Transgenic Crop Plants (eBook)

Transgenic Crop Plants 2
Title Page 3
Copyright Page 4
Preface 5
Contents 10
Contributors 12
Abbreviations 15
Chapter 1 21
Generation and Deployment of Transgenic Crop Plants: An Overview 21
1.1 Introduction 21
1.2 Target Cells and Organelles for Genetic Transformation 22
1.3 Methods for Introducing Genes into Plants 23
1.4 Vector Construction and Genes for Plant Transformation 26
1.4.1 Promoters for Plant Transformation 27
1.4.2 Reporter and Selectable Marker Genes 29
1.5 Methods for Screening of Genes Introduced into Putatively Transformed Plants 31
1.6 Gene Expression in Transgenic Plants 31
1.7 Target Genes for Genetic Transformation 32
1.7.1 Resistance to Biotic and Abiotic Stresses 33
1.7.2 Improvement of Quality 35
1.7.3 Biopharmaceuticals 36
1.7.4 Phytoremediation 37
1.7.5 Floriculture 37
1.8 Risks and Concerns 39
1.9 General Conclusions 39
References 40
Chapter 2 50
Explants Used for the Generation of Transgenic Plants 50
2.1 Introduction 50
2.2 Explants Used for the Transformation of Herbaceous Plants 51
2.2.1 Cereals 51
2.2.2 Brassica 51
2.2.3 Cassava 52
2.2.4 Potato 52
2.2.5 Sugarcane 52
2.2.6 Banana 53
2.2.7 Carnation 53
2.2.8 Tomato 53
2.2.9 Soybean 54
2.2.10 Alfalfa 55
2.2.11 Sunflower 55
2.2.12 Cucumber 55
2.2.13 Eggplant 56
2.2.14 Melon 56
2.2.15 Strawberry 56
2.3 Explants Used for the Transformation of Woody Plants 57
2.3.1 Almond 58
2.3.2 Apple 59
2.3.3 Apricot 59
2.3.4 Blueberry 59
2.3.5 Birch 60
2.3.6 Citrus 61
2.3.7 Cherry 61
2.3.8 Eucalyptus 62
2.3.9 Kiwi 62
2.3.10 Larch 63
2.3.11 Peach 63
2.3.12 Pear 64
2.3.13 Pine 64
2.3.14 Plum 64
2.3.15 Populus 65
2.3.16 Spruces 65
2.3.17 Walnut 66
2.4 Concluding Remarks 66
References 66
Chapter 3 76
Gene Transfer Methods 76
3.1 Introduction 76
3.2 Gene Delivery Methods 77
3.2.1 Biological Methods 80
3.2.1.1 Agrobacterium-Mediated Gene Transfer 80
3.2.1.2 Agroinfection 84
3.2.1.3 Virus-induced Gene Silencing (VIGS) 84
3.2.1.4 Other Microorganisms for DNA Delivery 85
3.3 Physical Methods 86
3.3.1 Liposome-Mediated Delivery 86
3.3.2 Nanoparticles 87
3.3.3 Microinjection 87
3.3.4 Silicon Carbide Whiskers 88
3.3.5 Microprojectile Bombardment 89
3.3.6 Electroporation 91
3.3.7 Other Potential Physical Methods 92
3.4 Combined Physical and Biological DNA Delivery 92
3.4.1 Agrolistic 92
3.4.2 Sonication-Assisted Delivery 93
3.5 Concluding Remarks 93
References 94
Chapter 4 103
Selection and Screening Strategies 103
4.1 Introduction 103
4.2 Selection Strategies 104
4.2.1 Positive Selection 104
4.2.1.1 Shoot/Root Phenotypic-Based Positive Selection 104
Isopentyl Transferase 104
Enhancer of Shoot Regeneration 1 105
Histidine Kinase 106
Homeodomain-Containing Knotted1 Protein 106
b-Glucuronidase 106
Root Locus (ROL) Proteins 107
4.2.1.2 Carbon-Based Positive Selection 107
Xylose Isomerase 107
Phosphomannose Isomerase 108
D-Arabitol Dehydrogenase 108
4.2.1.3 Auxotrophic Markers 108
4.2.1.4 Selection with Biotic and Abiotic Stresses 109
Pathogen Resistance 109
High Salt Tolerance 109
Heat Shock Tolerance 109
4.2.1.5 Antibiotics-Based Positive Selection 110
4.2.2 Negative Selection 110
4.2.2.1 Antibiotics 110
Neomycin Phosphotransferase 110
Hygromycin Phosphotransferase 111
Aminoglycoside-3-N-acetyltransferase (ACC3) and Aminoglycoside-6-N-acetyltransferase (ACC6) 112
Bleomycin-Binding Protein 112
Dihydropteroate Synthase 113
Streptothricin Acetyltransferase 113
Chloramphenicol Acetyltransferase 113
