Intelligent Gene Editing in Plants analyzes how AI-enabled design and CRISPR-based genome engineering are reshaping plant genetics, with a clear functional focus on delivering durable gains in crop productivity, stress tolerance, and nutritional quality.
The work unfolds in three parts: [i] a foundational survey of genome-editing technologies and the evolving role of AI in precise trait modifications and outcome prediction; [ii] a thorough exploration of applications and synergies, including AI-assisted gRNA optimization, off-target mitigation, regulatory-network analysis, and trait enhancement for disease resistance and climate resilience; and [iii] an emerging-horizons section on cis-regulatory edits, omics integration, synthetic biology, and next-generation editing.
Throughout, the volume interweaves practical experiences, cutting-edge methodologies, and case studies, alongside discussions of biosafety, ethical concerns, governance, and public perception, providing a holistic, decision-ready resource for students, researchers, practitioners, and regulatory authorities to navigate the opportunities and responsibilities of plant gene editing, with significant implications for sustainable agriculture and global food security.
The work unfolds in three parts: [i] a foundational survey of genome-editing technologies and the evolving role of AI in precise trait modifications and outcome prediction; [ii] a thorough exploration of applications and synergies, including AI-assisted gRNA optimization, off-target mitigation, regulatory-network analysis, and trait enhancement for disease resistance and climate resilience; and [iii] an emerging-horizons section on cis-regulatory edits, omics integration, synthetic biology, and next-generation editing.
Throughout, the volume interweaves practical experiences, cutting-edge methodologies, and case studies, alongside discussions of biosafety, ethical concerns, governance, and public perception, providing a holistic, decision-ready resource for students, researchers, practitioners, and regulatory authorities to navigate the opportunities and responsibilities of plant gene editing, with significant implications for sustainable agriculture and global food security.
Table of Contents
Part I. An introduction to gene editing technologies1. Gene editing technologies: A comprehensive overview
2. Revolution of CRISPR-Cas: Advancements in genome editing for agriculture
3. The CRISPR-Cas toolkit for gene editing in plants
4. CRISPR cargo delivery systems for intelligent plant genome engineering
5. Evolution of CRISPR technology, progress, and its future implications for crop improvement
6. Gene editing beyond food crops
7. Convergence of gene editing and AI: The future of gene editing in plants
8. From data to discovery: The role of AI in advancing gene editing
9. Machine learning approaches in gene editing
Part II. Applications and synergies of CRISPR and AI for plant gene editing
10. Practical design of gRNA: AI combined with CRISPR
11. AI for accurate prediction of on-target efficiency and minimization of off-targets in plants
12. AI for improved prediction of CRISPR repair outcomes
13. AI and CRISPR: studying gene functions and regulatory networks in plants
14. AI-driven gene editing for disease resistance in plants
15. Artificial intelligence tools for predicting off-targets in plant genome editing
16. AI and multiplex gene editing: The future of gene editing in plants
17. Artificial intelligence and CRISPR technologies for enhancing food security
18. Intelligent gene editing for stress tolerance in plants
19. AI-guided CRISPR in crop yield enhancement
20. AI-driven regulation of gene-edited plants
21. AI and CRISPR: Biosafety, governance, and public perception of gene-edited organisms
22. CRISPR meets AI: New frontiers in developing insect-resistant crops
Part III. Emerging horizons of CRISPR
23. Editing cis-regulatory elements to enhance desired traits in plants
24. AI integration with omics and CRISPR to decipher complex traits in plants
25. AI and next-generation gene editing tools
26. Future landscape of CRISPR and AI in plant gene editing
Authors
Aftab Ahmad Associate Professor, Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.Aftab Ahmad earned his PhD and completed postdoctoral research in plant molecular biology at the University of Shizuoka, Japan, under the prestigious 21st Century Center of Excellence Program. He also served as a Visiting Scientist in the Department of Plant Sciences at the University of California Davis, United States. With over a decade of teaching experience in biochemistry and molecular biology at the University of Agriculture, Faisalabad, Pakistan, Dr. Aftab now continues to advance plant genome editing research aimed at improving crop resilience and productivity at the Natural & Medical Sciences Research Center, University of Nizwa, Oman. He has published in leading international peer-reviewed journals such as Frontiers in Plant Science, Journal of Biomedical Science, Plant Molecular Biology Reporter, Journal of Cereal Science, Genetic Resources and Crop Evolution, and many more.
