C. Neal Stewart 
Plant Biotechnology and Genetics [EPUB ebook] 
Principles, Techniques, and Applications

Foreword xvi
Contributors xviii
Preface xx
1. The Impact of Biotechnology on Plant Agriculture 1
Graham Brookes
1.0 Chapter Summary and Objectives 1
1.0.1 Summary 1
1.0.2 Discussion Questions 1
1.1 Introduction 1
1.2 Cultivation of Biotechnology (GM) Crops 2
1.3 Why Farmers Use Biotech Crops 4
1.4 GM’s Effects on Crop Production and Farming 7
1.5 How the Adoption of Plant Biotechnology has Impacted the Environment 8
1.5.1 Environmental Impacts from Changes in Insecticide and Herbicide Use 8
1.5.2 Impact on GHG Emissions 11
1.6 Conclusions 13
Life Box 1.1 Norman E. Borlaug 14
Life Box 1.2 Mary-Dell Chilton 15
Life Box 1.3 Robert T. Fraley 17
References 19
2. Mendelian Genetics and Plant Reproduction 20
Matthew D. Halfhill and Suzanne I. Warwick
2.0 Chapter Summary and Objectives 20
2.0.1 Summary 20
2.0.2 Discussion Questions 20
2.1 Overview of Genetics 20
2.2 Mendelian Genetics 23
2.2.1 Law of Segregation 26
2.2.2 Law of Independent Assortment 26
2.3 Mitosis and Meiosis 27
2.3.1 Mitosis 29
2.3.2 Meiosis 29
2.3.3 Recombination 30
2.3.4 Cytogenetic Analysis 31
2.3.5 Mendelian Genetics and Biotechnology Summary 32
2.4 Plant Reproductive Biology 32
2.4.1 History of Research in Plant Reproduction 32
2.4.2 Mating Systems 32
2.4.3 Hybridization and Polyploidy 36
2.4.4 Mating Systems and Biotechnology Summary 38
2.5 Conclusion 38
Life Box 2.1 Richard A. Dixon 39
Life Box 2.2 Michael L. Arnold 40
References 42
3. Plant Breeding 43
Nicholas A. Tinker and Elroy R. Cober
3.0 Chapter Summary and Objectives 43
3.0.1 Summary 43
3.0.2 Discussion Questions 43
3.1 Introduction 44
3.2 Central Concepts in Plant Breeding 45
3.2.1 Simple vs. Complex Inheritance 45
3.2.2 Phenotype vs. Genotype 46
3.2.3 Mating Systems, Varieties, Landraces, and Pure Lines 47
3.2.4 Other Topics in Population and Quantitative Genetics 49
3.2.5 The Value of a Plant Variety Depends on Many Traits 51
3.2.6 A Plant Variety Must Be Environmentally Adapted 51
3.2.7 Plant Breeding is a Numbers Game 52
3.2.8 Plant Breeding is an Iterative and Collaborative Process 52
3.2.9 Diversity, Adaptation, and Ideotypes 53
3.2.10 Other Considerations 56
3.3 Objectives in Plant Breeding 56
3.4 Methods of Plant Breeding 57
3.4.1 Methods of Hybridization 58
3.4.2 Self?]Pollinated Species 58
3.4.3 Outcrossing Species 63
3.4.4 Clonally Propagated Species 67
3.5 Breeding Enhancements 68
3.5.1 Doubled Haploidy 68
3.5.2 Marker?]Assisted Selection 68
3.5.3 Mutation Breeding 70
3.5.4 Apomixis 71
3.6 Conclusions 71
Life Box 3.1 Gurdev Singh Khush 72
Life Box 3.2 P. Stephen Baenziger 74
Life Box 3.3 Steven D. Tanksley 75
References 77
4. Plant Development and Physiology 78
Glenda E. Gillaspy
4.0 Chapter Summary and Objectives 78
4.0.1 Summary 78
4.0.2 Discussion Questions 78
4.1 Plant Anatomy and Morphology 79
4.2 Embryogenesis and Seed Germination 80
