Cisgenic Crops: Potential and Prospects

Description

This book is the first attempt for in-depth compilation of current knowledge on cisgenic crops and their  potential prospects as a sustainable substitute for the controversial genetically modified crops. Innovative methodologies for the development of cisgenic crops for disease resistance, improved nutritional contents, suitability for organic farming, survival under climate change, and their role in conservation of plant genetic resources have been highlighted. Combined with molecular markers and genome editing, an advanced approach for crop improvement is reported. The book has 14 chapters authored by globally leading experts on the subject. This book is useful to the students, teachers, researchers and policy planners working across the disciplines of classical plant breeding up to the recent genetically modified and genome edited crops. 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