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Applications of Genome Engineering in Plants

1. Aufl.

von: Santosh Kumar Upadhyay
162,99 €
Verlag:	Wiley
Format:	PDF
Veröffentl.:	15.12.2023
ISBN/EAN:	9781394183890
Sprache:	englisch
Anzahl Seiten:	448

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Titelbeschreibung

Applications of Genome Engineering in Plants Understand the keys to creating the food of the future Genome engineering in plants is a field that has made enormous strides in recent years. In particular, the CRISPR-Cas system has been used in a number of crop species to make significant leaps forward in nutritional improvement, stress tolerance, crop yield, and more. As scientists work to meet global food needs and foster sustainable agriculture in a changing world, genome engineering promises only to become more important. Applications of Genome Engineering in Plants details the history of, and recent developments in, this essential area of biotechnology. It describes advances enabling nutritional improvement, nutraceuticals improvement, flavonoid enrichment, and many more crop enhancements, as well as subjects such as biosafety and regulatory mechanisms. The result is a thorough and essential overview for researchers and biotech professionals. Applications of Genome Engineering in Plants readers will also find: <ul><li>Chapters on trans-gene free editing or non-transgenic approaches to plant genomes</li> <li>Detailed discussion of topics including nanotechnology-facilitated genome editing, engineering for virus resistance in plants, and more</li> <li>Applications of genome editing in oil seed crops, vegetables, ornamental plants, and many others</li></ul> Applications of Genome Engineering in Plants is ideal for academics, scientists, and industry professionals working in biotechnology, agriculture, food science, and related subjects.

Inhaltsverzeichnis

List of Contributors xv Preface xix About the Editor xx 1 CRISPR/Cas-Mediated Genome Editing in Plants: A Historical Perspective 1 Anil Kumar, Shumayla, and Santosh Kumar Upadhyay 1.1 Introduction 1 1.2 Historical Background 2 1.3 Mechanism of CRISPR/Cas System 4 1.3.1 Acquisition of Spacers 4 1.3.2 Biogenesis 5 1.3.3 Interference with the Target 5 1.4 Breakthrough Studies in CRISPR/Cas System 5 1.5 CRISPR Types 6 1.6 Type of Cas Proteins 7 1.6.1 Cas 1 7 1.6.2 Cas 2 7 1.6.3 Cas 3 7 1.6.4 Cas 4 7 1.6.5 Cas 5 7 1.6.6 Cas 6 8 1.6.7 Cas 7 8 1.6.8 Cas 8 8 1.6.9 Cas 9 8 1.6.10 Cas 10 8 1.6.11 Cas 11 8 1.6.12 Cas 12 9 1.6.13 Cas 13 9 1.6.14 Cas 14 9 1.7 CRISPR/Cas Modification 9 1.7.1 Nickase 9 1.7.2 Dead Cas9 (dCas9) 10 1.7.3 Base Editors 10 1.7.4 Prime Editors 10 1.8 CRISPR/Cas as a Genome Editing Tool and Its Application 10 1.8.1 Gene Knockout 10 1.8.2 DNA Insertion 11 1.8.3 Base Editing 11 1.8.4 Gene Activation and/or Repression 12 1.8.5 Epigenetic Modifications 12 1.8.6 Localization 12 1.8.7 RNA Editing 13 1.9 Conclusion 13 References 13 2 CRISPR/Cas-Mediated Multiplex Genome Editing in Plants and Applications 20 R. Prajapati and K. Tyagi 2.1 Introduction 20 2.2 Construct Design for Multiplex CRISPR/Cas Genome Editing 22 2.3 Strategies for Processing Multiple-Guide RNAs 23 2.4 Delivery of CRISPR/Cas Construct into Plant Cells 24 2.4.1 Agrobacterium-Mediated Delivery 24 2.4.2 Virus-Mediated Delivery 24 2.4.3 Particle Bombardment-Based Delivery 25 2.5 Broader Implications of CRISPR/Cas Multiplex Gene Editing 