Plant Biotechnology and Genetics

C. Neal Stewart Jr. PhD, holds the Racheff Chair of Excellence in Plant Molecular Genetics and is a Professor in the Department of Plant Sciences at the University of Tennessee, Knoxville. Dr. Stewart serves on the editorial boards of BMC Biotechnology, Sensors, and Trends in Plant Science, and is an Associate Editor for In Vitro Developmental and Cellular Biology - Plant.

Preface. Foreword to Plant Biotechnology and Genetics. Contributors. 1. Plant Agriculture: The Impact of Biotechnology ( Graham Brookes ). 1.0 Chapter Summary and Objectives. 1.0.1 Summary. 1.0.2 Discussion Questions. 1.1 Introduction. 1.2 Biotechnology Crops Plantings. 1.3 Why Farmers Use Biotech Crops. 1.3.1 Herbicide-Tolerant Crops. 1.3.2 Insect-Resistant Crops. 1.3.3 Conclusion. 1.4 How the Adoption of Plant Biotechnology Has Impacted the Environment. 1.4.1 Environmental Impacts from Changes in Insecticide and Herbicide Use. 1.4.2 Impact on Greenhouse Gas (GHG) Emissions. 1.5 Conclusions. References. 2. Mendelian Genetics and Plant Reproduction ( Matthew D. Halfhill and Suzanne I. Warwick ). 2.0 Chapter Summary and Objectives. 2.0.1 Summary. 2.0.2 Discussion Questions. 2.1 Genetics Overview. 2.2 Mendelian Genetics. 2.2.1 Law of Segregation. 2.2.2 Law of Independent Assortment. 2.3 Mitosis and Meiosis. 2.3.1 Mitosis. 2.3.2 Meiosis. 2.3.3 Recombination. 2.3.4 Cytogenetic Analysis. 2.4 Plant Reproductive Biology. 2.4.1 History of Research. 2.4.2 Mating Systems. 2.4.2.1 Sexual Reproduction. 2.4.2.2 Asexual Reproduction. 2.4.2.3 Mating Systems Summary. 2.4.3 Hybridization and Polyploidy. 2.5 Conclusion. References. 3. Plant Breeding ( Nicholas A. Tinker ). 3.0 Chapter Summary and Objectives. 3.0.1 Summary. 3.0.2 Discussion Questions. 3.1 Introduction. 3.2 Central Concepts in Plant Breeding. 3.2.1 Simple versus Complex Inheritance. 3.2.2 Phenotype versus Genotype. 3.2.3 Mating Systems, Varieties, Landraces, and Pure Lines. 3.2.4 Other Topics in Population and Quantitative Genetics. 3.2.5 The Value of a Plant Variety Depends on Many Traits. 3.2.6 Varieties Must Be Adapted to Environments. 3.2.7 Plant Breeding Is a Numbers Game. 3.2.8 Plant Breeding Is an Iterative and Collaborative Process. 3.2.9 Diversity, Adaptation, and Ideotypes. 3.2.10 Other Considerations. 3.3 Objectives for Plant Breeding. 3.4 Methods of Plant Breeding. 3.4.1 Methods of Hybridization. 3.4.1.1 Self-Pollinated Species. 3.4.1.2 Outcrossing Species. 3.4.1.3 Synthetic Varieties. 3.4.1.4 Hybrid Varieties. 3.4.2 Clonally Propagated Species. 3.5 Breeding Enhancements. 3.5.1 Doubled Haploidy. 3.5.2 Marker-Assisted Selection. 3.5.3 Mutation Breeding. 3.5.4 Apomixis. 3.6 Conclusions. References. 4. Plant Development and Physiology ( Glenda E. Gillaspy ). 4.0 Chapter Summary and Objectives. 4.0.1 Summary. 4.0.2 Discussion Questions. 4.1 Plant Anatomy and Morphology. 4.2 Embryogenesis and Seed Germination. 4.2.1 Gametogenesis. 4.2.2 Fertilization. 4.2.3 Fruit Development. 4.2.4 Embryogenesis. 4.2.5 Seed Germination. 4.2.6 Photomorphogenesis. 4.3 Meristems. 4.3.1 Shoot Apical Meristem. 4.3.2 Root Apical Meristem and Root Development. 4.4 Leaf Development. 4.4.1 Leaf Structure. 4.4.2 Leaf Development Patterns. 4.5 Flower Development. 