3 Plant-Mediated Strategies to Elicit Stresses 136

6.3.1 Osmoadaptation 137

6.3.2 Antioxidative Enzyme Production 137

6.3.3 Effect of Stress on Plant Nutrient Uptake 137

6.4 Plant Growth Promoting Rhizobacteria-Mediated Beneficiaries to the Environment 138

6.4.1 PGPR as Abiotic Stress Ameliorating Agent 138

6.4.2 PGPR Action against Multiple Pathogens 139

6.4.3 Determinants of PGPR Colonization in Stressed Environment 140

6.4.4 PGPR-Mediated Induction of Defense Mechanism 143

6.4.5 Modulation of Plant Genes through Bacterial Intervention 144

6.5 PGPR-Based Practical Approaches to Stress Tolerance 145

6.5.1 Development and Commercialization of PGPRs: Approaches and Limitations 145

6.5.2 Implications of Bacterial Genes for Transgenic Development 146

6.6 Conclusions 147

References 147

7 Are Viruses Always Villains? The Roles Plant Viruses May Play in Improving Plant Responses to Stress 155
Stephen J. Wylie and Michael G.K. Jones

7.1 Introduction 155

7.2 Viruses Are Abundant and Diverse 156

7.3 Wild Versus Domesticated 156

7.4 New Encounters 157

7.5 Roles for Viruses in Adaptation and Evolution 158

7.6 Conclusions 160

References 160

8 Risk Assessment of Abiotic Stress Tolerant GM Crops 163
Paul Howles and Joe Smith

8.1 Introduction 163

8.2 Abiotic Stress 164

8.3 Abiotic Stress Traits are Mediated by Multiple Genes 165

8.4 Pleiotropy and Abiotic Stress Responses 167

8.5 General Concepts of Risk Analysis 168

8.6 Risk Assessment and Abiotic Stress Tolerance 169

8.6.1 Choice of Comparator 171

8.6.2 Production of an Allergenic or Toxic Substance 171

8.6.3 Invasiveness and Weediness 172

8.6.4 Pleiotropic Effects 173

8.6.5 Gene Transfer to Another Organism 175

8.7 Abiotic Stress Tolerance Engineered by Traditional Breeding and Mutagenesis 176

8.8 Conclusions 177

Acknowledgments 177

References 177

9 Biofertilizers: Potential for Crop Improvement under Stressed Conditions 183
Alok Adholeya and Manab Das

9.1 Introduction 183

9.2 What Is Biofertilizer? 184

9.3 How It Differs from Chemical and Organic Fertilizers 184

9.4 Type of Biofertilizers 184

9.5 Description and Function of Important Microorganisms Used as Biofertilizers 187

9.5.1 Rhizobia 187

9.5.2 Azotobacter and Azospirillum 187

9.5.3 Blue-Green Algae or Cyanobacteria 188

9.6 Phosphate Solubilizing Bacteria 189

9.7 Plant Growth Promoting Rhizobacteria 189

9.8 Mycorrhiza 189

9.9 Inoculation of Biofertilizers 190

9.9.1 Carrier Materials for Biofertilizers 190

9.10 Potential Role of Various Biofertilizers in Crop Production and Improvement 192

9.10.1 Bacterial Biofertilizers 192

9.10.2 Fungal Biofertilizers 194

9.11 Conclusions 195

References 195

PART III Species-Specific Case Studies 201

Section IIIA Graminoids 201

10 Rice: Genetic Engineering Approaches for Abiotic Stress Tolerance – Retrospects and Prospects 203
Salvinder Singh, M.K. Modi, Sarvajeet Singh Gill, and Narendra Tuteja

