Plant biotechnology and genetics : principles, techniques, and applications /

PLANT BIOTECHNOLOGY AND GENETICS 3
CONTENTS 9
Preface 19
Foreword to Plant Biotechnology and Genetics 21
Contributors 25
1. Plant Agriculture: The Impact of Biotechnology 27
1.0 Chapter Summary and Objectives 27
1.0.1 Summary 27
1.0.2 Discussion Questions 27
1.1 Introduction 27
1.2 Biotechnology Crops Plantings 28
1.3 Why Farmers Use Biotech Crops 30
1.3.1 Herbicide-Tolerant Crops 33
1.3.2 Insect-Resistant Crops 33
1.3.3 Conclusion 34
1.4 How the Adoption of Plant Biotechnology Has Impacted the Environment 34
1.4.1 Environmental Impacts from Changes in Insecticide and Herbicide Use 35
1.4.2 Impact on Greenhouse Gas (GHG) Emissions 38
1.5 Conclusions 40
References 45
2. Mendelian Genetics and Plant Reproduction 47
2.0 Chapter Summary and Objectives 47
2.0.1 Summary 47
2.0.2 Discussion Questions 47
2.1 Genetics Overview 48
2.2 Mendelian Genetics 51
2.2.1 Law of Segregation 54
2.2.2 Law of Independent Assortment 54
2.3 Mitosis and Meiosis 56
2.3.1 Mitosis 57
2.3.2 Meiosis 58
2.3.3 Recombination 58
2.3.4 Cytogenetic Analysis 59
2.4 Plant Reproductive Biology 60
2.4.1 History of Research 60
2.4.2 Mating Systems 61
2.4.2.1 Sexual Reproduction 61
2.4.2.2 Asexual Reproduction 64
2.4.2.3 Mating Systems Summary 64
2.4.3 Hybridization and Polyploidy 65
2.5 Conclusion 67
References 71
3. Plant Breeding 73
3.0 Chapter Summary and Objectives 73
3.0.1 Summary 73
3.0.2 Discussion Questions 73
3.1 Introduction 74
3.2 Central Concepts in Plant Breeding 75
3.2.1 Simple versus Complex Inheritance 75
3.2.2 Phenotype versus Genotype 77
3.2.3 Mating Systems, Varieties, Landraces, and Pure Lines 78
3.2.4 Other Topics in Population and Quantitative Genetics 81
3.2.5 The Value of a Plant Variety Depends on Many Traits 81
3.2.6 Varieties Must Be Adapted to Environments 82
3.2.7 Plant Breeding Is a Numbers Game 83
3.2.8 Plant Breeding Is an Iterative and Collaborative Process 83
3.2.9 Diversity, Adaptation, and Ideotypes 84
3.2.10 Other Considerations 87
3.3 Objectives for Plant Breeding 88
3.4 Methods of Plant Breeding 89
3.4.1 Methods of Hybridization 89
3.4.1.1 Self-Pollinated Species 90
3.4.1.2 Outcrossing Species 95
3.4.1.3 Synthetic Varieties 98
3.4.1.4 Hybrid Varieties 98
3.4.2 Clonally Propagated Species 90
3.5 Breeding Enhancements 100
3.5.1 Doubled Haploidy 100
3.5.2 Marker-Assisted Selection 101
3.5.3 Mutation Breeding 102
3.5.4 Apomixis 103
3.6 Conclusions 103
References 108
4. Plant Development and Physiology 109
4.0 Chapter Summary and Objectives 109
4.0.1 Summary 109
4.0.2 Discussion Questions 109
4.1 Plant Anatomy and Morphology 110
4.2 Embryogenesis and Seed Germination 111
4.2.1 Gametogenesis 111
4.2.2 Fertilization 114
4.2.3 Fruit Development 114
4.2.4 Embryogenesis 115
4.2.5 Seed Germination 117
4.2.6 Photomorphogenesis 117
4.3 Meristems 118
4.3.1 Shoot Apical Meristem 118
4.3.2 Root Apical Meristem and Root Development 120
4.4 Leaf Development 122
4.4.1 Leaf Structure 122
4.4.2 Leaf Development Patterns 123
4.5 Flower Development 124
4.5.1 Floral Evocation 124
4.5.2 Floral Organ Identity and the ABC Model 125
4.6 Hormone Physiology and Signal Transduction 127
4.6.1 Seven Plant Hormones and Their Actions 127
4.6.2 Plant Hormone Signal Transduction 129
4.6.2.1 Auxin and GA Signaling 130