25 2.5.1 Simultaneous Knockout of Multiple Genes 25 2.5.2 Targeted Chromosomal Deletions 26 2.5.3 Transcriptional Activation or Repression of Genes 26 2.5.4 Base Editing 26 2.6 Application of CRISPR/Cas Multiplex Gene Editing in Generating Disease Resistant Plants 27 2.6.1 Disease Resistance Against Viruses 27 2.6.2 Disease Resistance Against Fungi 28 2.6.3 Disease Resistance Against Bacteria 29 2.7 Application of CRISPR/Cas Multiplex Gene Editing in Abiotic Stress-Tolerant Crop Production 29 2.7.1 Drought Tolerance 30 2.7.2 Salinity Tolerance 30 2.7.3 Herbicide Resistance 31 2.8 Application of CRISPR/Cas Multiplex Gene Editing in Enhancing Crop Yield, Nutrition, and Related Traits 31 2.9 Conclusion 32 Acknowledgments 32 References 34 3 Cas Variants Increased the Dimension of the CRISPR Tool Kit 40 Sameer Dixit, Akanchha Shukla, Mahendra Pawar, and Jyothilakshmi Vadassery 3.1 Introduction 40 3.2 General Architecture and Mechanism of CRISPR-Cas System 41 3.3 Classification of CRISPR-Cas System 42 3.3.1 Class 1 CRISPR-Cas System 44 3.3.2 Class 2 CRISPR-Cas System 45 3.4 Different Application-Based CRISPR-Cas System 45 3.4.1 Cas 9 46 3.4.2 Cas 12 46 3.4.3 Cas 14 46 3.4.4 Cas 13 47 3.4.5 Cas 3 47 3.5 Advancement and Reengineering of CRISPR-Cas System 47 3.6 Conclusions 48 Acknowledgments 49 References 49 4 Advancement in Delivery Systems and Vector Selection for CRISPR/ Cas-Mediated Genome Editing in Plants 52 Sanskriti Vats, Sukhmandeep Kaur, Amit Chauhan, Dipul Kumar Biswas, and Rupesh Deshmukh 4.1 Introduction 52 4.2 Advancement in Delivery Systems and Vector Selection for CRISPR/ Cas-Mediated Genome Editing in Plants 53 4.2.1 Vector Selection Based on Application and Availability in Plants 53 4.2.2 Plant Transformation Methodologies 56 4.3 Emerging Advanced CRISPR/Cas Systems and the Increased Demand for Quick Transformation Protocols 57 4.4 Advancements in Agrobacterium-Meditated Stable Transformation of Plants 59 4.5 Improvement of Agrobacterium-Mediated Transformation System by Developmental Regulators and Modular Agrobacterium Strains 61 4.6 Non-Agrobacterium Systems for Plant Transformation 62 4.7 Viral Vectors for Delivery of CRISPR Reagents and Increasing Donor Titer 63 4.8 De novo Meristem Induction 65 4.9 Biolistics and Protoplast Systems for CRISPR-Based Genome Editing 66 4.9.1 Biolistic Approach 66 4.9.2 Protoplast Approach 67 4.10 Generation of Transgene-Free CRISPR-Edited Lines 68 4.10.1 Mendelian Segregation Analysis 68 4.10.2 Programmed Self-Elimination Method 68 4.10.3 Transient Expression of CRISPR/Cas9 Cassette 68 References 69 5 Role of Nanotechnology in the Advancement in Genome Editing in Plants 78 Mehtap AYDIN 5.1 An Overview of Plant Genome Editing 78 5.1.1 Meganuclease 79 5.1.2 Zinc Finger Nucleases 79 5.1.3 Transcription Activator-Like Effectors Nucleases 80 5.1.4 CRISPR/Cas9 Based Genome Editing 80 5.2 Nanoparticles used as Genome Editing Tools in Plants 80 5.2.1 Mesoporous Silica Nanoparticles 82 5.2.2 Carbon Nanotubes Carbon 82 5.2.3 Lipid-Based Nanoparticles 83 5.2.4 Polymer-Based Nanoparticles 83 5.3 Point of View: The Nanotechnology and Plant Genome Editing 83 5.4 The Approach to Transferring Biomolecules to Plants and Its Limitations 84 5.5 Role of Nanotechnology in Agriculture 84 5.6 Conclusion 86 References 86 6 Genome Editing for Crop Biofortification 91 Erum Shoeb, Srividhya Venkataraman, Uzma Badar, and Kathleen Hefferon 6.1 Introduction 91 