4.5.1 Floral Evocation. 4.5.2 Floral Organ Identity and the ABC Model. 4.6 Hormone Physiology and Signal Transduction. 4.6.1 Seven Plant Hormones and Their Actions. 4.6.2 Plant Hormone Signal Transduction. 4.6.2.1 Auxin and GA Signaling. 4.6.2.2 Cytokinin and Ethylene Signaling. 4.6.2.3 Brassinosteroid Signal Transduction. 4.7 Conclusions. References. 5. Tissue Culture: The Manipulation of Plant Development ( Vinitha Cardoza ). 5.0 Chapter Summary and Objectives. 5.0.1 Summary. 5.0.2 Discussion Questions. 5.1 Introduction. 5.2 History. 5.3 Media and Culture Conditions. 5.3.1 Basal Media. 5.3.2 Growth Regulators. 5.4 Sterile Technique. 5.4.1 Clean Equipment. 5.4.2 Surface Sterilization of Explants. 5.5 Culture Conditions and Vessels. 5.6 Culture Types and Their Uses. 5.6.1 Callus Culture. 5.6.1.1 Somaclonal Variation. 5.6.2 Cell Suspension Culture. 5.6.2.1 Production of Secondary Metabolites and Recombinant Proteins Using Cell Culture. 5.6.3 Anther/Microspore Culture. 5.6.4 Protoplast Culture. 5.6.4.1 Somatic Hybridization. 5.6.5 Embryo Culture. 5.6.6 Meristem Culture. 5.7 Regeneration Methods of Plants in Culture. 5.7.1 Organogenesis. 5.7.1.1 Indirect Organogenesis. 5.7.1.2 Direct Organogenesis. 5.7.2 Somatic Embryogenesis. 5.7.2.1 Synthetic Seeds. 5.8 Rooting of Shoots. 5.9 Acclimation. 5.10 Conclusions. Acknowledgments. References. 6. Molecular Genetics of Gene Expression ( Maria Gallo and Alison K. Flynn ). 6.0 Chapter Summary and Objectives. 6.0.1 Summary. 6.0.2 Discussion Questions. 6.1 The gene. 6.1.1 DNA Coding for a Protein via the Gene. 6.1.2 DNA as a Polynucleotide. 6.2 DNA Packaging into Eukaryotic Chromosomes. 6.3 Transcription. 6.3.1 Transcription of DNA to Produce Messenger RNA (mRNA). 6.3.2 Transcription Factors. 6.3.3 Coordinated Regulation of Gene Expression. 6.3.4 Chromatin as an Important Regulator of Transcription. 6.3.5 Regulation of Gene Expression by DNA Methylation. 6.3.6 Processing to Produce Mature mRNA. 6.4 Translation. 6.4.1 Initiation of Translation. 6.4.2 Translation Elongation. 6.4.3 Translation Termination. 6.5 Protein Postranslational Modification. References. 7. Recombinant DNA, Vector Design, and Construction ( Mark D. Curtis ). 7.0 Chapter Summary and Objectives. 7.0.1 Summary. 7.0.2 Discussion Questions. 7.1 DNA Modification. 7.2 DNA Vectors. 7.2.1 DNA Vectors for Plant Transformation. 7.2.2 Components for Efficient Gene Expression in Plants. 7.3 Greater Demands Lead to Innovation. 7.3.1 Site-Specific DNA Recombination. 7.3.1.1 Gateway Cloning. 7.3.1.2 CreatorTM Cloning. 7.3.1.3 Univector (EchoTM) Cloning. 7.4 Vector Design. 7.4.1 Vectors for High-Throughput Functional Analysis. 7.4.2 Vectors for RNA Interference (RNAi). 7.4.3 Expression Vectors. 7.4.4 Vectors for Promoter Analysis. 7.4.5 Vectors Derived from Plant Sequences. 7.4.6 Vectors for Multigenic Traits. 7.5 Targeted Transgene Insertions. 7.6 Safety Features in Vector Design. 7.7 Prospects. References. 8. Genes and Traits of Interest for Transgenic Plants ( Kenneth L. Korth ). 8.0 Chapter Summary and Objectives. 8.0.1 Summary. 8.0.2 Discussion Questions. 8.1 Introduction. 8.2 Identifying Genes of Interest via Genomic Studies. 8.3 Traits for Improved Crop Production. 