4.6.2.2 Cytokinin and Ethylene Signaling 131
4.6.2.3 Brassinosteroid Signal Transduction 131
4.7 Conclusions 132
References 136
5. Tissue Culture: The Manipulation of Plant Development 139
5.0 Chapter Summary and Objectives 139
5.0.1 Summary 139
5.0.2 Discussion Questions 139
5.1 Introduction 139
5.2 History 140
5.3 Media and Culture Conditions 141
5.3.1 Basal Media 141
5.3.2 Growth Regulators 142
5.4 Sterile Technique 144
5.4.1 Clean Equipment 144
5.4.2 Surface Sterilization of Explants 144
5.5 Culture Conditions and Vessels 145
5.6 Culture Types and Their Uses 146
5.6.1 Callus Culture 146
5.6.1.1 Somaclonal Variation 148
5.6.2 Cell Suspension Culture 148
5.6.2.1 Production of Secondary Metabolites and Recombinant Proteins Using Cell Culture 148
5.6.3 Anther/Microspore Culture 149
5.6.4 Protoplast Culture 149
5.6.4.1 Somatic Hybridization 150
5.6.5 Embryo Culture 150
5.6.6 Meristem Culture 150
5.7 Regeneration Methods of Plants in Culture 151
5.7.1 Organogenesis 151
5.7.1.1 Indirect Organogenesis 151
5.7.1.2 Direct Organogenesis 151
5.7.2 Somatic Embryogenesis 152
5.7.2.1 Synthetic Seeds 153
5.8 Rooting of Shoots 153
5.9 Acclimation 154
5.10 Conclusions 154
Acknowledgments 154
References 158
6. Molecular Genetics of Gene Expression 161
6.0 Chapter Summary and Objectives 161
6.0.1 Summary 161
6.0.2 Discussion Questions 161
6.1 The gene 161
6.1.1 DNA Coding for a Protein via the Gene 161
6.1.2 DNA as a Polynucleotide 162
6.2 DNA Packaging into Eukaryotic Chromosomes 162
6.3 Transcription 166
6.3.1 Transcription of DNA to Produce Messenger RNA (mRNA) 166
6.3.2 Transcription Factors 169
6.3.3 Coordinated Regulation of Gene Expression 170
6.3.4 Chromatin as an Important Regulator of Transcription 170
6.3.5 Regulation of Gene Expression by DNA Methylation 172
6.3.6 Processing to Produce Mature mRNA 172
6.4 Translation 174
6.4.1 Initiation of Translation 176
6.4.2 Translation Elongation 178
6.4.3 Translation Termination 178
6.5 Protein Postranslational Modification 178
References 182
7. Recombinant DNA, Vector Design, and Construction 185
7.0 Chapter Summary and Objectives 185
7.0.1 Summary 185
7.0.2 Discussion Questions 185
7.1 DNA Modification 186
7.2 DNA Vectors 189
7.2.1 DNA Vectors for Plant Transformation 192
7.2.2 Components for Efficient Gene Expression in Plants 193
7.3 Greater Demands Lead to Innovation 196
7.3.1 Site-Specific DNA Recombination 197
7.3.1.1 Gateway Cloning 198
7.3.1.2 Creator鈩?Cloning 201
7.3.1.3 Univector (Echo鈩? Cloning 201
7.4 Vector Design 203
7.4.1 Vectors for High-Throughput Functional Analysis 203
7.4.2 Vectors for RNA Interference (RNAi) 205
7.4.3 Expression Vectors 205
7.4.4 Vectors for Promoter Analysis 206
7.4.5 Vectors Derived from Plant Sequences 207
7.4.6 Vectors for Multigenic Traits 211
7.5 Targeted Transgene Insertions 212
7.6 Safety Features in Vector Design 212
7.7 Prospects 214
References 216
8. Genes and Traits of Interest for Transgenic Plants 219
8.0 Chapter Summary and Objectives 219
8.0.1 Summary 219
8.0.2 Discussion Questions 219
8.1 Introduction 220
8.2 Identifying Genes of Interest via Genomic Studies 220
8.3 Traits for Improved Crop Production 223
8.3.1 Herbicide Resistance 223
8.3.2 Insect Resistance 226
8.3.3 Pathogen Resistance 228
8.4 Traits for Improved Products and Food Quality 231
