CRISPRized Horticulture Crops

Genome Modified Plants and Microbes in Food and Agriculture

1st Edition - March 19, 2024
Editors: Kamel A Abd-Elsalam, Aftab Ahmad, Baohong Zhang
Language: English
Paperback ISBN:
9 7 8 - 0 - 4 4 3 - 1 3 2 2 9 - 2
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 1 3 2 3 0 - 8

CRISPRized Horticultural Crops: Genome Modified Plants and Microbes in Food and Agriculture summarizes applications of CRISPR/Cas systems and its advanced variants e.g., CRISPR/Cp… Read more

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CRISPRized Horticultural Crops: Genome Modified Plants and Microbes in Food and Agriculture summarizes applications of CRISPR/Cas systems and its advanced variants e.g., CRISPR/Cpf1, base editing and prime editing, for precise editing of horticultural crops. The book discusses vector transformations methods, epi-genome, deep learning, synthetic biology, and precision breeding for improving yield and quality related attributes in horticultural crops. With coverage of the relevant technologies and their applications, the book also includes bioinformatics and large-scale databases and their potential application in fruits, vegetables and ornamental plants and sections on regulatory concerns related to CRISPR edited crops.

Horticultural crops, including fruit, vegetable and ornamental plants are an important component of agriculture production systems and play an important role in sustaining human life.