Baohong Zhang THCAS Distinguished Professor, Department of Biology, East Carolina University, Greenville, NC, USA. Baohong Zhang is a THCAS Distinguished Professor in the Department of Biology at East Carolina University and an internationally recognized leader in genomics and biotechnology. He earned his bachelor's degree in Plant Genetics and Breeding from China Agricultural University and his PhD in Environmental Toxicology from Texas Tech University. For over 20 years, Dr. Zhang has conducted pioneering research in transgenic technologies, genome editing, and functional genomics, supported by major funding agencies such as the NSF, NIH, DoD, and USDA, as well as industry partners including the North Carolina Biotechnology Center and DuPont. He is a prolific author, with several publications listed as Highly Cited Papers by the ISI Web of Science. He is Editor-in-Chief, Associate Editor, or Guest Editor for multiple international journals, including Functional & Integrative Genomics, Plants, Scientific Reports, Plant Biotechnology Journal, Molecular Biotechnology, Plant Molecular Biology, and Journal of Cotton Research. A Fellow of the American Association for the Advancement of Science, Dr. Zhang has received numerous honors, including more recently the ECU Achievement in International Research and Creative Activity Award (2017), the Cotton Researcher of the Year (2018), the Lifetime Achievement Research Award (2019), and the Cotton Biotechnology Award (2020). Kamel A. Abd-Elsalam Research Professor, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt. Kamel A. Abd-Elsalam is currently a research professor at the Plant Pathology Research Institute, Agricultural Research Center, Giza. He earned his PhD in molecular plant pathology through a joint program between Christian Albrechts University of Kiel, Germany, and Suez Canal University, Egypt, followed by a postdoctoral fellowship at Christian Albrechts University. His research focuses on nanobiotechnology applications in agriculture and plant protection, and he has authored numerous peer-reviewed articles and edited books with major international publishers. His scientific contributions have been recognized nationally and regionally, including awards from the Federation of Arab Scientific Research Councils for research excellence in biotechnology and the Egyptian State Award for Agricultural Scientific Excellence from the Academy of Scientific Research and Technology. He has been recognized among the world's top 2% most influential scientists in nanobiotechnology for three consecutive years (2021-2023), according to global rankings developed by Stanford University. Since 2019, he has served as the Editor-in-Chief of two Elsevier book series, Nanobiotechnology for Plant Protection and Genome Modified Plants and Microbes in Food and Agriculture. Ahmed Al-Harrasi Professor and Chair, Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman. Ahmed Al-Harrasi is the Vice Chancellor for Graduate Studies, Research, and External Relations and teaches organic chemistry at the University of Nizwa, Oman, where he also founded and chairs the Natural and Medical Sciences Research Center. He earned his BSc (1997) in Chemistry from Sultan Qaboos University, and his MSc (2002) and PhD (2005) in Organic Chemistry from the Free University of Berlin as a DAAD Fellow under the supervision of Prof. Hans-Ulrich Reissig. He later pursued postdoctoral research in chemical biology as a Fulbright Scholar at Cornell University, United States. A Fellow of the Royal Society of Chemistry and a member of UNESCO's International Basic Sciences Program, Professor Al-Harrasi has led over 40 funded research projects and is an accomplished and prolific author. His contributions to research have been widely recognized through the Order of Royal Commendation from His Majesty. He is also a recipient of the National Research Award from the Research Council of Oman. From 2019 to 2024, he has been consistently listed among the World's Top 2% of Scientists by Stanford University.