ATP-binding Cassette (ABC) Transporter 114
4.2.2.2 Herbicides 114
Phosphinothricin Acetyltransferase 114
5-Enolpyruvyl-Shikimate-3-Phosphate Synthase and Glyphosate Oxidase 114
Acetolactate Synthase 116
Bromoxynil-Specific Nitrilase 117
Cytochrome P450 Monooxygenase 117
Protoporphyrinogen Oxidase 118
Organophosphate Hydrolase 118
Mutant a-Tubulin Genes 118
4.2.2.3 Other Toxic Compounds 119
2-Deoxyglucose 119
Betaine Aldehyde Dehydrogenase (BADH) 119
Dihydrodipicolinate Synthase and Aspartate Kinase 122
Tryptophan Decarboxylase 122
Dihydrofolate Reductase 123
Tryptophan Synthase b1 123
Peptide Deformylase 123
Threonine Deaminase 124
Anthranilate Synthase 124
D-Amino Acid Deaminase 125
Glutamate-1-semialdehyde Aminotransferase 125
Galactose-1-phosphate Uridyltransferase 126
Cyanamide Hydratase 126
Octopine Synthase 126
4.3 Screening Strategies 126
4.3.1 Scorable Markers 127
4.3.1.1 b-Galactosidase 127
4.3.1.2 GUS, b-Glucuronidase (uidA) 129
4.3.1.3 Luciferase 131
4.3.1.4 GFPs 131
4.3.1.5 Reef Coral Proteins 132
4.3.1.6 Oxalate Oxidases 133
4.3.1.7 Anthocyanin Formation (Maize R, C1, and B Transcription Factors) 133
4.3.1.8 Phytoene Synthase 134
4.3.1.9 NPTII 134
4.3.1.10 Opines 134
4.3.1.11 Chloramphenicol Acetyl Transferase 135
4.3.2 PCR-Based Screening 135
4.3.3 Southern Hybridization Analysis 137
4.3.4 ELISA 139
4.4 Marker-Removal Strategies 139
4.4.1 Cotransformation and Subsequent Segregation 140
4.4.2 Transposon-based Marker Gene Removal 142
4.4.3 Site-specific Recombination-mediated Marker Deletion 142
4.4.4 Intrachromosomal Homologous Recombination System 145
4.4.5 Cytokinin-Based Backbone-Free Approach 145
4.4.6 Radiation Method 145
4.5 Conclusions 146
Chapter 5 162
Levels and Stability of Expression of Transgenes 162
5.1 Introduction 162
5.2 Gene Design for Insertion 163
5.3 Quantification of Transgene Expression 163
5.4 Promoters 164
5.4.1 Types of Promoters and Their Applications in Transgenic Crops 165
5.4.1.1 Constitutive Promoters 165
5.4.1.2 Nonconstitutive (Tissue-Enhanced) Promoters 172
Roots 173
Root Nodules 173
Tubers 174
Leaves 175
Flowers 176
Pistils 177
Pollen/Anther 177
Fruit 179
Seeds 180
5.5 Factors Affecting Stability and Level of Transgene Expression 181
5.5.1 SAR/MAR Effect on Transgene Expression 181
5.5.2 Effect of 50 and 30 UTR Regions 182
5.5.3 Effect of Introns 184
5.5.4 Role of Transcription Factors 186
5.5.5 Effect of DNA Acetylation and Methylation 187
5.6 Conclusions 189
References 190
Chapter 6 204
Silencing as a Tool for Transgenic Crop Improvement 204
6.1 Introduction 204
6.2 Procedures for Development of RNAi-Based Transgenic Gene-Silencing Lines 205
6.3 Crop Improvements with Silencing Tools 206
6.3.1 RNAi for Resistance to Diseases and Pests 206
6.3.1.1 RNAi for Resistance to Viruses 206
6.3.1.2 RNAi for Resistance to Parasitic Nematodes 207
6.3.1.3 RNAi for Resistance to Insects 208
6.3.2 RNAi to Enhance Quality Traits 209
6.3.2.1 Decaffeinated Coffee 209
6.3.2.2 Reduction of Toxic Gossypol in Cotton 210
6.3.2.3 Tearless Onions 211
6.3.2.4 Low-acrylamide French Fries and Potato Chips 211
6.4 Limitations of RNAi-Silencing Technology 212
6.5 Future Directions 213
References 214
Chapter 7 217
Transgene Integration, Expression and Stability in Plants: Strategies for Improvements 217
7.1 Introduction 217
7.2 Methods for the Analysis of Transgenic Loci 218
7.3 Locus Structure in Plants Transformed by Agrobacterium tumefaciens 221
7.3.1 Principles of Gene Transfer 221
