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List of Contributors xv 1 Plant Tolerance to Environmental Stress: Translating Research from Lab to Land 1 P. Suprasanna and S. B. Ghag 1.1 Introduction 1 1.2 Drought Tolerance 3 1.3 Cold Tolerance 10 1.4 Salinity Tolerance 12 1.5 Need for More Translational Research 16 1.6 Conclusion 17 References 17 2 Morphological and Anatomical Modifications of Plants for Environmental Stresses 29 Chanda Bano, Nimisha Amist, and N. B. Singh 2.1 Introduction 29 2.2 Drought-induced Adaptations 32 2.3 Cold-induced Adaptations 33 2.4 High Temperature-induced Adaptations 34 2.5 UV-B-induced Morphogenic Responses 35 2.6 Heavy Metal-induced Adaptations 35 2.7 Roles of Auxin, Ethylene, and ROS 36 2.8 Conclusion 37 References 38 3 Stomatal Regulation as a Drought-tolerance Mechanism 45 Shokoofeh Hajihashemi 3.1 Introduction 45 3.2 Stomatal Morphology 46 3.3 Stomatal Movement Mechanism 47 3.4 Drought Stress Sensing 48 3.5 Drought Stress Signaling Pathways 48 3.5.1 Hydraulic Signaling 49 3.5.2 Chemical Signaling 49 3.5.2.1 Plant Hormones 49 3.5.3 Nonhormonal Molecules 52 3.5.3.1 Role of CO2 Molecule in Response to Drought Stress 52 3.5.3.2 Role of Ca2+ Molecules in Response to Drought Stress 53 3.5.3.3 Protein Kinase Involved in Osmotic Stress Signaling Pathway 53 3.5.3.4 Phospholipid Role in Signal Transduction in Response to Drought Stress 53 3.6 Mechanisms of Plant Response to Stress 54 3.7 Stomatal Density Variation in Response to Stress 56 3.8 Conclusion 56 References 57 4 Antioxidative Machinery for Redox Homeostasis During Abiotic Stress 65 Nimisha Amist, Chanda Bano, and N. B. Singh 4.1 Introduction 65 4.2 Reactive Oxygen Species 66 4.2.1 Types of Reactive Oxygen Species 67 4.2.1.1 Superoxide Radical (O2 ) 67 4.2.1.2 Singlet Oxygen (1O2) 68 4.2.1.3 Hydrogen Peroxide (H2O2) 69 4.2.1.4 Hydroxyl Radicals (OH ) 69 4.2.2 Sites of ROS Generation 69 4.2.2.1 Chloroplasts 70 4.2.2.2 Peroxisomes 70 4.2.2.3 Mitochondria 70 4.2.3 ROS and Oxidative Damage to Biomolecules 71 4.2.4 Role of ROS as Messengers 73 4.3 Antioxidative Defense System in Plants 74 4.3.1 Nonenzymatic Components of the Antioxidative Defense System 74 4.3.1.1 Ascorbate 74 4.3.1.2 Glutathione 75 4.3.1.3 Tocopherols 75 4.3.1.4 Carotenoids 76 4.3.1.5 Phenolics 76 4.3.2 Enzymatic Components 76 4.3.2.1 Superoxide Dismutases 77 4.3.2.2 Catalases 77 4.3.2.3 Peroxidases 77 4.3.2.4 Enzymes of the Ascorbate-Glutathione Cycle 78 4.3.2.5 Monodehydroascorbate Reductase 79 4.3.2.6 Dehydroascorbate Reductase 79 4.3.2.7 Glutathione Reductase 79 4.4 Redox Homeostasis in Plants 80 4.5 Conclusion 81 References 81 5 Osmolytes and their Role in Abiotic Stress Tolerance in Plants 91 Abhimanyu Jogawat 5.1 Introduction 91 5.2 Osmolyte Accumulation is a Universally Conserved Quick Response During Abiotic Stress 92 5.3 Osmolytes Minimize Toxic Effects of Abiotic Stresses in Plants 93 5.4 Stress Signaling Pathways Regulate Osmolyte Accumulation Under Abiotic Stress Conditions 94 5.5 Metabolic Pathway Engineering of Osmolyte Biosynthesis Can Generate Improved Abiotic Stress Tolerance in Transgenic Crop Plants 95 5.6 Conclusion and Future Perspectives 97 Acknowledgements 97 References 97 6 Elicitor-mediated Amelioration of Abiotic Stress in Plants 105 Nilanjan Chakraborty, Anik Sarkar, and Krishnendu Acharya 6.1 Introduction 105 6.2 