8.4.1 Nutritional Improvements 231
8.4.2 Modified Plant Oils 233
8.4.3 Pharmaceutical Products 234
8.4.4 Biofuels 235
8.5 Conclusions 236
References 241
9. Marker Genes and Promoters 243
9.0 Chapter Summary and Objectives 243
9.0.1 Summary 243
9.0.2 Discussion Questions 243
9.1 Introduction 244
9.2 Definition of Marker Genes 244
9.2.1 Selectable Marker Genes: An Introduction 244
9.2.2 Reporter Genes: An Introduction 248
9.3 Promoters 250
9.4 Selectable Marker Genes 253
9.4.1 Conditional Positive Selectable Marker Gene Systems 253
9.4.1.1 Selection on Antibiotics 254
9.4.1.2 Selection on Herbicides 255
9.4.1.3 Selection Using Nontoxic Metabolic Substrates 255
9.4.2 Nonconditional Positive Selection Systems 256
9.4.3 Conditional Negative Selection Systems 256
9.4.4 Nonconditional Negative Selection Systems 256
9.5 Nonselectable Marker Genes or Reporter Genes 257
9.5.1 尾-Glucuronidase 257
9.5.2 Luciferase 258
9.5.3 Green Fluorescent Protein 258
9.6 Marker-Free Strategies 259
9.7 Conclusions 263
References 268
10. Transgenic Plant Production 271
10.0 Chapter Summary and Objectives 271
10.0.1 Summary 271
10.0.2 Discussion Questions 271
10.1 Overview 272
10.2 Basic Components for Successful Gene Transfer to Plant Cells 272
10.2.1 Visualizing the General Transformation Process 272
10.2.2 DNA Delivery 273
10.2.3 Target Tissue Status 274
10.2.4 Selection and Regeneration 274
10.3 Agrobacterium 275
10.3.1 History of Our Knowledge of Agrobacterium 275
10.3.2 Use of the T-DNA Transfer Process for Transformation 277
10.3.3 Optimizing Delivery and Broadening the Range of Targets 279
10.3.4 Agroinfiltration 280
10.3.5 Arabidopsis Floral Dip 280
10.4 Particle Bombardment 281
10.4.1 History of Particle Bombardment 281
10.4.2 The Fate of Introduced DNA 283
10.4.3 The Power and Problems of Direct DNA Introduction 285
10.4.4 Improvements in Transgene Expression 285
10.5 Other Methods 286
10.5.1 The Need for Additional Technologies 286
10.5.2 Protoplasts 287
10.5.3 Whole-Tissue Electroporation 288
10.5.4 Silicon Carbide Whiskers 288
10.5.5 Viral Vectors 289
10.5.6 Laser Micropuncture 289
10.5.7 Nanofiber Arrays 289
10.6 The Rush to Publish 291
10.6.1 Controversial Reports of Plant Transformation 291
10.6.1.1 DNA Uptake in Pollen 291
10.6.1.2 Agrobacterium-Mediated Transformation of Maize Seedlings 291
10.6.1.3 Pollen Tube Pathway 292
10.6.1.4 Rye Floral Tiller Injection 292
10.6.1.5 Electrotransformation of Germinating Pollen Grain 293
10.6.1.6 Medicago Transformation via Seedling Infiltration 293
10.6.2 Criteria to Consider: Whether My Plant Is Transgenic 294
10.6.2.1 Resistance Genes 294
10.6.2.2 Marker Genes 294
10.6.2.3 Transgene DNA 295
10.7 A Look to the Future 295
References 298
11. Transgenic Plant Analysis 301
11.0 Chapter Summary and Objectives 301
11.0.1 Summary 301
11.0.2 Discussion Questions 301
11.1 Introduction 302
11.2 Directionally Named Analyses: As the Compass Turns 302
11.3 Initial Screens: Putative Transgenic Plants 303
11.3.1 Screens on Selection Media 303
11.3.2 Polymerase Chain Reaction 304
11.3.3 Enzyme-Linked Immunosorbent Assays (ELISAs) 305
11.4 Definitive Molecular Characterization 306
11.4.1 Intact Transgene Integration 306
11.4.2 Determining the Presence of Intact Transgenes or Constructs 310
11.4.3 Transgene Expression: Transcription 310