4.2.1 Gametogenesis 80
4.2.2 Fertilization 82
4.2.3 Fruit Development 83
4.2.4 Embryogenesis 83
4.2.5 Seed Germination 85
4.2.6 Photomorphogenesis 85
4.3 Meristems 86
4.3.1 Shoot Apical Meristem 86
4.3.2 Root Apical Meristem and Root Development 88
4.4 Leaf Development 89
4.4.1 Leaf Structure 89
4.4.2 Leaf Development Patterns 91
4.5 Flower Development 92
4.5.1 Floral Evocation 92
4.5.2 Floral Organ Identity and the ABC Model 93
4.6 Hormone Physiology and Signal Transduction 94
4.6.1 Seven Plant Hormones and Their Actions 94
4.6.2 Plant Hormone Signal Transduction 96
4.7 Conclusions 100
Life Box 4.1 Deborah Delmer 100
Life Box 4.2 Natasha Raikhel 102
Life Box 4.3 Brenda S.J. Winkel 103
References 105
5. Tissue Culture: The Manipulation of Plant Development 107
Vinitha Cardoza
5.0 Chapter Summary and Objectives 107
5.0.1 Summary 107
5.0.2 Discussion Questions 107
5.1 Introduction 107
5.2 History of Tissue Culture 108
5.3 Media and Culture Conditions 109
5.3.1 Basal Media 109
5.3.2 Growth Regulators 110
5.4 Sterile Technique 111
5.4.1 Clean Equipment 111
5.4.2 Surface Sterilization of Explants 112
5.5 Culture Conditions and Vessels 113
5.6 Culture Types and Their Uses 113
5.6.1 Callus and Somatic Embryo Culture 113
5.6.2 Cell Suspension Cultures 117
5.6.3 Anther/Microspore Culture 119
5.6.4 Protoplast Culture 119
5.6.5 Somatic Hybridization 120
5.6.6 Embryo Culture 120
5.6.7 Meristem Culture 121
5.7 Regeneration Methods of Plants in Culture 121
5.7.1 Organogenesis 121
5.7.2 Somatic Embryogenesis 123
5.7.3 Synthetic Seeds 123
5.8 Rooting of Shoots 123
5.9 Acclimation 124
5.10 Problems that can Occur in Tissue Culture 124
5.10.1 Culture Contamination 124
5.10.2 Hyperhydricity 124
5.10.3 Browning of Explants 124
5.11 Conclusions 125
Acknowledgments 125
Life Box 5.1 Glenn Burton Collins 125
Life Box 5.2 Martha S. Wright 127
Life Box 5.3 Vinitha Cardoza 128
References 129
6. Molecular Genetics of Gene Expression 133
Maria Gallo and Alison K. Flynn
6.0 Chapter Summary and Objectives 133
6.0.1 Summary 133
6.0.2 Discussion Questions 133
6.1 The Gene 133
6.1.1 DNA Coding for a Protein via the Gene 133
6.1.2 DNA as a Polynucleotide 134
6.2 DNA Packaging into Eukaryotic Chromosomes 134
6.3 Transcription 135
6.3.1 Transcription of DNA to Produce Messenger Ribonucleic Acid 135
6.3.2 Transcription Factors 140
6.3.3 Coordinated Regulation of Gene Expression 140
6.3.4 Chromatin as an Important Regulator of Transcription 141
6.3.5 Regulation of Gene Expression by DNA Methylation 142
6.3.6 RNA?]Directed Gene Silencing by Small RNAs 143
6.3.7 Processing to Produce Mature m RNA 143
6.4 Translation 144
6.4.1 Initiation of Translation 147
6.4.2 Elongation Phase of Translation 147
6.4.3 Translation Termination 147
6.5 Protein Postranslational Modification 147
Life Box 6.1 Maarten Chrispeels 150
Life Box 6.2 David W. Ow 152
References 154
7. Plant Systems Biology 155
Wusheng Liu and C. Neal Stewart, Jr.