Plant Hormones and Other Elicitor-mediated Abiotic Stress Tolerance in Plants 106 6.3 PGPR-mediated Abiotic Stress Tolerance in Plants 109 6.4 Signaling Role of Nitric Oxide in Abiotic Stresses 109 6.5 Future Goals 114 6.6 Conclusion 114 References 115 7 Role of Selenium in Plants Against Abiotic Stresses: Phenological and Molecular Aspects 123 Aditya Banerjee and Aryadeep Roychoudhury 7.1 Introduction 123 7.2 Se Bioaccumulation and Metabolism in Plants 124 7.3 Physiological Roles of Se 125 7.3.1 Seas Plant Growth Promoters 125 7.3.2 The Antioxidant Properties of Se 125 7.4 Se Ameliorating Abiotic Stresses in Plants 126 7.4.1 Se and Salt Stress 126 7.4.2 Se and Drought Stress 127 7.4.3 Se Counteracting Low-temperature Stress 128 7.4.4 Se Ameliorating the Effects of UV-B Irradiation 128 7.4.5 Se and Heavy Metal Stress 129 7.5 Conclusion 129 7.6 Future Perspectives 130 References 130 8 Polyamines Ameliorate Oxidative Stress by Regulating Antioxidant Systems and Interacting with Plant Growth Regulators 135 Prabal Das, Aditya Banerjee, and Aryadeep Roychoudhury 8.1 Introduction 135 8.2 PAs as Cellular Antioxidants 136 8.2.1 PAs Scavenge Reactive Oxygen Species 136 8.2.2 The Co-operative Biosynthesis of PAs and Proline 137 8.3 The Relationship Between PAs and Growth Regulators 137 8.3.1 Brassinosteroids and PAs 137 8.3.2 Ethylene and PAs 137 8.3.3 Salicylic Acid and PAs 138 8.3.4 Abscisic Acid and PAs 138 8.4 Conclusion and Future Perspectives 139 Acknowledgments 140 References 140 9 Abscisic Acid in Abiotic Stress-responsive Gene Expression 145 Liliane Souza Conceicao Tavares, Savio Pinho dos Reis, Deyvid Novaes Marques, Eraldo Jose Madureira Tavares, Solange da Cunha Ferreira, Francinilson Meireles Coelho, and Claudia Regina Batista de Souza 9.1 Introduction 145 9.2 Deep Evolutionary Roots 146 9.3 ABA Chemical Structure, Biosynthesis, and Metabolism 151 9.4 ABA Perception and Signaling 153 9.5 ABA Regulation of Gene Expression 154 9.5.1 Cis-regulatory Elements 155 9.5.2 Transcription Factors Involved in the ABA-Mediated Abiotic Stress Response 156 9.5.2.1 bZIP Family 157 9.5.2.2 MYC and MYB 157 9.5.2.3 NAC Family 159 9.5.2.4 AP2/ERF Family 160 9.5.2.5 Zinc Finger Family 162 9.6 Post-transcriptional and Post-translational Control in Regulating ABA Response 164 9.7 Epigenetic Regulation of ABA Response 167 9.8 Conclusion 168 References 169 10 Abiotic StressManagement in Plants: Role of Ethylene 185 Anket Sharma, Vinod Kumar, Gagan Preet Singh Sidhu, Rakesh Kumar, Sukhmeen Kaur Kohli, Poonam Yadav, Dhriti Kapoor, Aditi Shreeya Bali, Babar Shahzad, Kanika Khanna, Sandeep Kumar, Ashwani Kumar Thukral, and Renu Bhardwaj 10.1 Introduction 185 10.2 Ethylene: Abundance, Biosynthesis, Signaling, and Functions 186 10.3 Abiotic Stress and Ethylene Biosynthesis 187 10.4 Role of Ethylene in Photosynthesis Under Abiotic Stress 188 10.5 Role of Ethylene on ROS and Antioxidative System Under Abiotic Stress 194 10.6 Conclusion 196 References 196 11 Crosstalk Among Phytohormone Signaling Pathways During Abiotic Stress 209 Abhimanyu Jogawat 11.1 Introduction 209 11.2 Phytohormone Crosstalk Phenomenon and its Necessity 210 11.3 Various Phytohormonal Crosstalk Under Abiotic Stresses for Improving Stress Tolerance 210 11.3.1 Crosstalk Between ABA and GA 210 11.3.2 Crosstalk Between GA and ET 211 11.3.3 Crosstalk Between