Plant Biotechnology and Agriculture (eBook)

Front cover 1
Plant biotechnology and agriculture 4
Copyright page 5
Contents 8
Contributors 22
Foreword 26
Preface 28
Introduction to plant biotechnology 2011: Basic aspects and agricultural implications 30
A. Introduction to basic procedures in plant biotechnology 40
1 Genetics and genomics of crop domestication 42
Plants and Domestication 42
Scope 42
Domesticated crops 42
Weeds 43
Invasive species 43
Model species and crop sciences 44
Understanding Domestication Processes 44
Evidence of relatives and processes of early domestication 44
Genes of domestication 45
Genetic variation and domestication 45
Genetic control related to diversity and speciation 45
Domestication of maize 46
Domestication of legumes 46
Yield traits 47
Hybrid Species and New Polyploids in Domestication 47
Post-Domestication Selection 47
Modifications in crop characteristics 47
New Domestication 48
Domesticated species 48
Lost crops 48
Trees and biofuels 48
Genetics and breeding for new uses: Ecosystem services 49
Features of Domesticated Genomes 50
Superdomestication 53
Acknowledgments 55
2 The scope of things to come: New paradigms in biotechnology 58
Introduction 58
Progress Enabled by Next-Generation DNA Sequencing 59
Mapping of comprehensive, genome-wide, treatment-specific transcript profiles 62
Current next-gen sequencing 62
Behold the third generation 62
The Elephant in the Laboratory: Data Handling 63
From Sequences to Comparative Genomics 63
Transcriptome profiling 64
Broadening the Genomics Toolbox: Proteins and Metabolites 65
Proteomics advances 65
Metabolomics highlights 65
Genomics Unlimited: Getting Beyond Mere Genes 66
Into the Future: Genomics-Based Biotechnology and Agriculture 67
From models to crops, from labs to fields 67
Genetic resources from extremophile species 68
Exploring “unknown unknowns” 68
The importance of stress “tolerance” engineering 68
Acknowledgments 69
3 Protein targeting: Strategic planning for optimizing protein products through plant biotechnology 74
Introduction: Strategic Decisions about How to Express an Output Trait 74
Approaches 76
Routing proteins to the endomembrane system 76
Accumulating proteins in the ER 77
Accumulating proteins in ER-derived protein bodies 78
Accumulating proteins in the vacuole or vacuolar protein bodies 78
Accumulating proteins in the apoplast 79
Accumulating proteins in the chloroplast 79
Accumulating proteins on the surface of oil bodies 80
Seed-Based Expression Systems 80
Leaf Systems 83
Stable versus transient leaf expression systems 83
Protein bodies in leaves 86
Hairy Root Cultures 86
Advantages of the hairy root culture system 87
Recombinant proteins expressed with hairy root cultures 87
Hairy root cultures in bioreactors and scale-up 87
Summary and Conclusions 89
4 Proteomics and its application in plant biotechnology 94
Introduction 94
Mass Spectrometry-Based Proteomics 95
Sample preparation prior to mass spectrometry 95
Protein extraction and digestion 96
Protein and peptide fractionation 96
Mass spectrometry 96
Spectra assignment for peptide and protein identification 97
Quantitative proteomics 97
Post-translational modifications 97
Proteomics in Plant Biotechnology 98
What has been achieved so far in crop proteomics? 98
Arabidopsis thaliana as plant model organism 98
Crops and other economically relevant plant species 99
Future applications and perspectives 100
5 Plant metabolomics: Applications and opportunities for agricultural biotechnology 106
Introduction 106
Metabolite Networks: The Basics 107
Metabolomics: Technologies for Analyses 108
Analytical platforms 109
Data analysis and interpretation 110
Data pre-processing 111
Normalization and data transformation 111
Statistical analysis 111
Data visualization 112
Metabolomics: Applications in Agricultural Biotechnology 112
Metabolite profiling to test substantial equivalence 112
Phytochemical diversity, phenotyping, and classification 113
Postharvest quality of horticultural crops 113
Stress responses 113