8.3.1 Herbicide Resistance. 8.3.2 Insect Resistance. 8.3.3 Pathogen Resistance. 8.4 Traits for Improved Products and Food Quality. 8.4.1 Nutritional Improvements. 8.4.2 Modified Plant Oils. 8.4.3 Pharmaceutical Products. 8.4.4 Biofuels. 8.5 Conclusions. References. 9. Marker Genes and Promoters ( Brian Miki) . 9.0 Chapter Summary and Objectives. 9.0.1 Summary. 9.0.2 Discussion Questions. 9.1 Introduction. 9.2 Definition of Marker Genes. 9.2.1 Selectable Marker Genes: An Introduction. 9.2.2 Reporter Genes: An Introduction. 9.3 Promoters. 9.4 Selectable Marker Genes. 9.4.1 Conditional Positive Selectable Marker Gene Systems. 9.4.1.1 Selection on Antibiotics. 9.4.1.2 Selection on Herbicides. 9.4.1.3 Selection Using Nontoxic Metabolic Substrates. 9.4.2 Nonconditional Positive Selection Systems. 9.4.3 Conditional Negative Selection Systems. 9.4.4 Nonconditional Negative Selection Systems. 9.5 Nonselectable Marker Genes or Reporter Genes. 9.5.1 b-Glucuronidase. 9.5.2 Luciferase. 9.5.3 Green Fluorescent Protein. 9.6 Marker-Free Strategies. 9.7 Conclusions. References. 10. Transgenic Plant Production ( John Finer and Taniya Dhillon ). 10.0 Chapter Summary and Objectives. 10.0.1 Summary. 10.0.2 Discussion Questions. 10.1 Overview. 10.2 Basic Components for Successful Gene Transfer to Plant Cells. 10.2.1 Visualizing the General Transformation Process. 10.2.2 DNA Delivery. 10.2.3 Target Tissue Status. 10.2.4 Selection and Regeneration. 10.3 Agrobacterium. 10.3.1 History of Our Knowledge of Agrobacterium. 10.3.2 Use of the T-DNA Transfer Process for Transformation. 10.3.3 Optimizing Delivery and Broadening the Range of Targets. 10.3.4 Agroinfiltration. 10.3.5 Arabidopsis Floral Dip. 10.4 Particle Bombardment. 10.4.1 History of Particle Bombardment. 10.4.2 The Fate of Introduced DNA. 10.4.3 The Power and Problems of Direct DNA Introduction. 10.4.4 Improvements in Transgene Expression. 10.5 Other Methods. 10.5.1 The Need for Additional Technologies. 10.5.2 Protoplasts. 10.5.3 Whole-Tissue Electroporation. 10.5.4 Silicon Carbide Whiskers. 10.5.5 Viral Vectors. 10.5.6 Laser Micropuncture. 10.5.7 Nanofiber Arrays. 10.6 The Rush to Publish. 10.6.1 Controversial Reports of Plant Transformation. 10.6.1.1 DNA Uptake in Pollen. 10.6.1.2 Agrobacterium-Mediated Transformation of Maize Seedlings. 10.6.1.3 Pollen Tube Pathway. 10.6.1.4 Rye Floral Tiller Injection. 10.6.1.5 Electrotransformation of Germinating Pollen Grain. 10.6.1.6 Medicago Transformation via Seedling Infiltration. 10.6.2 Criteria to Consider: Whether My Plant Is Transgenic. 10.6.2.1 Resistance Genes. 10.6.2.2 Marker Genes. 10.6.2.3 Transgene DNA. 10.7 A Look to the Future. References. 11. Transgenic Plant Analysis ( Janice Zale ). 11.0 Chapter Summary and Objectives. 11.0.1 Summary. 11.0.2 Discussion Questions. 11.1 Introduction. 11.2 Directionally Named Analyses: As the Compass Turns. 11.3 Initial Screens: Putative Transgenic Plants. 11.3.1 Screens on Selection Media. 11.3.2 Polymerase Chain Reaction. 11.3.3 Enzyme-Linked Immunosorbent Assays (ELISAs). 11.4 Definitive Molecular Characterization. 11.4.1 Intact Transgene Integration. 11.4.2 Determining the Presence of Intact Transgenes or Constructs. 11.4.3 Transgene Expression: Transcription. 