ABA and ET 211 11.3.4 Crosstalk Between ABA and Auxins 212 11.3.5 Crosstalk Between ET and Auxins 213 11.3.6 Crosstalk Between ABA and CTs 213 11.4 Conclusion and Future Directions 213 Acknowledgements 215 References 215 12 PlantMolecular Chaperones: Structural Organization and their Roles in Abiotic Stress Tolerance 221 Roshan Kumar Singh, Varsha Gupta, and Manoj Prasad 12.1 Introduction 221 12.2 Classification of Plant HSPs 223 12.2.1 Structure and Functions of sHSP Family 223 12.2.2 Structure and Functions of HSP60 Family 224 12.2.3 Structure and Functions of the HSP70 Family 225 12.2.3.1 DnaJ/HSP40 227 12.2.4 Structure and Functions of HSP90 Family 228 12.2.5 Structure and Functions of HSP100 Family 229 12.3 Regulation of HSP Expression in Plants 230 12.4 Crosstalk Between HSP Networks to Provide Tolerance Against Abiotic Stress 231 12.5 Genetic Engineering of HSPs for Abiotic Stress Tolerance in Plants 232 12.6 Conclusion 234 Acknowledgements 234 References 234 13 Chloride (Cl ) Uptake, Transport, and Regulation in Plant Salt Tolerance 241 DB Shelke, GC Nikalje, TD Nikam, P Maheshwari, DL Punita, KRSS Rao, PB Kavi Kishor, and P. Suprasanna 13.1 Introduction 241 13.2 Sources of Cl Ion Contamination 242 13.3 Role of Cl in Plant Growth and Development 243 13.4 Cl Toxicity 244 13.5 Interaction of Soil Cl with Plant Tissues 245 13.5.1 Cl Influx from Soil to Root 245 13.5.2 Mechanism of Cl Efflux at the Membrane Level 245 13.5.3 Differential Accumulation of Cl in Plants and Compartmentalization 246 13.6 Electrophysiological Study of Cl Anion Channels in Plants 247 13.7 Channels and Transporters Participating in Cl Homeostasis 248 13.7.1 Slow Anion Channel and Associated Homologs 249 13.7.2 QUAC1 and Aluminum-activated Malate Transporters 251 13.7.3 Plant Chloride Channel Family Members 253 13.7.4 Phylogenetic Tree and Tissue Localization of CLC Family Members 255 13.7.5 Cation, Chloride Co-transporters 257 13.7.6 ATP-binding Cassette Transporters and Chloride Conductance Regulatory Protein 258 13.7.7 Nitrate Transporter1/Peptide Transporter Proteins 259 13.7.8 Chloride Channel-mediated Anion Transport 259 13.7.9 Possible Mechanisms of Cl Influx, Efflux, Reduced Net Xylem Loading, and its Compartmentalization 260 13.8 Conclusion and Future Perspectives 260 References 261 14 The Root Endomutualist Piriformospora indica: A Promising Bio-tool for Improving Crops under Salinity Stress 269 Abhimanyu Jogawat, Deepa Bisht, Nidhi Verma, Meenakshi Dua, and Atul Kumar Johri 14.1 Introduction 269 14.2 P. indica: An Extraordinary Tool for Salinity Stress Tolerance Improvement 269 14.3 Utilization of P. indica for Improving and Understanding the Salinity Stress Tolerance of Host Plants 270 14.4 P. indica-induced Biomodulation in Host Plant under Salinity Stress 270 14.5 Activity of Antioxidant Enzymes and ROS in Host Plant During Interaction with P. indica 272 14.6 Role of Calcium Signaling and MAP Kinase Signaling Combating Salt Stress 272 14.7 Effect of P. indica on Osmolyte Synthesis and Accumulation 273 14.8 Salinity Stress Tolerance Mechanism in Axenically Cultivated and Root Colonized P. indica 274 14.9 Conclusion 277 Acknowledgments 278 Conflict of Interest 278 References 278 15 Root Endosymbiont-mediated Priming of Host Plants for Abiotic Stress Tolerance 283 Abhimanyu Jogawat, Deepa Bisht, and Atul Kumar