Cisgenic Crops: Potential and Prospects

Preface
Contents
Contributors
1 The Origin of Cisgenesis, and Its Evolving Definition
1.1 Birth of the Concept of Cisgenesis in Two Interdisciplinary Groups
1.1.1 The Word ‘Cisgenesis’ Was Coined in 1999 in an Interdisciplinary Working Group of Dutch Scientists
1.1.2 An Interdisciplinary European Project Team Developed a ‘Cisgenic’ Strawberry
1.2 Cisgenesis and Intragenics
1.3 Stricter Definition of Cisgenesis
1.4 Cisgenesis and the European GMO Regulation
1.5 A Likely Future Direction: Allele Replacement
References
2 Cisgenesis: Enabling an Innovative Green Agriculture by Deploying Genes from the Breeders’ Gene Pool
2.1 Introduction
2.2 Traditional Breeding and the Bottle Neck of Linkage Drag
2.3 Genetic Modification of Crop Plants with Transgenes
2.3.1 Genetic Modification of Crop Plants with Cisgenes
2.4 Advantages of Cisgenesis in Breeding
2.4.1 Seed Propagation
2.4.2 Vegetative Propagation
2.5 The Case of Improving Potato
2.5.1 The Problem and Part of the Solution
2.5.2 Short History of Resistance Breeding Against Phytophthora Infestans
2.5.3 Jumping Back and Forth in 4x-2x-4x ploidy Levels
2.5.4 S Gene Derived Resistance to Phytophthora Infestans
2.5.5 Why Cisgenesis in Potato?
2.5.6 Cisgenic and Transgenic R Genes in Potato
2.5.7 Ins and Outs of Marker Free Transformation of Potato
2.5.8 Combination of Recessive and Dominant Resistance Genes
2.6 Conclusions and Perspectives
2.7 Annexes
References
3 Cisgenesis and Intragenesis: Innovative Tools for Crop Improvement
3.1 Introduction
3.2 Comparison of Cisgenesis, Intragenesis, Transgenesis and Conventional Breeding
3.2.1 Genetic Differences
3.2.2 Objectives
3.2.3 Consumer Attitudes
3.2.4 Scientific and Legislative Position
3.3 Application of Cisgenesis and Intragenesis in the Improvement of Crops
3.4 Legal Framework, Safety and Public Perception
3.5 Conclusion and Future Perspectives
References
4 Cis Genesis of Crops
4.1 Introduction
4.2 Examples of Cisgenesis Technology Used in Crops
4.2.1 Apple
4.2.2 Grapevines and Powdery Mildew Fungus Disease
4.3 Poplar
4.4 Potato
4.5 Barley and Other Crops
4.6 Public Perception, Consumer Acceptance and Government Regulation
4.7 The Potential of Cisgenesis for Organic Farming
4.8 Conclusions
References
5 Cisgenesis and Plant Breeding: A Review
5.1 Introduction
5.2 Evolution of Traditional Plant Breeding Techniques
5.3 Transgenic Selection Approach
5.4 Cisgenesis, a New Tool in Plant Breeding
5.5 Regulation of Cisgenic Plants
5.6 Closing Comments
References
6 Opportunities for Generic Cisgenic Crops
6.1 Introduction
6.2 Generic Biotechnology in Agriculture
6.2.1 Agbiogeneric and Off-Patent Events
6.3 Considerations for the Development Agbiogeneric Crops
6.4 Freedom to Operate Analysis
6.5 Technical Considerations
6.6 Regulatory Considerations in Colombia
6.7 Generic Biotechnology for Colombia
6.8 Current Status of Generic Crops
6.9 Cisgenic Commercial Crops
6.10 Late Blight-Resistant Potato as a Model Generic Cisgenic Crop
6.10.1 Late Blight in Potato
6.11 Late Blight Resistance: Conventional and Biotechnological Approaches
6.12 IP Evaluation of Commercial Cisgenic Potatoes
6.13 Gene Identification and FTO
6.14 Conclusions
References
7 Cisgenesis and Organic Farming
7.1 Introduction
7.2 Cisgenesis
7.2.1 Technique Classification Scheme
7.3 Organic Farming
7.3.1 Principles
7.3.2 Statements
7.3.3 Prehispanic Farming
7.3.4 Soil Preparation and Management
7.3.5 Sowing
7.3.6 Plague Insects and Diseases
7.3.7 Irrigation
7.3.8 Fertilizers
7.3.9 Ecological Management of Plagues
7.4 Discussion
7.4.1 Is Alternative Agriculture Profitable?
7.4.2 Organic Certification for Export
7.4.3 Marketing Organic Produce
7.5 Conclusions
References
8 Cisgenic Crops and Disease Resistance
8.1 Introduction
8.2 Cisgensis
8.3 Intragenesis
8.4 Need of Cisgenesis
8.5 Development of Cis/Intragenics: General Outline
8.6 Cisgenesis Versus Traditional Breeding
8.7 Breeding Crops for Disease Resistance
8.8 Cis/Intragenesis in Plant Disease Resistance
8.9 Conclusions
References
9 Cisgenesis and Intragenesis as a Biotechnological Tool to Improve Abiotic Stress Tolerance in Commercial Crops