11.4.3.1 Northern Blot Analysis 310
11.4.3.2 Quantitative Real-Time Reverse Transcriptase (RT)-PCR 311
11.4.4 Transgene Expression: Translation: Western Blot Analyses 312
11.5 Digital Imaging 313
11.6 Phenotypic Analysis 313
11.7 Conclusions 313
References 314
12. Regulations and Biosafety 317
12.0 Chapter Summary and Objectives 317
12.0.1 Summary 317
12.0.2 Discussion Questions 317
12.1 Introduction 317
12.2 History of Genetic Engineering and its Regulation 319
12.3 Regulation of GE 322
12.3.1 United States 322
12.3.1.1 USDA 323
12.3.1.2 FDA 323
12.3.1.3 EPA 324
12.3.2 EU 325
12.3.3 Canada 326
12.3.4 International Perspectives 327
12.4 Conclusions 328
References 335
13. Field Testing of Transgenic Plants 337
13.0 Chapter Summary and Objectives 337
13.0.1 Summary 337
13.0.2 Discussion Questions 337
13.1 Introduction 338
13.2 Environmental Risk Assessment (Era) Process 338
13.2.1 Initial Evaluation (ERA Step 1) 339
13.2.2 Problem Formulation (ERA Step 2) 339
13.2.3 Controlled Experiments and Gathering of Information (ERA Step 3) 339
13.2.4 Risk Evaluation (ERA Step 4) 339
13.2.5 Progression through a Tiered Risk Assessment 339
13.3 An Example Risk Assessment: The Case of Bt Maize 340
13.3.1 Effect of Bt Maize Pollen on Nontarget Caterpillars 341
13.3.2 Statistical Analysis and Relevance for Predicting Potential Adverse Effects on Butterflies 343
13.4 Proof of Safety versus Proof of Hazard 345
13.5 Proof of Benefits: Agronomic Performance 345
13.6 Conclusions 346
References 349
14. Intellectual Property in Agricultural Biotechnology: Strategies for Open Access 351
14.0 Chapter Summary and Objectives 351
14.0.1 Summary 351
14.0.2 Discussion Questions 351
14.1 Introduction 352
14.2 Intellectual Property Defined 353
14.3 Intellectual Property in Relation to Agricultural Research 355
14.4 Development of an \u201cAnticommons\u201d in Agricultural Biotechnology 355
14.4.1 Transformation Methods 357
14.4.2 Selectable Markers 358
14.4.3 Constitutive Promoters 358
14.4.4 Tissue- or Development-Specific Promoters 358
14.4.5 Subcellular Localization 359
14.5 Freedom to Operate (FTO) 359
14.6 Strategies for Open Access 362
14.7 Conclusions 364
References 365
15. Why Transgenic Plants Are So Controversial 369
15.0 Chapter Summary and Objectives 369
15.0.1 Summary 369
15.0.2 Discussion Questions 369
15.1 Introduction 369
15.1.1 The Frankenstein Backdrop 370
15.1.2 Agricultural Innovations and Questions 370
15.2 Perceptions of Risk 371
15.3 Responses to Fear 373
15.4 Feeding Fear: Case Studies 374
15.4.1 Pusztai\u2019s Potatoes 375
15.4.2 Monarch Butterfly Flap 375
15.5 How Many Benefits are Enough 376
15.6 Continuing Debates 377
15.6.1 Process versus Product 377
15.6.2 Health Concerns 378
15.6.3 Environmental Concerns 379
15.6.4 Consumer Choice 379
15.7 Business and Control 379
15.8 Conclusions 380
References 380
16. The Future of Plant Biotechnology 383
16.0 Chapter Summary and Objectives 383
16.0.1 Summary 383
16.0.2 Discussion Questions 383
16.1 Introduction 383
16.2 Site-Specific Recombination Systems to Provide Increased Precision 385
16.2.1 Removal of DNA from Transgenic Plants or Plant Parts 387
16.2.2 More Precise Integration of DNA 388
16.3 Zinc-Finger Nucleases 389
16.4 The Future of Food (and Fuel and Pharmaceuticals) 390
16.5 Conclusions 391
References 394
Index 397