Johri 15.1 Introduction 283 15.2 Bacterial Symbionts-mediated Abiotic Stress Tolerance Priming of Host Plants 284 15.3 AM Fungi-mediated Alleviation of Abiotic Stress Tolerance of Vascular Plants 286 15.4 Other Beneficial Fungi and their Importance in Abiotic Stress Tolerance Priming of Plants 287 15.4.1 Piriformospora indica: A Model System for Bio-priming of Host Plants Against Abiotic Stresses 288 15.4.2 Fungal Endophytes, AM-like Fungi, and Other DSE-mediated Bio-priming ofHost Plants for Abiotic Stress Tolerance 289 15.5 Implication of Transgenes from Symbiotic Microorganisms in the Era of Genetic Engineering and Omics 289 15.6 Conclusion and Future Perspectives 290 Acknowledgements 291 References 291 16 Insight into the Molecular Interaction Between Leguminous Plants and Rhizobia Under Abiotic Stress 301 Sumanti Gupta and Sampa Das 16.1 Introduction 301 16.1.1 Why is Legume-Rhizobium Interaction Under the Scientific Scanner? 301 16.2 Legume-Rhizobium Interaction Chemistry: A Brief Overview 302 16.2.1 Nodule Structure and Formation:The Sequential Events 302 16.2.2 Nod Factor Signaling: From Perception to Nodule Inception 304 16.2.3 Reactive Oxygen Species:The Crucial Role of the Mobile Signal in Nodulation 305 16.2.4 Phytohormones: Key Players on All Occasions 306 16.2.5 Autoregulation of Nodulation: The Self Control fromWithin 306 16.3 Role of Abiotic Stress Factors in Influencing Symbiotic Relations of Legumes 307 16.3.1 How Do Abiotic Stress Factors Alter Rhizobial Behavior During Symbiotic Association? 307 16.3.2 Abiotic Agents Modulate Symbiotic Signals of Host Legumes 308 16.3.3 Abiotic Stress Agents as Regulators of Defense Signals of Symbiotic Hosts During Interaction with Other Pathogens 309 16.4 Conclusion: The Lessons Unlearnt 309 References 310 17 Effect of Nanoparticles on Oxidative Damage and Antioxidant Defense Systemin Plants 315 Savita Sharma, Vivek K. Singh, Anil Kumar, and Sharada Mallubhotla 17.1 Introduction 315 17.2 Engineered Nanoparticles in the Environment 317 17.3 Nanoparticle Transformations 318 17.4 Plant Response to Nanoparticle Stress 320 17.5 Generation of Reactive Oxygen Species (ROS) 323 17.6 Nanoparticle Induced Oxidative Stress 324 17.7 Antioxidant Defense System in Plants 326 17.8 Conclusion 327 References 328 18 Marker-assisted Selection for Abiotic Stress Tolerance in Crop Plants 335 Saikat Gantait, Sutanu Sarkar, and Sandeep Kumar Verma 18.1 Introduction 335 18.2 Reaction of Plants to Abiotic Stress 336 18.3 Basic Concept of Abiotic Stress Tolerance in Plants 337 18.4 Genetics of Abiotic Stress Tolerance 338 18.5 Fundamentals of Molecular Markers and Marker-assisted Selection 339 18.5.1 Molecular Markers 339 18.5.2 Marker-assisted Selection 341 18.6 Marker-assisted Selection for Abiotic Stress Tolerance in Crop Plants 341 18.6.1 Marker-assisted Selection for Heat Tolerance 342 18.6.1.1 Wheat (Triticum aestivum) 342 18.6.1.2 Cowpea (Vigna unguiculata) 343 18.6.1.3 Oilseed Brassica 343 18.6.1.4 Grape (Vitis species) 343 18.7 Marker-assisted Selection for Drought Tolerance 344 18.7.1.1 Maize (Zea mays) 344 18.7.1.2 Chickpea (Cicer arietinum) 345 18.7.1.3 Oilseed Brassica 346 18.7.1.4 Coriander (Coriandrum sativum) 346 18.7.2 Marker-assisted Selection for Salinity Tolerance 347 18.7.2.1 Rice (Oryza sativa) 347 18.7.2.2 Mungbean (Vigna radiata) 348 18.7.2.3 