7.3.2 T-DNA Locus Structure 222
7.3.3 T-DNA Integration Mechanism 223
7.3.4 Cotransfer of Vector Backbone Sequences 225
7.4 Locus Structure in Plants Transformed by Direct DNA Transfer 226
7.4.1 Principles of Gene Transfer 226
7.4.2 Transgenic Locus Structure 227
7.4.3 Mechanisms of Transgene Integration 231
7.5 Locus Structure and Transgene Stability 235
7.5.1 Position Effects 235
7.5.2 Locus Structure Effects 236
7.5.3 Overcoming Position and Locus Structure Effects by Buffering the Transgene 237
7.5.4 Overcoming Position and Locus Structure Effects by Homologous Recombination 238
7.5.5 Overcoming Position and Locus Structure Effects by Organelle Transformation 239
7.5.6 Overcoming Position and Locus Structure Effects by Site-specific Recombination 240
7.5.7 Overcoming Position and Locus Structure Effects Using Minichromosomes 241
7.6 Epigenetic Silencing Phenomena Resulting From Complex Locus Structures and High-Level Expression 242
7.7 Conclusions 244
References 245
Chapter 8 254
Organelle Transformations 254
8.1 Introduction 254
8.2 Overview of Organelle Transformation 255
8.2.1 Plastids 255
8.2.2 Mitochondria 258
8.3 Achievements and Technique Used in Organelle Transformation 258
8.3.1 Plastids 258
8.3.1.1 Biolistics Transformation 258
8.3.1.2 Electroporation 260
8.3.1.3 Other Systems 260
8.3.2 Mitochondria 260
8.4 Conclusions 260
References 261
Chapter 9 265
Biosynthesis and Biotransformation 265
9.1 Introduction 265
9.2 Biosynthesis of Useful Secondary Metabolites by Plant Cell Cultures 265
9.2.1 Useful Secondary Metabolites Produced by Cell Suspension Cultures 266
9.2.1.1 Shikonin 266
9.2.1.2 Paclitaxel 268
9.2.1.3 Other Useful Metabolites Produced in the Undifferentiated Cells 269
9.2.2 Useful Secondary Metabolites Produced by Hairy Root Cultures 270
9.2.2.1 Tropane Alkaloids 271
9.2.2.2 Camptothecin 272
9.2.2.3 Morphine 273
9.2.2.4 Other Useful Metabolites Produced by Hairy Root Cultures 274
9.2.3 Useful Secondary Products That Are Hardly Produced by Plant Cell Cultures 275
9.2.3.1 Vinca Alkaloids 275
9.2.3.2 Glycyrrhizin 277
9.3 Biotransformation 278
9.3.1 Glycosylation 278
9.3.1.1 Arbutin 279
9.3.1.2 Curcumin 279
9.3.1.3 Capsaicin 280
9.3.1.4 Monoterpene Alcohols 281
9.3.2 Hydroxylation 282
9.3.2.1 Digitoxin 282
9.3.3 Miscellaneous 283
9.3.3.1 Podophyllotoxin 283
9.3.3.2 Scopolamine 283
References 284
Chapter 10 289
Metabolic Engineering of Pathways and Gene Discovery 289
10.1 Introduction 289
10.2 The Beginnings and Early Years of Metabolic Engineering 290
10.3 The Basic Goals and Strategies of Metabolic Engineering 291
10.3.1 Biochemical Pathways 291
10.3.2 Functional Genomics 291
10.3.3 Compartmentalization, Transport, and Storage 292
10.3.4 Basic Strategies 292
10.4 Engineering Primary Metabolic Pathways 294
10.4.1 Carbohydrate Metabolism 294
10.4.2 Amino Acid Metabolism 295
10.4.3 Polyamine Metabolism 296
10.4.4 Lipid Metabolism 298
10.4.5 Metabolic Engineering in Chloroplast Genome 300
10.5 Engineering Secondary Metabolic Pathways 302
10.5.1 Transcription Factors as Tools for Metabolic Engineering 302
10.5.2 Flavonoids 303
10.5.2.1 Isoflavone Biosynthesis and Metabolic Engineering 305
10.5.2.2 Anthocyanin Biosynthesis and Metabolic Engineering 306
10.6 Future Roadmap 308
10.6.1 Food for the World 309
10.6.2 Biofortification of Plant-Based Foods 309
10.6.3 Biofuel From Plants 310
10.7 Conclusion: Factories of the Future 311
References 312
Index 321