7.0 Chapter Summary and Objectives 155
7.0.1 Summary 155
7.0.2 Discussion Questions 155
7.1 Introduction 155
7.2 Defining Plant Systems Biology 157
7.3 Properties of Plant Systems 158
7.4 A Framework of Plant Systems Biology 159
7.4.1 Comprehensive Quantitative Data Sets 160
7.4.2 Network Analysis 161
7.4.3 Dynamic Modeling 161
7.4.4 Exploring Systems and Models Toward Refinement 161
7.5 Disciplines and Enabling Tools of Plant Systems Biology 162
7.5.1 Plant Genomics 162
7.5.2 Plant Transcriptomics 166
7.5.3 Plant Proteomics 168
7.5.4 Plant Metabolomics 170
7.5.5 Bioinformatics 172
7.6 Conclusions 176
Life Box 7.1 C. Robin Buell 177
Life Box 7.2 Zhenbiao Yang 178
References 179
8. Recombinant DNA, Vector Design, and Construction 181
Mark D. Curtis and David G.J. Mann
8.0 Chapter Summary and Objectives 181
8.0.1 Summary 181
8.0.2 Discussion Questions 181
8.1 DNA Modification 181
8.2 DNA Vectors 186
8.2.1 DNA Vectors for Plant Transformation 188
8.2.2 Components for Efficient Gene Expression in Plants 190
8.3 Greater Demands Lead to Innovation 192
8.3.1 ‘Modern’ Cloning Strategies 192
8.4 Vector Design 197
8.4.1 Vectors for High?]Throughput Functional Analysis 197
8.4.2 Vectors for Gene Down?]Regulation Using RNA Interference (RNAi) 199
8.4.3 Expression Vectors 199
8.4.4 Vectors for Promoter Analysis 200
8.4.5 Vectors Derived from Plant Sequences 201
8.4.6 Vectors for Multigenic Traits 203
8.5 Targeted Transgene Insertions 204
8.6 Prospects 205
Life Box 8.1 Wayne Parrott 206
Life Box 8.2 David Mann 207
References 208
9. Genes and Traits of Interest 211
Kenneth L. Korth
9.0 Chapter Summary and Objectives 211
9.0.1 Summary 211
9.0.2 Discussion Questions 211
9.1 Introduction 212
9.2 Identifying Genes of Interest via Genomics and other Omics Technologies 212
9.3 Traits for Improved Crop Production Using Transgenics 214
9.3.1 Herbicide Resistance 215
9.3.2 Insect Resistance 218
9.3.3 Pathogen Resistance 220
9.3.4 Traits for Improved Products and Food Quality 222
9.4 Conclusion 227
Life Box 9.1 Dennis Gonsalves 227
Life Box 9.2 Ingo Potrykus 229
References 231
10. Promoters and Marker Genes 233
Wusheng Liu, Brian Miki and C. Neal Stewart, Jr.