6.2 Current Global Status of Micronutrient Malnutrition 92 6.3 Importance of Biofortification in Ensuring Food Security 92 6.4 Strategies for Biofortification 93 6.4.1 Chloroplast Metabolic Engineering for Developing Nutrient-Dense Food Crops 94 6.5 Biofortification Through Agronomic Practices 96 6.6 Genome Editing Is a Powerful Tool 98 6.6.1 Meganucleases (MegNs) 99 6.6.2 Zinc Finger Nucleases 100 6.6.3 TALENs 100 6.6.4 CRISPR/Cas- 9 101 6.7 Examples of Biofortification Using Genome Editing Technologies 102 6.7.1 Amino Acid Biofortification 102 6.7.2 GABA Biofortification 102 6.7.3 Improvement of Oil Content and Quality 105 6.7.4 Improvement of Resistant Starch Content 105 6.7.5 Improvement of Micronutrient Bioavailability 105 6.7.6 Crops Enriched in Iron 105 6.7.7 Zn-enriched Crops 106 6.7.8 Crops Enriched in Vitamin A 106 6.7.9 Crops Enriched in Vitamin E 107 6.7.10 Engineering Crops Adapted to Growing in Toxic Environments 107 6.7.11 CRISPR-Cas9-enabled Decrease in Anti-nutrients 107 6.7.12 Benefits of Genome Editing over Other Technologies for Biofortification 108 6.8 Regulation of Genome Editing 108 6.9 Conclusions and Future Prospects 109 References 109 7 Genome Editing for Nutritional Improvement of Crops 122 Pooja Kanwar Shekhawat, Hasthi Ram, and Praveen Soni Abbreviations 122 7.1 Introduction 124 7.2 Evolution of Techniques for Improvement of Crops’ Genomes 124 7.3 Genome Editing for Nutritional Improvement 125 7.3.1 Improvement in Cereal Crops 126 7.3.2 Improvement in Oilseed Crops 138 7.3.3 Improvements in Horticulture Crops 139 7.4 Regulation of Genome Edited Crops: Current Status 141 7.5 Future Perspectives and Conclusion 142 Author Contribution 142 Acknowledgment 142 References 143 8 Genome-Editing Tools for Engineering of MicroRNAs and Their Encoded Peptides, miPEPs, in Plants 153 Ravi Shankar Kumar, Hiteshwari Sinha, Tapasya Datta, Ashish Sharma, and Prabodh Kumar Trivedi 8.1 Introduction 153 8.1.1 ZINC Finger Nucleases 154 8.1.2 TALE Nucleases 155 8.1.3 CRISPR/Cas 9 156 8.2 CRISPR–Cas9-Mediated DNA Interference in Bacterial Adaptive Immunity 157 8.2.1 Types of CRISPR Systems 158 8.2.2 The Cas9 Enzyme 158 8.3 CRISPR/Cas9 Effector Complex Assembly 159 8.4 The Mechanism of CRISPR/Cas9-Mediated Genome Engineering 159 8.4.1 Comparison with Other Technologies for Genome Editing 160 8.4.2 Limitations of the Cas9 System 160 8.4.3 miRNAs 162 8.4.4 Biogenesis of miRNA 162 8.4.5 miRNA and Gene Regulations 163 8.5 Role of Genome-Editing in miRNA Expression 164 8.6 Applications of the CRISPR/Cas9 System in miRNA Editing 165 8.6.1 microRNA-Encoded Peptide 166 8.6.2 Biogenesis of miPEPs 166 8.6.3 Role of miPEP 167 8.7 miPEPs Act as the Master Regulator in Plant Growth and Development 167 8.8 Conclusions and Future Prospect 168 Acknowledgments 169 References 169 9 Genome Editing for Trait Improvement in Ornamental Plants 177 Yang Zhou, Yuxin Li, and Wen Liu 9.1 Introduction 177 9.2 Application of Gene Editing Technology in Color Regulation of Ornamental Plants 178 9.3 Application of Gene Editing Technology in Ornamental Plants Preservation 179 9.4 Application of Gene Editing Technology in Shape and Organ Regulation of Ornamental Plants 180 9.5 Application of Gene Editing Technology in Other Traits of Ornamental Plants 180 9.6 Conclusions and Perspectives 181 Acknowledgments 181 References 181 10 Abiotic Stress Tolerance in Plants by Genome Editing Applications 185 Elif Karlik