Genome and Epigenome Editing for Stress-Tolerant Crops

Jen-Tsung Chen is Professor of Cell Biology at the Department of Life Sciences, National University of Kaohsiung, Taiwan, where he teaches courses on cell biology, genomics, proteomics, plant physiology, and plant biotechnology. His research focuses on bioactive compounds, plant molecular biology, bioinformatics, and systems pharmacology. Dr. Chen is an editorial board member for several prestigious journals, including Plant Methods and GM Crops & Food. He has authored multiple books on drug discovery, nanotechnology, plant functional genomics, and CRISPR-based plant genome editing. Dr. Chen was included in the “World’s Top 2% Scientists” by Stanford University and Elsevier in 2023 and 2024.

• List of Contributors xviiPreface xxiii1 Mitigating Heat Stress Response in CRISPR/Cas-Mediated Edited Crops by Altering the Expression Pattern of Noncoding DNA 1Emanpreet Kaur, Louie Cris Lopos, and Andriy Bilichak1.1 Introduction 11.2 Impact of Climate Change and Heat Stress on Crop Productivity 21.3 Strategies for Mitigating Heat Stress Response Through Gene Editing and Derivative Technologies 81.4 Conclusions and Future Perspectives 17References 182 Design Future Crops with Stress Resilience by CRISPR/Cas Reprogramming Noncoding RNAs 33Hidam Bishworjit Singh, Niraj Kumar, Riwandahun Marwein, Ajay Kumar Keot, Manash Pratim Sarmah, and Dhanawantari L. Singha2.1 Introduction 332.2 Noncoding RNAs Associated with Drought in Plants 352.3 Noncoding RNA Associated with Salt Stress Tolerance in Plant 352.4 Important to Edit Noncoding RNA by CRISPR/Cas to Reprogram Them 362.5 Gene-Editing Mechanism in Plants with CRISPR/Cas Technology 372.6 Functions of Different Cas Proteins 392.7 Different Cas9 Variants for Genome Editing in Plants 402.8 Success in CRISPR/Cas-Editing Noncoding RNA Genes in Plants 412.9 Challenges Associated with Editing Noncoding RNA in Plants 412.10 Conclusion and Future Directions 43References 433 Improving Plant Abiotic Stress Tolerance by Modulating LncRNAs Using CRISPR/Cas9 Technology 49Muhammad Waseem, Sana Basharat, Iffat Shaheen, Liu Pingwu, Muhammad Shareef, and Nimra Shahid3.1 Introduction 493.2 The CRISPR-Cas Technology 503.3 Mechanistic Overview of CRISPR/Cas9-Based Editing 523.4 Impact of lncRNAs on Plant Abiotic Stress 543.5 CRISPR/Cas lncRNA Editing Improves Plant Abiotic Stress Tolerance 573.6 Future Directions and Perspective 583.7 Conclusion 59References 594 CRISPR/Cas-Modified Long Noncoding RNAs for Regulating Plant Abiotic Responses 65Diliane Harumi Yaguinuma, Jardel de Oliveira, Fernanda Freitas de Oliveira, and Tiago Benedito dos Santos4.1 Introduction 654.2 Long Noncoding RNA (lncRNA) from Plants May Also be Related to Stress 684.3 Conclusion 74References 745 Functional Analysis of Plant Noncoding Genomes UsingCRISPR-Cas9-Mediated Approaches 87Anna Rera, Privilege Chikove, Nyashadzashe Shengezi, Angeline Jurry, and Jyoti Prakash Sahoo5.1 Introduction 875.2 Noncoding Genome in Plants 885.3 CRISPR-Cas9 Technology 905.4 Applications of CRISPR-Cas9 in Plant Genomics 915.5 Designing CRISPR-Cas9 Experiments for Noncoding Regions 935.6 Techniques for Characterizing CRISPR-Cas9-Mediated Mutations 945.7 Future Prospects 975.8 Conclusion 97References 976 Small RNA-Mediated Plant Protection Constructed by CRISPR/Cas Genome Editing 101Alagu Manickavelu6.1 Introduction 1016.2 Principles of Small RNA-Mediated Plant Defense Mechanisms 1026.3 