Cover image
Title page
Copyright
Contents
Contributors
Editor’s Biography
Series Preface
Preface
Section I The CRISPR/Cas toolkit for horticultural crops
CHAPTER 1 CRISPRized fruit, vegetable, and ornamental crops: A note from editors
1.1 Introduction
1.2 What are genome-editing techniques?
1.3 CRISPR: a revolutionary technique for genetic improvement of plants
1.4 Accelerating horticultural plant domestication
1.5 Challenges
1.6 Conclusion
References
CHAPTER 2 Evolution of genome editing technologies
2.1 Introduction
2.2 DNA repairs system: a key in developing genome editing tools
2.3 The rise of the genome editing era
2.4 Advances in genome editing era
2.5 Applications of gene editing technologies in agriculture
2.6 Application of gene editing technologies in horticulture crops
2.7 Conclusion and future prospect
References
CHAPTER 3 CRISPR-Cas: Effectors, mechanism, and classification
3.1 Introduction
3.2 Objectives
3.3 CRISPR-Cas9; from adoptive immunity to gene editing tool
3.4 CRISPR-Cas9 system structure
3.5 CRISPR-Cas system working principle
3.6 Approaches for the classification of CRISPR-Cas system
3.7 Classification of CRISPR-Cas systems
3.8 Distribution of CRISPR-Cas system
3.9 Core and ancillary Cas genes
3.10 Origin and evolution of CRISPR-Cas9
3.11 Anti-CRISPR defense
3.12 Conclusion
References
CHAPTER 4 Bioinformatics tools and databases in genome editing for plants
4.1 Introduction
4.2 Mechanism of genome editing techniques
4.4 gRNA designing process: a brief overview
4.5 Bioinformatics tools for designing gRNA
4.6 gRNA design tools: plant-specific databases
4.7 Challenges and future prospects
4.8 Conclusion
References
CHAPTER 5 CRISPR workflow solutions: Cargos and versatile delivery platforms in genome editing
5.1 Introduction
5.2 CRISPR delivery formats
5.3 Viral-mediated CRISPR delivery
5.4 Nonviral and chemical based CRISPR delivery methods
5.5 Physical delivery methods
5.6 Delivery of CRISPR-Cas systems in plants
5.7 Future outlooks in CRISPR-Cas system delivery
References
CHAPTER 6 CRISPR-based techniques and their application in plants
6.1 Introduction
6.2 Components and basic structure of the CRISPR-Cas system
6.3 CRISPR-Cas system classification
6.4 CRISPR-Cas system applications
6.5 Application of the CRISPR tool in plants
6.6 Plant genome editing
6.7 Applications of the CRISPR-Cas system in plants
6.8 Limitations of gene editing using CRISPR-Cas in plants
6.9 Conclusion and future prospects
Acknowledgment
References
CHAPTER 7 Base editing and prime editing in horticulture crops: Potential applications, challenges, and prospects
7.1 Introduction
7.2 Base editor
7.3 Prime editing
7.4 Edits for important agronomic characteristics
7.5 Challenges and future prospects
7.6 Conclusion
References
CHAPTER 8 Multiplex genome editing in plants through CRISPR-Cas
8.1 Introduction
8.2 CRISPR-Cas9: a powerful approach for multiplex gene editing
8.3 Strategies of multiplex gene editing: unlocking the power of precise genetic modifications
8.4 Multiplex gene editing: reshaping the crop genetic improvement
8.5 Applications of multiplex gene editing
8.6 Tackling complexity: insights and challenges of multiplex genome editing
8.7 Conclusion and future prospects
References
CHAPTER 9 CRISPR-Cas technologies for food and nutritional security
9.1 Introduction
9.2 History of CRISPR
9.3 Development of biofortified crops employing CRISPR-Cas mechanism
9.4 A breakthrough in editing a plant genome
9.5 Expanding the CRISPR-Cas editing toolkit
9.6 Recent frontiers in the CRISPR-Cas system
9.7 CRISPR-Cas for abiotic stresses
9.8 Targeting structural and regulatory genes
9.9 Application of CRISPR-Cas against abiotic stresses
9.10 Stress resilience crops for improved agricultural yield
9.11 Challenges and future prospects
9.12 Conclusion
References
Section II CRISPR mediated genome editing in horticultural crops
CHAPTER 10 CRISPR-Cas9 genome editing of crops: Food and nutritional security
10.1 Introduction
10.2 Components of CRISPR-Cas9 toolbox
10.3 Process of genome editing via CRISPR-Cas9
10.4 Genomics of produced crops
10.5 Human exposure and public acceptance of the CRISPR-Cas9 system
10.6 CRISPR-mediated genome modification for food security
10.7 Regulatory landscape of genome-modified crops
10.8 Applications of the CRISPR-Cas9 toolbox
10.9 Challenges pertaining to genome-modification and editing
10.10 Conclusion and future prospects
Acknowledgment
References
CHAPTER 11 CRISPR-based precision breeding of fruits, vegetables, and ornamental plants
11.1 Introduction
11.2 CRISPR-Cas system
11.3 CRISPR-Cas applications for crop improvement
11.4 CRISPRized vegetable crops
11.5 CRISPRized fruit crops
11.6 CRISPRized ornamental crops
11.7 Conclusions and future perspectives
References
CHAPTER 12 Deep learning for genomics and epi-genomics in horticulture crops improvement
12.1 Introduction
12.2 Common deep learning algorithms
12.3 Deep learning in genomics
12.4 Deep learning for genomics in horticultural crop improvement
12.5 Epigenetic interactions in plants
12.6 Epigenomic practices in crop improvement
12.7 Deep learning approaches to investigate epigenomic effects on plants
12.8 Applications of deep-learning approaches in horticulture crops improvement
12.9 Conclusion and future prospects
References
CHAPTER 13 Plant modification techniques in horticulture and DNA-free CRISPR-based genome editing in plants
13.1 Introduction
13.2 Plant transformation
13.3 Transformation methods
13.4 Transformation in horticultural crops
13.5 Genome editing technology
13.6 Application and current status of genome editing in plants
13.7 Limitations and future prospects
13.8 Conclusion
References
CHAPTER 14 CRISPR vegetables: Challenges and opportunities
14.1 Introduction
14.2 Brief overview of the CRISPR-Cas9 system and its advancement
14.3 CRISPR-Cas9-based gene editing technology: opportunities for improving vegetable crops
14.4 Challenges associated with the application of CRISPR-Cas in vegetable crops
14.5 The CRISPR-Cas system's ethical implications
14.6 Intellectual property (IP) and regulatory frameworks
14.7 Future scope
14.8 Conclusion
Acknowledgment
References
CHAPTER 15 CRISPR-Cas-mediated genome editing in tomatoes and potatoes
15.1 Introduction
15.2 CRISPR-Cas system
15.3 Delivery methods
15.4 Functional studies
15.5 Biotic factors
15.6 Abiotic stresses
15.7 Ripening and shelf life
15.8 Quality improvement