10.0 Chapter Summary and Objectives 233
10.0.1 Summary 233
10.0.2 Discussion Questions 233
10.1 Introduction 234
10.2 Promoters 234
10.2.1 Constitutive Promoters 235
10.2.2 Tissue?]Specific Promoters 236
10.2.3 Inducible Promoters 237
10.2.4 Synthetic Promoters 239
10.3 Marker Genes 239
10.3.1 Selectable Marker Genes 242
10.3.2 Reporter Genes 246
10.4 Marker?]Free Strategies 250
10.5 Conclusions 254
Life Box 10.1 Fredy Altpeter 255
Life Box 10.2 Taniya Dhillon 257
References 259
11. Transgenic Plant Production 262
John J. Finer
11.0 Chapter Summary and Objectives 262
11.0.1 Summary 262
11.0.2 Discussion Questions 262
11.1 Overview of Plant Transformation 263
11.1.1 Introduction 263
11.1.2 Basic Components for Successful Gene Transfer to Plant Cells 263
11.2 Agrobacterium Tumefaciens 265
11.2.1 History of Agrobacterium Research 266
11.2.2 Use of the T?]DNA Transfer Process for Transformation 268
11.2.3 Optimizing Delivery and Broadening the Taxonomical Range of Targets 269
11.2.4 Strain and Cultivar Compatibility 270
11.2.5 Agroinfiltration 271
11.2.6 Arabidopsis Floral Dip (Clough and Bent 1998) 271
11.3 Particle Bombardment 272
11.3.1 History of Particle Bombardment 272
11.3.2 The Fate of the Introduced DNA into Plant Cells 274
11.3.3 The Power and Problems of Direct DNA Introduction 275
11.3.4 Improvements in the Control of Transgene Expression 276
11.4 Other Methods of Transformation 276
11.4.1 The Need for Additional Technologies 276
11.4.2 Protoplasts 277
11.4.3 Whole Tissue Electroporation 278
11.4.4 Silicon Carbide Whiskers 278
11.4.5 Viral Vectors 278
11.4.6 Laser Micropuncture 279
11.4.7 Nanofiber Arrays 279
11.5 The Rush to Publish 280
11.5.1 Controversial Reports of Plant Transformation 280
11.5.2 Criteria to Consider in Judging Novel Plant Transformation Methods 284
11.6 A Look to the Future 286
Life Box 11.1 Ted Klein 286
Life Box 11.2 John Finer 287
Life Box 11.3 Kan Wang 289
References 291
12. Analysis of Transgenic Plants 293
C. Neal Stewart, Jr.
12.0 Chapter Summary and Objectives 293
12.0.1 Summary 293
12.0.2 Discussion Questions 293
12.1 Essential Elements of Transgenic Plant Analysis 293
12.2 Assays for Transgenicity, Insert Copy Number, and Segregation 295
12.2.1 Polymerase Chain Reaction 295
12.2.2 Quantitative PCR 295
12.2.3 Southern (DNA) Blot Analysis 296
12.2.4 Segregation Analysis of Progeny 300
12.3 Transgene Expression 301
12.3.1 Transcript Abundance 301
12.3.2 Protein Abundance 302
12.4 Knockdown or Knockout Analysis Rather than Overexpression Analysis 304
12.5 The Relationship Between Molecular Analyses and Phenotype 305
Life Box 12.1 Hong S. Moon 305
Life Box 12.2 Neal Stewart 306
Life Box 12.3 Nancy A. Reichert 308
References 310
13. Regulations and Biosafety 311
Alan Mc Hughen
13.0 Chapter Summary and Objectives 311
13.0.1 Summary 311
13.0.2 Discussion Questions 311
13.1 Introduction 311
13.2 History of Genetic Engineering and Its Regulation 313
13.3 Regulation of GM Plants 315
13.3.1 New Technologies 316
13.3.2 US Regulatory Agencies and Regulations 317
13.3.3 European Union 319
13.3.4 Canada 321
13.3.5 International Perspectives 321
13.4 Regulatory Flaws and Invalid Assumptions 323
13.4.1 Conventional Plant Breeding has Higher Safety than Biotechnology?]Derived GM 324
13.4.2 GMOs Should Be Regulated Because They’re GMOs and Un?]natural 324
13.4.3 Even though Product Risk is Important, It is Reasonable that Process (GMO) Should Trigger Regulation 324
13.4.4 Since GM Technology is New, It Might Be Hazardous and Should Be Regulated 325
13.4.5 If We Have a Valid Scientific Test, Then It Should Be Used in Regulations 326
13.4.6 Better Safe than Sorry: Overregulation is Better than Underregulation 326
13.5 Conclusion 327
Life Box 13.1 Alan Mc Hughen 328
Life Box 13.2 Raymond D. Shillito 329
References 331
14. Field Testing of Transgenic Plants 333
Detlef Bartsch, Achim Gathmann, Christiane Saeglitz and Arti Sinha
14.0 Chapter Summary and Objectives 333
14.0.1 Summary 333