Oilseed Brassica 349 18.7.2.4 Tomato (Solanum lycopersicum) 350 18.7.3 Marker-assisted Selection for Low Temperature Tolerance 351 18.7.3.1 Barley (Hordeum vulgare) 351 18.7.3.2 Pea (Pisum sativum) 353 18.7.3.3 Oilseed Brassica 354 18.7.3.4 Potato (Solanum tuberosum) 355 18.8 Outlook 356 References 356 19 Transgenes: The Key to Understanding Abiotic Stress Tolerance in Rice 369 Supratim Basu, Lymperopoulos Panagiotis, Joseph Msanne, and Roel Rabara 19.1 Introduction 369 19.2 Drought Effects in Rice Leaves 370 19.3 Molecular Analysis of Drought Stress Response 370 19.4 Omics Approach to Analysis of Drought Response 371 19.4.1 Transcriptomics 371 19.4.2 Metabolomics 372 19.4.3 Epigenomics 373 19.5 Plant Breeding Techniques to Improve Rice Tolerance 374 19.6 Marker-assisted Selection 374 19.7 Transgenic Approach: Present Status and Future Prospects 375 19.8 Looking into the Future for Developing Drought-tolerant Transgenic Rice Plants 376 19.9 Salinity Stress in Rice 376 19.10 Candidate Genes for Salt Tolerance in Rice 378 19.11 QTL Associated with Rice Tolerance to Salinity Stress 379 19.12 The Saltol QTL 380 19.13 Conclusion 381 References 381 20 Impact of Next-generation Sequencing in Elucidating the Role of microRNA Related to Multiple Abiotic Stresses 389 Kavita Goswami, Anita Tripathi, Budhayash Gautam, and Neeti Sanan-Mishra 20.1 Introduction 389 20.2 NGS Platforms and their Applications 390 20.2.1 NGS Platforms 390 20.2.1.1 Roche 454 390 20.2.1.2 ABI SoLid 391 20.2.1.3 ION Torrent 392 20.2.1.4 Illumina 393 20.2.2 Applications of NGS 394 20.2.2.1 Genomics 395 20.2.2.2 Metagenomics 396 20.2.2.3 Epigenomics 396 20.2.2.4 Transcriptomics 397 20.3 Understanding the Small RNA Family 398 20.3.1 Small Interfering RNAs 398 20.3.2 microRNA 402 20.4 Criteria and Tools for Computational Classification of Small RNAs 402 20.4.1 Pre-processing (Quality Filtering and Sequence Alignment) 403 20.4.2 Identification and Prediction of miRNAs and siRNAs 403 20.5 Role of NGS in Identification of Stress-regulated miRNA and their Targets 407 20.5.1 miR156 408 20.5.2 miR159 408 20.5.3 miR160 409 20.5.4 miR164 409 20.5.5 miR166 409 20.5.6 miR167 409 20.5.7 miR168 410 20.5.8 miR169 410 20.5.9 miR172 410 20.5.10 miR393 410 20.5.11 miR396 411 20.5.12 miR398 411 20.6 Conclusion 411 Acknowledgments 412 References 412 21 Understanding the Interaction of Molecular Factors During the Crosstalk Between Drought and Biotic Stresses in Plants 427 Arnab Purohit, Shreeparna Ganguly, Rituparna Kundu Chaudhuri, and Dipankar Chakraborti 21.1 Introduction 427 21.2 Combined Stress Responses in Plants 428 21.3 Combined Drought-Biotic Stresses in Plants 428 21.3.1 Plant Responses Against Biotic Stress during Drought Stress 429 21.3.2 Plant Responses Against Drought Stress during Biotic Stress 430 21.4 Varietal Failure Against Multiple Stresses 430 21.5 Transcriptome Studies of Multiple Stress Responses 431 21.6 Signaling Pathways Induced by Drought-Biotic Stress Responses 432 21.6.1 Reactive Oxygen Species 432 21.6.2 Mitogen-activated Protein Kinase Cascades 433 21.6.3 Transcription Factors 434 21.6.4 Heat Shock Proteins and Heat Shock Factors 436 21.6.5 Role of ABA Signaling during Crosstalk 437 21.7 Conclusion 438 Acknowledgments 439 Conflict of Interest 439 References 439 Index 447

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