15.9 Self-incompatibility in potatoes
15.10 Conclusion
References
CHAPTER 16 Gene editing with CRISPR in root and tuber crops
16.1 Introduction
16.2 Applications of CRISPR-Cas9 technology in major root and tuber crops
16.3 Conclusion and Future Prospects
References
CHAPTER 17 Improvement of ornamental plants through CRISPR-Cas
17.1 Introduction
17.2 Genetic engineering and manipulation strategy
17.3 CRISPR-Cas system
17.4 Classification of CRISPR-Cas system and its mode of action
17.5 CRISPR-Cas-9 complex transduction mechanism
17.6 Recently improved traits of ornamental plants using genome editing
17.7 Genetic engineering for stress tolerance in ornamental plants
17.8 Postharvesting and genetic engineering
17.9 Genome editing in ornamental plants
17.10 Conclusion and future prospects
References
CHAPTER 18 CRISPR-Cas9 technology for enhancement of fruit quality
18.1 Introduction
18.2 CRISPR-Cas system overview
18.3 Overview of genome editing in fruit crops
18.4 Opportunities and future challenges of fruit quality enhancement
18.5 Conclusion and future prospects
References
CHAPTER 19 CRISPR-Cas9 systems for the improvement of solanaceous vegetable crops
19.1 Introduction
19.2 Solanaceous crops
19.3 Interaction of solanaceous crops with the challenging environment
19.4 Genetic and genomic resources for solanaceous crop improvement
19.5 Genome editing by sequence-specific nucleases
19.6 Application of CRISPR-Cas9 in solanaceous vegetable crops
19.7 Other horticultural crops employing CRISPR-Cas9
19.8 Challenges of CRISPR-Cas9 genome editing
19.9 Future of genome editing in horticultural crops
19.10 Conclusion and future prospects
References
CHAPTER 20 Gene editing for abiotic stress resistance in horticultural crops
20.1 Introduction
20.2 Genome modifying system
20.3 Tolerance for drought in crops
20.4 Tolerance for salinity in crops
20.5 Tolerance of heat stress in crops
20.6 Tolerance of cold stress in crops
20.7 Tolerance for soil toxicity and heavy metals
20.8 Conclusion and future prospects
References
CHAPTER 21 Editing of banana, apple, and grapevine genomes using the CRISPR-Cas9 system
21.1 Introduction
21.2 New breeding technologies
21.3 CRISPR-Cas9-mediated genome editing in apple
21.4 CRISPR-Cas9-mediated genome editing in banana
21.5 CRISPR-Cas9-mediated genome editing in grapevine
21.6 Conclusion and future prospects
References
CHAPTER 22 CRISPR applications in medicinal and aromatic plants
22.1 Introduction
22.2 CRISPR-Cas research with a historical perspective
22.3 The working mechanism of CRISPR-Cas
22.4 Application of CRISPR-Cas in medicinal and aromatic plants
22.5 Utilization in Salvia miltiorrhiza
22.6 Utilization in Dendrobium officinale
22.7 Utilization in Symphytum officinale L
22.8 Utilization in Cannabis sativa
22.9 Utilization in Camelina sativa
22.10 Utilization in Citrus sinensis
22.11 Potential applications of CRISPR in improving the quality of medicinal plants
22.12 CRISPR-Cas system limitations
22.13 Conclusion and future prospects
References
CHAPTER 23 CRISPR edited floriculture crops: A revolutionary technique to increase flower production, their color and longevity
23.1 Introduction
23.2 CRISPR-Cas in floriculture
23.3 Economic importance of floriculture plants-floral status in the market
23.4 Biosynthetic pathways
23.5 Current status of genetic engineering in floriculture plants
23.6 Breeding techniques to enhance floral fragrances
23.7 Enhancing flower scents using genetic engineering
23.8 Development of new breeding techniques in floriculture
23.9 Molecular markers
23.10 Genomics
23.11 Development of transgenics
23.12 Regulation
23.13 Conclusion and future prospects
References
CHAPTER 24 CRISPR genome editing of woody trees: Current status and future prospects
24.1 Introduction
24.2 Major platforms for genome editing in woody trees
24.3 Recent developments in CRISPR genome editing of woody trees
24.4 Current challenges
24.5 Conclusion and future prospects
Acknowledgment
References
Section III Regulation and commercialization of CRISPR edited crops
CHAPTER 25 Regulatory, ethical, social, and biosafety concerns in genome-edited horticultural crops
25.1 Introduction
25.2 Recent developments in CRISPR-Cas
25.3 CRISPR-Cas-mediated gene editing in plants
25.4 Regulatory classification of CRISPR based modifications
25.5 How CRISPR crops are different from conventional GMOs
25.6 Transgene-free CRISPR crops
25.7 Potential risks associated with CRISPR crops
25.8 Regulatory triggers of CRISPR crops
25.9 Deregulation of CRISPR crops
25.10 Global regulatory oversights of CRISPR crops
25.11 Biosafety concerns of CRISPR
25.12 Social concerns
25.13 Ethical concerns
25.14 Conclusion
References
CHAPTER 26 Regulatory, ethical, and social aspects of CRISPR crops
26.1 Introduction
26.2 Techniques involved in genome editing techniques
26.3 CRISPR-Cas reagents and their cargos
26.4 Methods of transplantation in plants
26.5 Site-directed nuclease systems
26.6 Battle of triggers
26.7 Regulations for plants with novel traits
26.8 Regulatory impacts on innovation and international trade
26.9 Concerns associated with GeneEd crops
26.10 Biosafety and regulation of genetically modified plants only heading
26.11 International considerations
26.12 Public acceptance and social concerns of genetically modified organisms
26.13 Genome-edited crops and ethical values
26.14 Economic issues
26.15 Research governance
26.16 What CRISPR crop developer to focus on for public trust?
26.17 Conclusion
References
CHAPTER 27 Commercialization of CRISPR-edited crops: Opportunities and challenges
27.1 Introduction
27.2 CRISPR-Cas systems deployed for crop improvement
27.3 Commercialization of CRISPR-Cas crops
27.4 Conclusion
Acknowledgment
References
CHAPTER 28 Global patent landscape in CRISPR-Cas
28.1 Introduction
28.2 Developments in CRISPR-Cas systems: An overview
28.3 Applications of CRISPR-Cas systems
28.4 CRISPR patent process
28.5 A brief guide to the global patent landscape in CRISPR
28.6 Trends in CRISPR commercialization and product development
28.7 Conclusion and future prospects
References
CHAPTER 29 Biosafety and biosecurity consideration in CRISPR-Cas
29.1 Introduction
29.2 CRISPR-Cas potential of harm
29.3 Natural exposure to CRISPR-Cas
29.4 Biosafety and biosecurity challenges
29.5 Biosafety and CRISPR-Cas
29.6 Biosecurity and CRISPR-Cas
29.7 Recommendations/measurements
29.8 Conclusion
References
Index