10.1 Introduction 204

10.2 Single Action Genes 204

10.2.1 Osmoprotectants 204

10.2.2 Late Embryogenesis Abundant Proteins 207

10.2.3 Detoxifying Genes 208

10.2.4 Multifunctional Genes for Lipid Biosynthesis 210

10.2.5 Heat Shock Protein Genes 211

10.2.6 Regulatory Genes 212

10.2.7 Transcription Factors 212

10.2.8 Other Transcription Factors 215

10.2.9 Signal Transduction Genes 216

10.2.10 Functional Proteins 217

10.2.11 ROS Scavenging System 217

10.2.12 Sodium Transporters 218

10.3 Choice of Promoters 220

10.4 Physiological Evaluation of Stress Effect 221

10.5 Means of Stress Impositions, Growth Conditions, and Evaluations 222

10.6 Adequate Protocols to Apply Drought and Salinity Stress 223

10.7 Conclusions 224

References 225

11 Rice: Genetic Engineering Approaches to Enhance Grain Iron Content 237
Salvinder Singh, D. Sudhakar, and M.K. Modi

11.1 Introduction 237

11.2 Micronutrient Malnutrition 237

11.2.1 Approaches to Decrease Micronutrient Deficiencies and/or Malnutrition 238

11.2.2 Importance of Iron in Human Physiology 239

11.2.3 Source of Iron for Human Nutrition 239

11.2.4 Approaches to Decrease Micronutrient Deficiencies 240

11.2.5 Pharmaceutical Preparation 241

11.2.6 Disease Reduction 241

11.3 Food Fortification 241

11.4 Biofortification 242

11.4.1 Biofortification through Classical Breeding Approach 243

11.4.2 Biofortification through Genetic Engineering Approach 244

11.4.3 Biofortification by Decreasing Antinutrient Contents 245

11.4.4 Biofortification by Increasing Iron Bioavailability Promoting Compounds 246

11.5 Iron Uptake and Transport in Plants 247

11.5.1 The Reduction Strategy 247

11.5.2 The Chelation Strategy 248

11.5.3 Regulation of the Reduction Strategy 248

11.5.4 Iron Signaling and Sensing in Plants 249

11.5.5 Iron Transport within the Plant 249

11.5.5.1 Intercellular Iron Transport 249

11.5.5.2 Subcellular Iron Transport 250

11.5.5.3 Vacuoles 251

11.5.5.4 Chloroplasts 251

11.5.5.5 Mitochondria 252

11.6 Conclusions 252

References 253

12 Pearl Millet: Genetic Improvement in Tolerance to Abiotic Stresses 261
O.P. Yadav, K.N. Rai, and S.K. Gupta

12.1 Introduction 262

12.2 Drought: Its Nature and Effects 264

12.2.1 Seedling Phase 264

12.2.2 Vegetative Phase 264

12.2.3 Reproductive Phase 265

12.3 Genetic Improvement in Drought Tolerance 265

12.3.1 Conventional Breeding 266

12.3.1.1 Selection Environment 266

12.3.1.2 Selection Criteria 268

12.3.1.3 Yield Improvement 270

12.3.2 Molecular Breeding 273

12.4 Heat Tolerance 274

12.4.1 Tolerance at Seedling Stage 274

12.4.2 Tolerance at Reproductive Stage 275

12.5 Salinity Tolerance 277

References 279

13 Bamboo: Application of Plant Tissue Culture Techniques for Genetic Improvement of Dendrocalamus strictus Nees 289
C.K. John and V.A. Parasharami

13.1 Introduction 289

13.2 Vegetative Propagation 290

13.3 Micropropagation 291

13.4 Genetic Improvement for Abiotic Stress Tolerance 291

13.5 Dendrocalamus strictus 292

13.6 Future Prospects 299

References 299

Section IIIB Leguminosae 303

14 Groundnut: Genetic Approaches to Enhance Adaptation of Groundnut (Arachis Hypogaea, L.) to Drought 305
R.C. Nageswara Rao, M.S. Sheshshayee, N. Nataraja Karaba, Rohini Sreevathsa, N. Rama, S. Kumaraswamy, T.G. Prasad, and M. Udayakumar