Urhan 10.1 Introduction 185 10.2 Drought Tolerance 187 10.3 Salinity Tolerance 191 10.4 Temperature Stress Tolerance 196 10.4.1 Heat Stress Tolerance 196 10.4.2 Cold Stress Tolerance 199 10.5 Conclusions 202 References 203 11 Genome Editing for Improvement of Nutrition and Quality in Vegetable Crops 222 Payal Gupta, Suhas G. Karkute, Prasanta K. Dash, and Achuit K. Singh 11.1 Vegetables and Human Nutrition 222 11.2 Important Quality Parameters of Vegetables 223 11.3 Approaches for Improving Nutrition Content in Vegetables 223 11.3.1 Breeding for Improving Nutrition in Vegetable Crops 224 11.3.2 Genome Editing Technologies 225 11.3.2.1 CRISPR/Cas9 and Advances in Genome Editing 225 11.3.2.2 Mechanism of CRISPR/Cas-Mediated Genome Editing in Plants 226 11.4 Applications of Genome Editing for Improvement of Vegetable Nutrition and Quality 227 11.4.1 Improvement in the Appearance in Terms of Shape and Size 229 11.4.2 Improvement of the Shelf-Life 229 11.4.3 Improvement of the Ripening Time 230 11.4.4 Improvement in Colour of the Fruit/Vegetable 230 11.4.5 Biofortification of Vegetable Crops Through Genome Editing 231 11.4.5.1 Metabolic Engineering of Carotenoid Biosynthesis Pathway 231 11.4.5.2 Increasing γ-Amino Butyric Acid and Vitamin D Content 232 11.4.6 Improvement of Starch Content 232 11.4.7 Elimination of Anti-Nutritional Factors 232 11.5 Challenges and Future Prospects 233 11.6 Conclusion 234 References 234 12 Insight into the Flavonoids Enrichment in Plants by Genome Engineering 242 Elena V. Mikhaylova 12.1 The Importance of Flavonoids 242 12.2 Flavonoid Biosynthesis Pathway 244 12.3 In Planta Flavonoid Enrichment via Genome Editing 247 12.4 Biotechnological Production of Flavonoids 252 12.5 Conclusions 253 References 253 13 Genome Engineering in Medicinal Plants for Improved Therapeutics: Current Scenario and Future Perspective 260 Buket Çakmak Güner 13.1 Introduction 260 13.2 Genome Engineering in Plants 261 13.2.1 Agrobacterium-Mediated Transformation 261 13.2.2 Biolistic or Particle Bombardment-Mediated Transformation 262 13.2.3 Electroporation-Mediated Transformation 262 13.2.4 Chemical-Mediated Transformation 262 13.3 Genome Editing in Plants 263 13.3.1 Applications in Medicinal Plants 264 13.4 Medicinal Plants: Comparison of Traditional and Scientific Use 266 13.5 Chemical Components of Medicinal Plants 266 13.6 Using Biotechnological Techniques in Medicinal Plant Production 267 13.7 In Vitro Culture Techniques in Herbal Medicine 268 13.7.1 Plant Tissue Culture in Herbal Medicine 268 13.7.2 Hairy Root Cultures in Herbal Medicine 269 13.7.3 Callus and Cell Suspension Culture in Herbal Medicine 270 13.7.4 Micropropagation in Herbal Medicine 270 13.7.5 Elicitation 270 13.7.6 Bioreactors for Large Scale Up 270 13.8 Pharmaceutical Products from Medicinal Plants: Current Situation 271 13.8.1 Antimicrobial Molecules 271 13.8.2 Antioxidant Molecules 271 13.8.3 Anticancer Molecules 273 13.8.4 Cardiovascular Molecules 273 13.9 Future Perspective and Conclusion 274 References 275 14 Nutraceuticals Enrichment by Genome Editing in Plants 282 Luis Alfonso Jiménez-Ortega, Jesus Christian Grimaldi-Olivas, Brandon Estefano Morales-Merida, and J. Basilio Heredia 14.1 Introduction 282 14.2 Functional and Biofortified Foods: Phytochemicals, Nutraceuticals, and Micronutrients 283 14.3 Metabolic Engineering to Enhance the Production of Phenolic Compounds 283 14.3.1 Biosynthetic Pathway of