Genome and Epigenome Editing for Stress-Tolerant Crops

List of Contributors xvii Preface xxiii 1 Mitigating Heat Stress Response in CRISPR/Cas-Mediated Edited Crops by Altering the Expression Pattern of Noncoding DNA 1 Emanpreet Kaur, Louie Cris Lopos, and Andriy Bilichak 1.1 Introduction 1 1.2 Impact of Climate Change and Heat Stress on Crop Productivity 2 1.3 Strategies for Mitigating Heat Stress Response Through Gene Editing and Derivative Technologies 8 1.4 Conclusions and Future Perspectives 17 References 18 2 Design Future Crops with Stress Resilience by CRISPR/Cas Reprogramming Noncoding RNAs 33 Hidam Bishworjit Singh, Niraj Kumar, Riwandahun Marwein, Ajay Kumar Keot, Manash Pratim Sarmah, and Dhanawantari L. Singha 2.1 Introduction 33 2.2 Noncoding RNAs Associated with Drought in Plants 35 2.3 Noncoding RNA Associated with Salt Stress Tolerance in Plant 35 2.4 Important to Edit Noncoding RNA by CRISPR/Cas to Reprogram Them 36 2.5 Gene-Editing Mechanism in Plants with CRISPR/Cas Technology 37 2.6 Functions of Different Cas Proteins 39 2.7 Different Cas9 Variants for Genome Editing in Plants 40 2.8 Success in CRISPR/Cas-Editing Noncoding RNA Genes in Plants 41 2.9 Challenges Associated with Editing Noncoding RNA in Plants 41 2.10 Conclusion and Future Directions 43 References 43 3 Improving Plant Abiotic Stress Tolerance by Modulating LncRNAs Using CRISPR/Cas9 Technology 49 Muhammad Waseem, Sana Basharat, Iffat Shaheen, Liu Pingwu, Muhammad Shareef, and Nimra Shahid 3.1 Introduction 49 3.2 The CRISPR-Cas Technology 50 3.3 Mechanistic Overview of CRISPR/Cas9-Based Editing 52 3.4 Impact of lncRNAs on Plant Abiotic Stress 54 3.5 CRISPR/Cas lncRNA Editing Improves Plant Abiotic Stress Tolerance 57 3.6 Future Directions and Perspective 58 3.7 Conclusion 59 References 59 4 CRISPR/Cas-Modified Long Noncoding RNAs for Regulating Plant Abiotic Responses 65 Diliane Harumi Yaguinuma, Jardel de Oliveira, Fernanda Freitas de Oliveira, and Tiago Benedito dos Santos 4.1 Introduction 65 4.2 Long Noncoding RNA (lncRNA) from Plants May Also be Related to Stress 68 4.3 Conclusion 74 References 74 5 Functional Analysis of Plant Noncoding Genomes UsingCRISPR-Cas9-Mediated Approaches 87 Anna Rera, Privilege Chikove, Nyashadzashe Shengezi, Angeline Jurry, and Jyoti Prakash Sahoo 5.1 Introduction 87 5.2 Noncoding Genome in Plants 88 5.3 CRISPR-Cas9 Technology 90 5.4 Applications of CRISPR-Cas9 in Plant Genomics 91 5.5 Designing CRISPR-Cas9 Experiments for Noncoding Regions 93 5.6 Techniques for Characterizing CRISPR-Cas9-Mediated Mutations 94 5.7 Future Prospects 97 5.8 Conclusion 97 References 97 6 Small RNA-Mediated Plant Protection Constructed by CRISPR/Cas Genome Editing 101 Alagu Manickavelu 6.1 Introduction 101 6.2 Principles of Small RNA-Mediated Plant Defense Mechanisms 102 6.3 CRISPR/Cas-Mediated Engineering of Small RNA Pathways 104 6.4 Case Studies: Small RNA-Mediated Plant Protection Enhanced by CRISPR/Cas 106 6.5 Challenges and Limitations 108 6.6 Future Prospects 109 6.7 Conclusion 110 References 111 7 Plant Immunity Released by CRISPR/Cas Technology-Mediated Modifying Long Noncoding RNAs 115 Ananya Choudhury, Pritilagna Panigrahi, Swatismita Deo, Bhupati Nayak, Dhaarani V., Swarnalata Tripathy, Jyoti Prakash Sahoo, and Swapan Kumar Tripathy 