14.1 Introduction 306

14.1.1 Importance of Groundnut 306

14.1.2 Origin and Diversity 307

14.1.3 Area, Production, and Productivity 307

14.1.4 Major Abiotic Stresses 307

14.2 Response to Water Deficits at the Crop Level 309

14.2.1 Effects of Water Deficits on Yield 309

14.2.2 Effects of Multiple Water Deficits 309

14.2.3 Effects of Water Deficit at Different Stages of Crop Growth 311

14.2.3.1 Germination and Emergence 311

14.2.3.2 Vegetative Phase 312

14.2.3.3 Reproductive Phase 313

14.2.4 Effects of Water Deficits on Some Physiological Processes 313

14.2.4.1 Water Deficit and Temperature Interaction 314

14.2.4.2 Water Uptake and Plant–Water Relations 315

14.2.4.3 N Fixation 315

14.2.4.4 Photosynthesis and Transpiration 316

14.2.4.5 Partitioning of Dry Matter to Pods and Harvest Index 317

14.2.5 Effects of Water Deficit on Seed Quality 318

14.2.5.1 Protein 318

14.2.5.2 Oil Content and Quality 318

14.2.5.3 Aflatoxin 319

14.3 Some Physiological Mechanisms Contributing to Drought Tolerance in Groundnut 320

14.3.1 Water Extraction Efficiency 321

14.3.2 Transpiration Efficiency 321

14.3.3 Surrogate Measures of TE 322

14.3.4 Epicuticular Wax 324

14.3.5 Survival under and Recovery from Drought 324

14.3.6 Acquired Thermotolerance 325

14.4 Integration of Physiological Traits to Improve Drought Adaptation of Groundnut 326

14.5 Status of Genomic Resources in Groundnut 330

14.5.1 Marker Resources in Groundnut 330

14.5.2 Drought-Specific ESTs Libraries in Groundnut 331

14.6 Molecular Breeding and Genetic Linkage Maps in Groundnut 337

14.6.1 Genetic Linkage Maps for Groundnut 338

14.7 Transgenic Approach to Enhance Drought Tolerance 339

14.7.1 Transgenics: An Option to Pyramid Drought Adaptive Traits 340

14.8 Summary and Future Perspectives 343

14.8.1 Options and Approaches 344

14.8.2 Molecular Breeding a Potential Option for Genetic Improvement in Groundnut 344

14.8.3 Transgenics: A Potential Future Alternative Strategy 345

Acknowledgments 345

References 345

15 Chickpea: Crop Improvement under Changing Environment Conditions 361
B.K. Sarmah, S. Acharjee, and H.C. Sharma

15.1 Introduction 362

15.2 Abiotic Constraints to Chickpea Production 363

15.3 Modern Crop Breeding Approaches for Abiotic Stress Tolerance 364

15.3.1 Drought, Salinity, and Low Temperature 364

15.4 Genetic Engineering of Chickpea for Tolerance to Abiotic Stresses 365

15.4.1 Drought and Salinity 365

15.4.2 Elevated CO2 Concentrations 366

15.5 Biotic Constraints in Chickpea Production 366

15.5.1 Insect Pests 366

15.5.2 Diseases 368

15.5.3 Biological Nitrogen Fixation 369

15.6 Modern Molecular Breeding Approaches for Biotic Stress Tolerance 369

15.6.1 Pod Borers 369

15.6.2 Ascochyta and Fusarium 370

15.6.3 Wide Hybridization 371

15.7 Application of Gene Technology 372

15.7.1 Pod Borers 372

15.8 Conclusion 372

References 373

16 Grain Legumes: Biotechnological Interventions in Crop Improvement for Adverse Environments 381
Pooja Bhatnagar-Mathur, Paramita Palit, Ch Sridhar Kumar, D. Srinivas Reddy, and Kiran K. Sharma

16.1 Introduction 382

16.2 Grain Legumes: A Brief Introduction 382

16.3 Major Constraints for Grain Legume Production 383

16.3.1 Biotic Stresses 383

16.3.1.1 Fungal Diseases 384

16.3.1.2 Viral Diseases 385

16.3.1.3 Insect Pests 385

16.3.1.4 Parasitic Weeds 385

16.3.2 Abiotic Stresses: A Threat to Grain Legumes 386

16.3.2.1 Heat Stress 386

16.3.2.2 Salinity 386

16.4 Biotechnological Interventions in Grain Legume Improvement 387

16.4.1 Groundnut 387

16.4.1.1 Biotechnology for Tolerance to Abiotic Stresses 388

16.4.1.2 Biotechnology for Resistance to Biotic Stresses 389

16.4.2 Chickpea 391

16.4.2.1 Biotechnology for Tolerance to Abiotic Stresses 392

16.4.2.2 Biotechnology for Resistance to Biotic Stresses 394

16.4.3 Pigeonpea 395

16.4.3.1 Biotechnology for Tolerance to Abiotic Stresses 396

16.4.3.2 Biotechnology for Resistance to Biotic Stresses 397

16.4.4 Soybean 398

16.4.4.1 Biotechnology for Tolerance to Abiotic Stresses 398

16.4.4.2 Biotechnology for Resistance to Biotic Stresses 400

16.4.5 Cowpea 401

16.4.5.1 Biotechnology for Tolerance to Abiotic Stresses 402

16.4.5.2 Biotechnology for Resistance to Biotic Stresses 403

16.4.6 Common Beans 403

16.4.6.1 Biotechnology for Tolerance to Abiotic Stresses 403

16.4.6.2 Biotechnology for Resistance to Biotic Stresses 404

16.4.7 Lentils 405

16.4.7.1 Biotechnology for Tolerance to Abiotic Stresses 405

16.4.7.2 Biotechnology for Resistance to Biotic Stresses 406

16.5 Future Prospects 407

16.6 Integration of Technologies 407

16.7 Conclusion 408

References 409

17 Pulse Crops: Biotechnological Strategies to Enhance Abiotic Stress Tolerance 423
S. Ganeshan, P.M. Gaur, and R.N. Chibbar