CRISPR/Cas-Mediated Engineering of Small RNA Pathways 1046.4 Case Studies: Small RNA-Mediated Plant Protection Enhanced by CRISPR/Cas 1066.5 Challenges and Limitations 1086.6 Future Prospects 1096.7 Conclusion 110References 1117 Plant Immunity Released by CRISPR/Cas Technology-Mediated Modifying Long Noncoding RNAs 115Ananya Choudhury, Pritilagna Panigrahi, Swatismita Deo, Bhupati Nayak, Dhaarani V., Swarnalata Tripathy, Jyoti Prakash Sahoo, and Swapan Kumar Tripathy7.1 Introduction 1157.2 Plant Immunity 1167.3 Long Noncoding RNAs and CRISPR/Cas Technology 1167.4 Enhancing Plant Immunity Through lncRNA Modification 1177.5 Key Roles of lncRNAs in Plant Immunity 1187.6 Application of CRISPR/Cas Technology-Mediated Modifying Long Noncoding RNAs 1187.7 Ethical Regulations, Bioethical Uses, and Future Prospects 1197.8 Conclusion 121References 1228 Plant Stress Memory Rewrite by CRISPR/Cas-Mediated Approaches 127Srutirekha Mishra, Subhashree Priyadarshinee Sahoo, Subhalaxmi Swain, Laxmipriya Pati, Dhaarani V., Swarnalata Tripathy, Jyoti Prakash Sahoo, and Swapan Kumar Tripathy8.1 Introduction 1278.2 Understanding Plant Stress Response 1288.3 Plant Stress Memory and Its Affecting Factors 1298.4 Molecular and Epigenetic Mechanism of Plant Stress Memory 1308.5 Exploring CRISPR/Cas Approaches to Write Plant Stress Memory 1318.6 Genome-Editing Technique Based on CRISPR/Cas 9 1318.7 The CRISPR-Cas Genome Modification Mechanism 1328.8 Ethical Issues 1348.9 Future Prospects 1358.10 Conclusion 135References 1359 Salinity-Tolerant Crop Breeding Through Reprogramming Noncoding RNAs Mediated by CRISPR/Cas9 Technology 141Santanu Samanta and Aryadeep Roychoudhury9.1 Introduction 1419.2 Negative Impact of Salinity Stress on Plants 1429.3 Why Developing Salinity-Tolerant Crops Is a Necessity? 1439.4 Breeding for Salt-Tolerant Crops Against Salinity Stress 1439.5 An Overview of ncRNAs in Plants 1449.6 Mechanistic Insights of CRISPR/Cas9 Tool 1479.7 Targeting/Reprogramming ncRNAs Using CRISPR/Cas9 Tools 1489.8 Concluding Remarks 149References 15010 Genetic Engineering of Cis-Regulatory Elements by CRISPR/Cas Technology for Crop Improvement 157Afreen Anis, Soumyashree Dash, Soumita Karmakar, and Jyoti Prakash Sahoo10.1 Introduction 15710.2 CRISPR/Cas System Advancements 15710.3 CRISPR/Cas9 Application for Improving Crop Quality 15910.4 Cis-regulatory Components in Introns, Promoters, and Intergenic Areas 16010.5 Natural Variation Affecting Cis-Regulatory Elements in Crops by InDels, SNPs, and Transposable Elements 16110.6 Ways to Use the CRISPR/Cas-Editing System for Transgene-Free Genetic Engineering 16310.7 The Genome-Wide Association Study’s (GWAS) Identification of CREs that are Vital to Agriculture 16310.8 Customized CRE Alterations 16310.9 CRE Editing with CRISPR/Cas 16510.10 Methods for Improving Horticultural Crops Through CRISPR/Cas-Mediated Cis-Engineering Applications16710.11 Opportunities and Challenges 16810.12 Conclusion 171References 17111 Harnessing CRISPR Technology to Edit Noncoding RNAs for Enhanced Disease Resistance in Crops 179Abhik Sarkar, Subham Ghosh, Dipro Sinha, Parinita Das, Sneha Murmu, and Himanshushekhar Chaurasia11.1 Introduction 17911.2 A Brief Overview of CRISPR/Cas Technology 18111.3 Overview of Noncoding RNAs 18711.4 CRISPR/Cas-Edited Crops for Disease Resistance and Limitations 19011.5 Modulation of Noncoding RNAs in CRISPR/Cas-Edited Crops 19311.6 Example of CRISPR-Cas-Edited Crops with Modified