7.1 Introduction 115 7.2 Plant Immunity 116 7.3 Long Noncoding RNAs and CRISPR/Cas Technology 116 7.4 Enhancing Plant Immunity Through lncRNA Modification 117 7.5 Key Roles of lncRNAs in Plant Immunity 118 7.6 Application of CRISPR/Cas Technology-Mediated Modifying Long Noncoding RNAs 118 7.7 Ethical Regulations, Bioethical Uses, and Future Prospects 119 7.8 Conclusion 121 References 122 8 Plant Stress Memory Rewrite by CRISPR/Cas-Mediated Approaches 127 Srutirekha Mishra, Subhashree Priyadarshinee Sahoo, Subhalaxmi Swain, Laxmipriya Pati, Dhaarani V., Swarnalata Tripathy, Jyoti Prakash Sahoo, and Swapan Kumar Tripathy 8.1 Introduction 127 8.2 Understanding Plant Stress Response 128 8.3 Plant Stress Memory and Its Affecting Factors 129 8.4 Molecular and Epigenetic Mechanism of Plant Stress Memory 130 8.5 Exploring CRISPR/Cas Approaches to Write Plant Stress Memory 131 8.6 Genome-Editing Technique Based on CRISPR/Cas 9 131 8.7 The CRISPR-Cas Genome Modification Mechanism 132 8.8 Ethical Issues 134 8.9 Future Prospects 135 8.10 Conclusion 135 References 135 9 Salinity-Tolerant Crop Breeding Through Reprogramming Noncoding RNAs Mediated by CRISPR/Cas9 Technology 141 Santanu Samanta and Aryadeep Roychoudhury 9.1 Introduction 141 9.2 Negative Impact of Salinity Stress on Plants 142 9.3 Why Developing Salinity-Tolerant Crops Is a Necessity? 143 9.4 Breeding for Salt-Tolerant Crops Against Salinity Stress 143 9.5 An Overview of ncRNAs in Plants 144 9.6 Mechanistic Insights of CRISPR/Cas9 Tool 147 9.7 Targeting/Reprogramming ncRNAs Using CRISPR/Cas9 Tools 148 9.8 Concluding Remarks 149 References 150 10 Genetic Engineering of Cis-Regulatory Elements by CRISPR/Cas Technology for Crop Improvement 157 Afreen Anis, Soumyashree Dash, Soumita Karmakar, and Jyoti Prakash Sahoo 10.1 Introduction 157 10.2 CRISPR/Cas System Advancements 157 10.3 CRISPR/Cas9 Application for Improving Crop Quality 159 10.4 Cis-regulatory Components in Introns, Promoters, and Intergenic Areas 160 10.5 Natural Variation Affecting Cis-Regulatory Elements in Crops by InDels, SNPs, and Transposable Elements 161 10.6 Ways to Use the CRISPR/Cas-Editing System for Transgene-Free Genetic Engineering 163 10.7 The Genome-Wide Association Study’s (GWAS) Identification of CREs that are Vital to Agriculture 163 10.8 Customized CRE Alterations 163 10.9 CRE Editing with CRISPR/Cas 165 10.10 Methods for Improving Horticultural Crops Through CRISPR/Cas-Mediated Cis-Engineering Applications167 10.11 Opportunities and Challenges 168 10.12 Conclusion 171 References 171 11 Harnessing CRISPR Technology to Edit Noncoding RNAs for Enhanced Disease Resistance in Crops 179 Abhik Sarkar, Subham Ghosh, Dipro Sinha, Parinita Das, Sneha Murmu, and Himanshushekhar Chaurasia 11.1 Introduction 179 11.2 A Brief Overview of CRISPR/Cas Technology 181 11.3 Overview of Noncoding RNAs 187 11.4 CRISPR/Cas-Edited Crops for Disease Resistance and Limitations 190 11.5 Modulation of Noncoding RNAs in CRISPR/Cas-Edited Crops 193 11.6 Example of CRISPR-Cas-Edited Crops with Modified Noncoding RNAs 196 11.7 Future Perspectives and Challenges 197 11.8 Conclusion 198 References 198 12 Temperature-Smart Crops Through Edited Noncoding RNAs Using CRISPR/Cas Technology 203 Sharia Yesmin Labonno, Marium Khatun, Sumi Sarkar, and