Phenolic Compounds 283 14.3.1.1 Phenolic Acids 283 14.3.1.2 Flavonoids 284 14.3.2 Tools to Increase the Production of Phenolic Compounds in Plants and Crops 285 14.4 Metabolic Engineering to Enhance the Production of Terpenes 286 14.4.1 Biosynthetic Pathway of Terpenes 287 14.4.2 Tools to Increase the Production of Terpenes in Plants and Crops 287 14.5 Metabolic Engineering to Enhance the Production of Alkaloids 289 14.5.1 Biosynthetic Pathway of Alkaloids 289 14.5.2 Tools to Increase the Production of Alkaloids in Plants and Crops 291 14.6 Metabolic Engineering to Enhance the Production of Vitamins and Minerals 292 14.6.1 Tools to Increase the Production of Vitamins in Plants and Crops 292 14.6.2 Tools to Increase the Production of Minerals in Plants and Crops 295 14.7 Metabolic Engineering to Enhance the Production of Polyunsaturated Fatty Acids 296 14.7.1 Biosynthetic Pathway of Polyunsaturated Fatty Acids 296 14.7.2 Tools to Increase the Production of Polyunsaturated Fatty Acids in Plants and Crops 297 14.8 Metabolic Engineering to Enhance the Production of Bioactive Peptides 298 14.8.1 Tools to Increase the Production of Bioactive Peptides in Plants and Crops 298 14.9 Conclusions 299 References 299 15 Exploration of Genome Editing Tools for microRNA Engineering in Plants 310 Hengyi Xu 15.1 Introduction 310 15.2 The Biogenesis of the miRNA and RNA Silencing in Plant 311 15.3 MIRs as a Family in Plant 313 15.4 The miRNA Engineering Methods in Plant 315 15.5 The PAM of CRISPR/Cas and Strategy in Construct Design for miRNA Knock-Out 316 15.6 Evolving CRISPR/Cas Tools, Strategies, and Their Potential Uses in MIR Regulation 317 15.7 Conclusion and Future Perspectives 319 References 320 16 Application of Genome Editing in Pulses 326 Nikhil Malhotra 16.1 Introduction 326 16.2 Genome Editing for Crop Improvement in Pulses 327 16.2.1 Chickpea (Cicer arietinum) 327 16.2.2 Cowpea (Vigna unguiculata) 328 16.2.3 Soybean (Glycine max) 328 16.2.4 Non-Edited Grain Legumes 329 16.2.4.1 Common Bean (Phaseolus vulgaris) 329 16.2.4.2 Dry Pea (Pisum sativum) 330 16.2.4.3 Faba Bean (Vicia faba) 330 16.2.4.4 Mung Bean (Vigna radiata) 331 16.2.4.5 Lentil (Lens culinaris) 332 16.3 Conclusion and Future Prospects 332 References 333 17 Genome Editing for Microbial Pathogens Resistance in Crops 339 Mudasir Ahmad Bhat, Saima Jan, Sumreen Amin Shah, and Arif Tasleem Jan 17.1 Introduction 339 17.2 Effects of Climate Change on Crop Productivity 340 17.3 CRISPR/Cas-Mediated Genome Editing in Plants 341 17.3.1 CRISPR/cpf 1 342 17.3.2 CRISPRi 342 17.4 CRISPR-Based Engineering of Crop Plants 343 17.4.1 Gene Disruption via Indel in Coding Sequences 343 17.4.2 Gene Disruption via Indel in Promoter Regions 343 17.4.3 Gene Deletion via Multiplex sgRNAs 344 17.4.4 Gene Insertion via Homology-Directed Repair 344 17.5 CRISPR/Cas in Imparting Tolerance to Biotic Factors 344 17.5.1 CRISPR in Developing Resistance to Viruses 345 17.5.2 CRISPR in Developing Resistance to Fungal Pathogens 345 17.5.3 CRISPR in Developing Resistance to Different Bacteria 349 17.6 CRISPR/Cas in Abiotic Stress Tolerance in Crops 350 17.6.1 CRISPR/Cas in Temperature Stress Tolerance 350 17.6.2 Drought Stress Responses 352 17.6.3 Salinity Stress Responses 353 17.6.4 Metal Stress Tolerance 354 17.7 Conclusion 355 Author Contributions 356 Funding 356 Acknowledgements 356 Conflicts of Interest 356 References 356 18 Genome Editing for Raising Crops