11.4.3.1 Northern Blot Analysis. 11.4.3.2 Quantitative Real-Time Reverse Transcriptase (RT)-PCR. 11.4.4 Transgene Expression: Translation: Western Blot Analyses. 11.5 Digital Imaging. 11.6 Phenotypic Analysis. 11.7 Conclusions. References. 12. Regulations and Biosafety ( Alan McHughen ). 12.0 Chapter Summary and Objectives. 12.0.1 Summary. 12.0.2 Discussion Questions. 12.1 Introduction. 12.2 History of Genetic Engineering and its Regulation. 12.3 Regulation of GE. 12.3.1 United States. 12.3.1.1 USDA. 12.3.1.2 FDA. 12.3.1.3 EPA. 12.3.2 EU. 12.3.3 Canada. 12.3.4 International Perspectives. 12.4 Conclusions. References. 13. Field Testing of Transgenic Plants ( Detlef Bartsch, Achim Gathmann, Christiane Saeglitz, and Arti Sinha ). 13.0 Chapter Summary and Objectives. 13.0.1 Summary. 13.0.2 Discussion Questions. 13.1 Introduction. 13.2 Environmental Risk Assessment (Era) Process. 13.2.1 Initial Evaluation (ERA Step 1). 13.2.2 Problem Formulation (ERA Step 2). 13.2.3 Controlled Experiments and Gathering of Information(ERA Step 3). 13.2.4 Risk Evaluation (ERA Step 4). 13.2.5 Progression through a Tiered Risk Assessment. 13.3 An Example Risk Assessment: The Case of Bt Maize. 13.3.1 Effect of Bt Maize Pollen on Nontarget Caterpillars. 13.3.2 Statistical Analysis and Relevance for Predicting Potential Adverse Effects on Butterflies. 13.4 Proof of Safety versus Proof of Hazard. 13.5 Proof of Benefits: Agronomic Performance. 13.6 Conclusions. References. 14. Intellectual Property in Agricultural Biotechnology: Strategies for Open Access ( Alan B. Bennett, Cecilia Chi-Ham, Gregory Graff, and Sara Boettiger ). 14.0 Chapter Summary and Objectives. 14.0.1 Summary. 14.0.2 Discussion Questions. 14.1 Introduction. 14.2 Intellectual Property Defined. 14.3 Intellectual Property in Relation to Agricultural Research. 14.4 Development of an "Anticommons" in Agricultural Biotechnology. 14.4.1 Transformation Methods. 14.4.2 Selectable Markers. 14.4.3 Constitutive Promoters. 14.4.4 Tissue- or Development-Specific Promoters. 14.4.5 Subcellular Localization. 14.5 Freedom to Operate (FTO). 14.6 Strategies for Open Access. 14.7 Conclusions. References. 15. Why Transgenic Plants Are So Controversial ( Douglas Powell ). 15.0 Chapter Summary and Objectives. 15.0.1 Summary. 15.0.2 Discussion Questions. 15.1 Introduction. 15.1.1 The Frankenstein Backdrop. 15.1.2 Agricultural Innovations and Questions. 15.2 Perceptions of Risk. 15.3 Responses to Fear. 15.4 Feeding Fear: Case Studies. 15.4.1 Pusztai's Potatoes. 15.4.2 Monarch Butterfly Flap. 15.5 How Many Benefits are Enough. 15.6 Continuing Debates. 15.6.1 Process versus Product. 15.6.2 Health Concerns. 15.6.3 Environmental Concerns. 15.6.4 Consumer Choice. 15.7 Business and Control. 15.8 Conclusions. References. 16. The Future of Plant Biotechnology ( C. Neal Stewart, Jr. and David W. Ow ). 16.0 Chapter Summary and Objectives. 16.0.1 Summary. 16.0.2 Discussion Questions. 16.1 Introduction. 16.2 Site-Specific Recombination Systems to Provide Increased Precision. 16.2.1 Removal of DNA from Transgenic Plants or Plant Parts. 16.2.2 More Precise Integration of DNA. 16.3 Zinc-Finger Nucleases. 16.4 The Future of Food (and Fuel and Pharmaceuticals). 16.5 Conclusions. References. Index.