Abul Kalam Mohammad Aminul Islam 12.1 Introduction 203 12.2 The Function of ncRNAs in Response to Temperature Stress in Plants 204 12.3 CRISPR/Cas Technology for Editing Noncoding RNAs 206 12.4 CRISPR/Cas9 Editing of Noncoding RNAs (ncRNAs) for Cold and Heat Tolerance 208 12.5 Applications in Cold and Heat Tolerance 209 12.6 Case Studies: Temperature-Smart Crops Developed Through ncRNA Editing 209 12.7 Challenges and Future Directions 212 12.8 Future Prospects for Temperature-Smart Crops 213 12.9 Conclusions 215 References 216 13 Technical Advancements in Functional Mutagenesis of Plant Long Noncoding RNAs Using CRISPR/Cas Technology 219 Tushar K. Dutta 13.1 Introduction 219 13.2 The Complex Architecture of Plant lncRNAs 220 13.3 The Diverse and Dynamic Functions of Plant lncRNAs 221 13.4 Utility and Challenges of CRISPR/Cas System for Deciphering lncRNA Functions 225 13.5 Functional Analysis of Different Plant lncRNAs Using CRISPR/Cas System 228 13.6 Conclusion and Future Directions 231 References 232 14 Plant Gene Silencing Modified by CRISPR/Cas-Reprogrammed Small Interfering RNAs for Regulating Abiotic Stress Responses 239 Noru Rajasekhar Reddy, Janapareddy Rajesh, Kadiyala Kavya, Lellapalli Rithesh, Abhishek Kumar, and Pooja 14.1 Introduction 239 14.2 CRISPR/Cas System: Principles and Applications 242 14.3 Role of Small Interfering RNAs in Gene Silencing 247 14.4 CRISPR/Cas-Mediated Reprogramming of siRNAs for Gene Silencing 249 14.5 Regulation of Abiotic Stress Responses Through Gene Silencing 250 14.6 Conclusion 254 References 255 15 Functional Analysis and Modification of Plant MicroRNA by CRISR/Cas System for Stress Tolerance 265 Rida Zahid, Ifrah Imran, Muhammad Waseem Sajjad, Muhammad Arslan Mahmood, Anam Ishtiaq, Saqib Siddique, Rabia Rehman, Imran Amin, and Rubab Zahra Naqvi 15.1 Introduction 265 15.2 miRNA Role in Plants 266 15.3 In Silico Approaches to Identifying miRNA 271 15.4 CRISPR-Based Editing of miRNA in Plants for Stress Control 278 15.5 Conclusion and Future Prospects 283 References 283 16 Employment of RNA Interference and CRISPR/Cas Machinery for Disease Resistance in Crops 293 Ifrah Imran, Muhammad Jawad Akbar Awan, Mariam Akhtar, Muhammad Waseem Sajjad, Muhammad Ismail Buzdar, Rida Zahid, Jahan Khan, Imran Amin, and Rubab Zahra Naqvi 16.1 Introduction 293 16.2 The Editors of Nature 295 16.3 The Mechanisms of Silence: Understanding RNA Interference 299 16.4 Advancing Agriculture: Engineered RNA Interference for Enhanced Crop Performance 301 16.5 RNAi Approaches: Targeted Silence to Combat Crop Diseases 302 16.6 Sculpting Genetic Frontiers: CRISPR and Its Triumphs in Crop Disease Management 306 16.7 Conclusion 310 References 312 17 Antiabiotic Stress Capacities of Crops Gained by CRISPR/Cas-Edited Small RNAs 321 Arfa Saifullah, Asad Azeem, Ghulam Mustafa, Muhammad Sarwar Khan, Sehrish Shehzadi, Aqsa Parvaiz, Maria Rehman, and Faiz Ahmad Joyia 17.1 Introduction 321 17.2 CRISPR/Cas Technology: Mechanism and Applications 322 17.3 CRISPR/Cas-Mediated Editing of sRNA for Stress Tolerance 324 17.4 Application of CRISPR/Cas-Edited sRNA in Stress Tolerance 325 17.5 Challenges and Future Prospects of CRISPR/Cas-Edited Small RNAs for Abiotic Stress Resistance in Crops 327 17.6 Conclusion 329 References 330 Index 335