for Arid Lands: A Perspective of Increasing Stress Tolerance 369 Pooja Jangir, Purva Khandelwal, and Praveen Soni Abbreviations 369 18.1 Introduction 370 18.2 Genome Editing Toolbox 371 18.3 Plants’ Responses to Drought and Heat 373 18.4 Increasing Drought Tolerance in Plants Through Genome Editing 375 18.4.1 Transcription Factors 375 18.4.2 Phytohormone Signaling 381 18.4.3 Morphology and Drought Avoidance 382 18.4.4 MicroRNAs 382 18.4.5 Nutrient and Yield Traits 383 18.5 Increasing Heat Tolerance in Plants Through Genome Editing 383 18.6 Conclusion and Future Perspective 385 Author Contributions 386 Conflicts of Interest 386 Acknowledgment 386 References 386 19 Genome Engineering for the Development of Climate-Resilient Crop Plants 394 Bhavuk Gupta, Ayush Khandelwal, Brijesh Kumar, and Purva Bhalothia 19.1 Introduction 394 19.2 Effect of Climate Change on Crop Plants 395 19.2.1 Effect on Photosynthesis and CO 2 Fixation 397 19.2.2 Effect of Temperature 397 19.2.3 Effect of Change in Precipitation 398 19.2.4 Effect of Salinity 398 19.3 Genome Engineering in Crop Improvement 398 19.4 Traditional and Modern Molecular Breeding for Crop Improvement 400 19.4.1 Classical Plant Breeding 400 19.4.2 Genetic Engineering 401 19.4.3 RNA Interference 401 19.4.4 Phenomics and Genomics 401 19.4.5 Role of miRNAs 402 19.4.6 Zinc Finger Nucleases 402 19.4.7 TALENs 403 19.4.8 CRISPR/Cas 9 403 19.5 Genome Engineering in Development of Climate Resilient Crops 404 19.6 Status of Improved Crops with Genetic Engineering 405 19.7 Problems Associated with Genetic Engineering 406 19.8 Future Aspects 407 19.9 Conclusion 407 References 408 Index 412

Autorenportrait

Santosh Kumar Upadhyay is an Assistant Professor in the Department of Botany, Panjab University, Chandigarh, India. His research focuses on functional genomics in plants, especially the use of the CRISPR-Cas system for genetic engineering.

Back cover copy

Understand the keys to creating the food of the future Genome engineering in plants is a field that has made enormous strides in recent years. In particular, the CRISPR-Cas system has been used in a number of crop species to make significant leaps forward in nutritional improvement, stress tolerance, crop yield, and more. As scientists work to meet global food needs and foster sustainable agriculture in a changing world, genome engineering promises only to become more important. Applications of Genome Engineering in Plants details the history of, and recent developments in, this essential area of biotechnology. It describes advances enabling nutritional improvement, nutraceuticals improvement, flavonoid enrichment, and many more crop enhancements, as well as subjects such as biosafety and regulatory mechanisms. The result is a thorough and essential overview for researchers and biotech professionals. Applications of Genome Engineering in Plants readers will also find: <ul><li>Chapters on trans-gene free editing or non-transgenic approaches to plant genomes</li> <li>Detailed discussion of topics including nanotechnology-facilitated genome editing, engineering for virus resistance in plants, and more</li> <li>Applications of genome editing in oil seed crops, vegetables, ornamental plants, and many others</li></ul> Applications of Genome Engineering in Plants is ideal for academics, scientists, and industry professionals working in biotechnology, agriculture, food science, and related subjects.