17.1 Pulse Crops: Definition and Major and Minor Pulse Crops 423

17.2 Pulse Production: Global and Different Countries from FAOStat 424

17.3 Abiotic Stresses Affecting Pulse Crops 424

17.4 Mechanisms Underlying Stress Tolerance: A Generalized Picture 426

17.5 Strategies to Enhance Abiotic Stress Tolerance: Conventional 428

17.5.1 Breeding 428

17.5.2 Mining Germplasm Resources 430

17.5.3 Variation Creation: Traditional Mutagenesis and TILLING 430

17.6 Strategies to Enhance Abiotic Stress Tolerance: Biotechnology and Genomics 432

17.6.1 Genetic Mapping and QTL Analysis 432

17.6.2 Transcriptomic Resources 434

17.6.3 Transgenic Approaches 435

17.6.4 In Vitro Regeneration and Transformation 436

17.7 Concluding Remarks 438

References 438

Section IIIC Rosaceae 449

18 Improving Crop Productivity and Abiotic Stress Tolerance in Cultivated Fragaria Using Omics and Systems Biology Approach 451
Jens Rohloff, Pankaj Barah, and Atle M. Bones

18.1 Introduction 451

18.2 Abiotic Factors and Agronomic Aspects 453

18.2.1 Botany and Agricultural History 453

18.2.1.1 Botany and Distribution 453

18.2.1.2 Nutritionals and Phytochemicals 454

18.2.1.3 Economic Aspects of Production and Environment 455

18.2.2 Abiotic Factors in Strawberry Production 458

18.2.2.1 Light 458

18.2.2.2 Temperature 459

18.2.2.3 Water 459

18.2.2.4 Soil 460

18.2.2.5 Atmospheric Gases and Airborne Contamination 460

18.2.2.6 Abiotic Stress Alleviation through Agricultural Practice 461

18.2.3 Fragaria Breeding toward Abiotic Factors 461

18.2.3.1 Cultivation and Berry Production 461

18.2.3.2 Fresh Market Quality and Consumer Demand 462

18.2.3.3 Postharvest and Food Chain 462

18.2.3.4 Processing and Industry 462

18.2.3.5 Classical Breeding of Varieties and Hybrids 463

18.2.3.6 Marker-Assisted Breeding (MAB) 463

18.3 Genetically Modified (GM) Plants 466

18.4 Omics Approaches toward Abiotic Stress in Fragaria 467

18.4.1 Genomic Approaches toward Fragaria 467

18.4.1.1 Case I: Genomic Approaches toward Cold Acclimation/Freezing Tolerance in Fragaria 468

18.4.2 Proteomic Approaches toward Fragaria 469

18.4.2.1 Case II: Proteomic Approaches toward Cold Acclimation/Freezing Tolerance in Fragaria 469

18.4.3 Metabolomic Approaches toward Fragaria 470

18.4.3.1 Case III: Metabolomic Approaches toward Cold Acclimation/Freezing Tolerance in Fragaria 471

18.5 Systems Biology as Suitable Tool for Crop Improvement 473

18.5.1 Omics Data Integration for Improving Plant Productivity/Translational Research 474

18.5.2 Plant/Crops Systems Biology 476

18.5.3 Pathway Modeling and the Concept of “Virtual Plant” 477

18.5.4 Network-Based Approaches 477

18.5.4.1 Correlation Studies Using Multivariate Data 478

18.5.4.2 Protein–Protein Interaction (PPI) Networks 478

18.5.4.3 Gene Regulatory Networks 478

18.5.4.4 Coexpression Networks 479

18.6 Conclusions and Future Prospects 479

18.6.1 Technology-Driven Innovations for Fragaria Breeding and Development 480

18.6.2 Biology-Related Issues for Improvements in the Fragaria Genus 480

Acknowledgments 480

References 480

19 Rose: Improvement for Crop Productivity 485
Madhu Sharma, Kiran Kaul, Navtej Kaur, Markandey Singh, Devendra Dhayani, and Paramvir Singh Ahuja

19.1 Introduction 485

19.2 Abiotic Stress and Rose Yield 487

19.2.1 Drought Stress 487

19.2.1.1 Ethylene Biosynthesis 490

19.2.2 Salt Stress 491

19.2.3 Light Stress 493

19.2.4 Low-Temperature Stress 494

19.2.5 High-Temperature Stress 494

19.3 Abiotic Stress and Reactive Oxygen Species 497

19.4 Stress-Related Genes Associated with Abiotic Stress Tolerance in Rose and Attempts to Transgenic Development 497

19.5 Conclusions 499

Acknowledgments 500

References 500

Index 507