Kamel A Abd-Elsalam

Prof. Kamel A. Abd-Elsalam, Ph.D., is currently a research professor at the Plant Pathology Research Institute, Agricultural Research Center, Giza. Kamel earned his Ph.D. in Molecular Plant Pathology from Christian Alberchts University of Kiel (Germany) and Suez Canal University (Egypt). Dr. Kamel’s research interests include developing, improving, and deploying plant biosecurity diagnostic tools; understanding and exploiting fungal pathogen genomes; and developing eco-friendly hybrid nanomaterials for controlling toxicogenic fungi, plant diseases, and agroecosystems applications. He published 20 books related to nano-biotechnology applications in agriculture and plant protection. Since 2019, he has served as the Editor-in-Chief of the Elsevier book series “Nanobiotechnology for Plant Protection.” He also serves as the Series Editor of the Elsevier book series “Genome Modified Plants and Microbes in Food and Agriculture.”

Affiliations and expertise

Molecular Plant Pathologist, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt

Aftab Ahmad

Dr Aftab Ahmad is currently working as Assistant Professor at Department of Biochemistry/ US-Pakistan Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad (UAF), Pakistan. Dr Aftab’s research interests include developing virus resistant and salt tolerant plants using CRISPR/Cas technology. He has published more than 15 research articles in international peer reviewed journals including Journal of Biomedical Sciences, Scientific Reports-Nature, PLOS One, Journal of Translational Medicine, Plant Molecular Biology Reporter, Molecules, Journal of Cereal Science, and Genetic Resources and Crop Evolution. Dr Aftab pursued his PhD and postdocs in Plant Molecular Biology from University of Shizuoka, Japan under Center of Excellence (COE, 21st Century) program. Dr Aftab also served as visiting scientist in department of plant sciences, University of California, Davis, USA. Dr Aftab has been teaching biochemistry and molecular biology at UAF and his research focuses in the area of CRISPR/Cas based genome editing in plants.

Affiliations and expertise

Biochemistry/Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, Pakistan

Baohong Zhang

Dr. Baohong Zhang is a full Professor at East Carolina University. His major research interest is on plant genetics and genomics with a focus on epigenetics and small RNA regulation. Dr. Zhang has developed a somatic embryogenesis and plant regeneration system for cotton tissue culture and transgenics; based on this, he also developed a system for CRISPR/Cas9 genome editing in cotton. He has published more than 200 papers with more than 9000 citations. During the past 20 years of his research and teaching, Dr. Zhang has been promoting genomics and biotechnology through research and education for a diversity of people. He has served on a various editorial boards of international journals and served as reviewers for more than 100 peer-reviewed journals as well as review panels for more than 30 national and international funding agencies. Dr. Zhang has delivered many keynote and/or invited lectures at different institutes and international conferences.

Affiliations and expertise

Full Professor, East Carolina University, Greenville, NC, USA

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CRISPRized Horticulture Crops

Genome Modified Plants and Microbes in Food and Agriculture

Purchase options

Institutional subscription on ScienceDirect

Kamel A Abd-Elsalam

Aftab Ahmad

Baohong Zhang