14.0.2 Discussion Questions 333
14.1 Introduction 334
14.2 Environmental Risk Assessment Process 334
14.2.1 Initial Evaluation (Era Step 1) 334
14.2.2 Problem Formulation (ERA Step 2) 335
14.2.3 Controlled Experiments and Gathering of Information (ERA Step 3) 335
14.2.4 Risk Evaluation (ERA Step 4) 335
14.2.5 Progression through a Tiered Risk Assessment 335
14.3 An Example Risk Assessment: The Case of Bt Maize 336
14.3.1 Effect of Bt Maize Pollen on Nontarget Caterpillars 337
14.3.2 Statistical Analysis and Relevance for Predicting Potential Adverse Effects on Butterflies 339
14.4 Proof of Safety Versus Proof of Hazard 340
14.5 Modeling the Risk Effects on a Greater Scale 340
14.6 Proof of Benefits: Agronomic Performance 341
14.7 Conclusions 342
Life Box 14.1 Tony Shelton 343
Life Box 14.2 Detlef Bartsch 344
References 346
15. Intellectual Property in Agricultural Biotechnology: Strategies for Open Access 347
Monica Alandete?]Saez, Cecilia Chi?]Ham, Gregory Graff, Sara Boettiger and Alan B. Bennett
15.0 Chapter Summary and Objectives 347
15.0.1 Summary 347
15.0.2 Discussion Questions 347
15.1 Intellectual Property and Agricultural Biotechnology 348
15.1.1 What is Intellectual Property? 349
15.1.2 What is a Patent? 349
15.2 The Relationship Between Intellectual Property and Agricultural Research 351
15.3 Patenting Plant Biotechnology: Has an Anti?]Commons Developed? 352
15.3.1 Transformation Methods 352
15.3.2 Selectable Markers 353
15.3.3 Promoters 354
15.3.4 Subcellular Localization 354
15.3.5 The Importance of Combining IP?]Protected Components in Transgenic Crops 355
15.4 What is Freedom to Operate (FTO)? 355
15.4.1 The Importance of FTO 355
15.4.2 FTO Case Study: the Tomato E8 Promoter 356
15.5 Strategies for Open Access 358
15.6 Conclusions 359
Life Box 15.1 Alan Bennett 360
Life Box 15.2 Maud Hinchee 361
References 363
16. Why Transgenic Plants Are So Controversial 366
Jennifer Trumbo and Douglas Powell
16.0 Chapter Summary and Objectives 366
16.0.1 Summary 366
16.0.2 Discussion Questions 366
16.1 Introduction 367
16.1.1 The Frankenstein Backdrop 367
16.1.2 Agricultural Innovations and Questions 367
16.2 Perceptions of Risk 368
16.3 Responses of Fear 370
16.4 Feeding Fear: Case Studies 372
16.4.1 Pusztai’s Potatoes 372
16.4.2 Monarch Butterfly Flap 373
16.5 How Many Benefits are Enough? 373
16.6 Continuing Debates 375
16.6.1 Process vs. Product 375
16.6.2 Health Concerns 375
16.6.3 Environmental Concerns 376
16.6.4 Consumer Choice 376
16.7 Business and Control 376
16.8 Conclusions 377
Life Box 16.1 Tony Conner 378
Life Box 16.2 Channapatna S. Prakash 379
References 381
17. The Future: Advanced Plant Biotechnology, Genome Editing, and Synthetic Biology 383
Wusheng Liu and C. Neal Stewart, Jr.
17.0 Chapter Summary and Objectives 383
17.0.1 Summary 383
17.0.2 Discussion Questions 383
17.1 Introduction: The Birth of Synthetic Biology 384
17.2 Defining Synthetic Biology for Plants 385
17.2.1 Design Cycles of Synthetic Biology 385
17.2.2 Foundations of Synthetic Biology 387
17.2.3 Components of Plant Synthetic Biology 388
17.3 Enabling Tools for Plant Synthetic Biology 389
17.3.1 Computer?]Aided Design 389
17.3.2 Synthetic Promoters 389
17.3.3 Precise Genome Editing 389
17.4 Synthetic Biology Applications in Plants 393
17.4.1 Synthetic Inducible Promoters 394
17.4.2 A Device for Monitoring Auxin?]Induced Plant IAA Degradation in Yeast 395
17.4.3 Circuits for Phytosensing of Explosives or Bacterial Pathogens in Transgenic Plants 395
17.5 Conclusions 397
Life Box 17.1 Joshua Yuan 397
Life Box 17.2 Wusheng Liu 398
References 399
Index 402

C. Neal Stewart, Ph D, is Racheff Chair of Excellence in Plant Molecular Genetics and Professor, Department of Plant Sciences, University of Tennessee. In addition to the prior edition of Plant Biotechnology, he has written Weedy and Invasive Plant Genomics, Plant Transformation Technologies, and Research Ethics for Scientists: A Companion for Students, all published by Wiley.