Noncoding RNAs 19611.7 Future Perspectives and Challenges 19711.8 Conclusion 198References 19812 Temperature-Smart Crops Through Edited Noncoding RNAs Using CRISPR/Cas Technology 203Sharia Yesmin Labonno, Marium Khatun, Sumi Sarkar, and Abul Kalam Mohammad Aminul Islam12.1 Introduction 20312.2 The Function of ncRNAs in Response to Temperature Stress in Plants 20412.3 CRISPR/Cas Technology for Editing Noncoding RNAs 20612.4 CRISPR/Cas9 Editing of Noncoding RNAs (ncRNAs) for Cold and Heat Tolerance 20812.5 Applications in Cold and Heat Tolerance 20912.6 Case Studies: Temperature-Smart Crops Developed Through ncRNA Editing 20912.7 Challenges and Future Directions 21212.8 Future Prospects for Temperature-Smart Crops 21312.9 Conclusions 215References 21613 Technical Advancements in Functional Mutagenesis of Plant Long Noncoding RNAs Using CRISPR/Cas Technology 219Tushar K. Dutta13.1 Introduction 21913.2 The Complex Architecture of Plant lncRNAs 22013.3 The Diverse and Dynamic Functions of Plant lncRNAs 22113.4 Utility and Challenges of CRISPR/Cas System for Deciphering lncRNA Functions 22513.5 Functional Analysis of Different Plant lncRNAs Using CRISPR/Cas System 22813.6 Conclusion and Future Directions 231References 23214 Plant Gene Silencing Modified by CRISPR/Cas-Reprogrammed Small Interfering RNAs for Regulating Abiotic Stress Responses 239Noru Rajasekhar Reddy, Janapareddy Rajesh, Kadiyala Kavya, Lellapalli Rithesh, Abhishek Kumar, and Pooja14.1 Introduction 23914.2 CRISPR/Cas System: Principles and Applications 24214.3 Role of Small Interfering RNAs in Gene Silencing 24714.4 CRISPR/Cas-Mediated Reprogramming of siRNAs for Gene Silencing 24914.5 Regulation of Abiotic Stress Responses Through Gene Silencing 25014.6 Conclusion 254References 25515 Functional Analysis and Modification of Plant MicroRNA by CRISR/Cas System for Stress Tolerance 265Rida Zahid, Ifrah Imran, Muhammad Waseem Sajjad, Muhammad Arslan Mahmood, Anam Ishtiaq, Saqib Siddique, Rabia Rehman, Imran Amin, and Rubab Zahra Naqvi15.1 Introduction 26515.2 miRNA Role in Plants 26615.3 In Silico Approaches to Identifying miRNA 27115.4 CRISPR-Based Editing of miRNA in Plants for Stress Control 27815.5 Conclusion and Future Prospects 283References 28316 Employment of RNA Interference and CRISPR/Cas Machinery for Disease Resistance in Crops 293Ifrah Imran, Muhammad Jawad Akbar Awan, Mariam Akhtar, Muhammad Waseem Sajjad, Muhammad Ismail Buzdar, Rida Zahid, Jahan Khan, Imran Amin, and Rubab Zahra Naqvi16.1 Introduction 29316.2 The Editors of Nature 29516.3 The Mechanisms of Silence: Understanding RNA Interference 29916.4 Advancing Agriculture: Engineered RNA Interference for Enhanced Crop Performance 30116.5 RNAi Approaches: Targeted Silence to Combat Crop Diseases 30216.6 Sculpting Genetic Frontiers: CRISPR and Its Triumphs in Crop Disease Management 30616.7 Conclusion 310References 31217 Antiabiotic Stress Capacities of Crops Gained by CRISPR/Cas-Edited Small RNAs 321Arfa Saifullah, Asad Azeem, Ghulam Mustafa, Muhammad Sarwar Khan, Sehrish Shehzadi, Aqsa Parvaiz, Maria Rehman, and Faiz Ahmad Joyia17.1 Introduction 32117.2 CRISPR/Cas Technology: Mechanism and Applications 32217.3 CRISPR/Cas-Mediated Editing of sRNA for Stress Tolerance 32417.4 Application of CRISPR/Cas-Edited sRNA in Stress Tolerance 32517.5 Challenges and Future Prospects of CRISPR/Cas-Edited Small RNAs for Abiotic Stress Resistance in Crops 32717.6 Conclusion 329References 330Index 335