9.1 How Global Warming is Stressing Plants Around the Globe
9.2 Conventional and Modern Biotechnology to Generate Abiotic Stress-Tolerant Crops
9.3 Cisgenesis and Intragenesis to Improve Abiotic Stress Tolerance in Commercially Relevant Crops
9.4 Intragenic and Cisgenic Crops Tolerant to Abiotic Stress
9.4.1 Proof of Concept for Cisgenic Grapevine Development
9.4.2 NCED Assessment for Improving Drought Tolerance in Vitis Vinifera
9.4.3 Drought-Tolerant Perennial Ryegrass
9.4.4 Alfalfa with Lower Lignin Content
9.5 Discussion
9.6 Conclusions and Future Perspectives
References
10 DNA Markers: An Essential Tool for Cis-genic Improvement of Rice
10.1 A Preamble on Use of DNA Markers in Rice Crop Improvement
10.2 A Glimpse into DNA Markers Used for Cis-genic Improvement of Rice
10.3 Marker-assisted Cis-genic Improvement of Rice
10.3.1 Development of Genetic Maps
10.3.2 Mapping of Genes
10.3.3 Synteny/Comparative Mapping
10.3.4 A Progeny Selection in Backcross Breeding and Gene Pyramiding
10.3.5 Genetic Diversity Assessment and Parental Selection in Rice Breeding
10.3.6 Seed Purity Testing
10.4 Limitations to Adoption of DNA Marker Technologies for Rice Cis-genic Improvement and the Way Forward
10.4.1 Technology and Resource Limitations
10.4.2 Lack of Skilled Personnel
10.4.3 Lack of Diversity or Restricted Access to Germplasm
10.4.4 Poor Marker-Trait Association and Unavailability of ‘Ideal’ DNA Markers
10.4.5 Social Unawareness of DNA Marker Work
10.5 Conclusions
References
11 Cisgenic Crops: Major Strategies to Create Cisgenic Plants Based on Genome Editing
11.1 Introduction
11.1.1 Brief History of Genetically Modified Organisms (GMOs)
11.1.2 Transgenic Plants
11.1.3 Legislations of Transgenic and Edited Crops
11.2 Cisgenesis, Intragenesis and Genome Editing
11.2.1 Cisgenesis and Intragenesis
11.2.2 Plant Genome Editing
11.3 Examples of Genome Editing Techniques
11.3.1 Oligonucleotide-Directed Mutagenesis (ODM)
11.3.2 Genome Editing with Engineered Nucleases
11.4 Methods to Generate Cisgenic Plants
11.4.1 Transformation Without Selection
11.4.2 Site-Specific Recombination
11.4.3 Co-transformation
11.5 Cisgenic Crops
11.6 Development of Cisgenic Crops Based on Genome Editing
11.6.1 Gene Replacement and TR-HDR
11.6.2 Prime Editing
11.6.3 Complex Trait Locus (CTL) Approach
11.7 Safety of Cisgenic Plants
11.8 Perspectives
References
12 Cisgenesis and Genome Editing: A Combined Approach for Improved Plant Breeding
12.1 Introduction
12.2 Plant Breeding in Agricultural Productivity
12.3 Genetic Modifications of Conventional Plant Breeding Techniques
12.4 Molecular Genetics and Genomics in Plant Breeding
12.5 New Agricultural Biotechnology Techniques
12.6 Cisgenesis: A New Plant Breeding Technique for Crop Improvement
12.6.1 Cisgenesis Versus Conventional Plant Breeding
12.6.2 Cisgenesis Versus Transgenesis
12.7 Genome Editing: Alterations of Specific Nucleotide Sequences to Modify the Genetic Materials in Crop
12.8 Genome Editing in Crop Improvement
12.9 Cisgenesis and Genome Editing: A Combined Approach for Speed and Smart Breeding
12.10 Conclusions
References
13 Cisgenesis in the Era of Genome Editing and Modern Plant Biotechnology
13.1 Introduction
13.2 Cisgenesis and Intragenesis
13.3 Crop Improvement Through Cisgenesis and Intragenesis
13.4 Genome Editing Approach for Creation of Cisgenic Plants
13.4.1 Meganucleases
13.4.2 Zinc-Finger Nucleases
13.4.3 TALENs
13.4.4 CRISPR/Cas System
13.4.5 CRISPR_Cpf1 or CRISPR_Cas12a
13.4.6 Promoter Engineering
13.5 Removal of the Selection Marker
13.6 Haploid Induction and Use of Genome Editing for Cisgenesis
13.7 Safety and Regulation
13.8 Conclusions
References
14 The Application of the Bioinformatic, Biotechnological, Agronomic, and Genetic Improvement Tools Can Help to Develop Plant Species in Less Time, and with Better Characteristics
14.1 Introduction
14.2 Cis and Transgenesis Differences
14.3 Bioinformatics Tools Approach
14.3.1 The Approach
14.3.2 Approach Description (Pipeline)
14.3.3 Data Bases
14.3.4 Softwares, Models, and Algorithms
14.4 Conclusions
References