Functional genomics 114
Breeding and metabolite quantitative trait loci 114
Metabolomics: Challenges and Future Perspectives 115
From model organisms to crop plants 115
Compartmentation of plant metabolism 115
High-resolution sampling 115
Primary and secondary metabolism pose different challenges 115
Identifying the metabolome 116
Measurements of metabolic flux 116
Outlook 117
Acknowledgments 117
6 Plant genome sequencing: Models for developing synteny maps and association mapping 122
Introduction 122
Genome Sequencing 123
Strategies for plant genome sequencing 123
High-throughput sequencing technologies 125
Single molecule and real-time sequencing 125
Assembly and alignment programs 125
Genome browsers 126
Models for Developing Syntenic Maps 127
Definitions 127
Intraspecies comparison 127
Cytogenetics for interspecies comparison 128
Sequence comparison 128
Macro- versus micro-synteny 128
Nature of the differences 128
Applications of syntenic maps 130
Tools and limitations 130
Association Mapping 130
Definitions 130
Population size and structure 131
Markers and marker density 132
Implications 133
7 Agrobacterium-mediated plant genetic transformation 138
Introduction 138
The Genetic Transformation Process 138
Agrobacterium as a Tool for Plant Transformation 143
Novel and Specialized Vectors for Plant Transformation 145
Manipulating the Plant Genome to Improve and Control Transformation 147
Using Novel Selection Methods and Restriction Enzymes to Control T-DNA Integration 148
Conclusions and Future Prospects 149
Acknowledgments 150
8 Biolistic and other non-Agrobacterium technologies of plant transformation 156
Introduction 156
Other Non-Agrobacterium Transformation 156
Electrophoretic transfection 156
Electroporation 157
Bioactive-beads-mediated gene transfer 157
Microinjection 157
Pollen-tube pathway 158
Silica carbide whisker-mediated transformation 158
Biolistic Transformation 159
The invention 159
Electric discharge particle acceleration 159
Current status of the “invention” hardware 160
Advantages of Biolistic Transformation 160
Implications of Biolistics in Agricultural Biotechnology 161
Application of biolistics in agriculture crops 161
Papaya: A case study of biolistic transformation 161
Papaya and papaya ringspot virus 161
Papaya and PRSV in Hawaii 164
Biolistic approach to transform papaya for resistance to PRSV 164
Testing, deregulation, commercialization, and impact of the transgenic papaya in Hawaii 166
Characteristics of transgene inserts in biolistically transformed line 55-1 and its derivatives 166
9 Plant tissue culture for biotechnology 170
Introduction 170
Plant Tissue Culture Technology 170
The basic laboratory setup 170
Preparation of tissue for culturing 171
Nutrient media 171
Types of culture 172
Environmental aspects of tissue culture 172
Modes of regeneration 173
Implications for Agricultural Biotechnology 173
Haploid tissue culture 174
Somatic embryogenesis 174
Artificial seeds 174
In vitro flowering 175
Future Perspectives 175
Acknowledgments 175
B. Breeding biotechnologies 178
10 Somatic (asexual) procedures (haploids, protoplasts, cell selection) and their applications 180
General Introduction 180
Somatic Embryogenesis 180
Introduction 180
Patterns of somatic embryogenesis 181
Factors affecting somatic embryo induction 181
Explant and genotype 181
Chemical factors 181
Other inductive factors 182
Histodifferentiation 182
Plant maturation 182
Plant regeneration 183
Gene expression during somatic embryogenesis 183
Mass propagation and somaclonal variation 183
Haploid Technology 183
Introduction 183
Cytological basis underlying haploid plant induction 184
Factors affecting the induction of microspore embryos 185
Plant genotype 185
Developmental stage of the microspore 185
Stress pre-treatment 185
Culture medium 186
Growth regulators 186
Haploid induction via ovary and ovule cultures 186
Protoplast and Somatic Hybridization 187
Introduction 187
Types of somatic hybrids 187
Protoplast fusion methods 187
Selection of somatic hybrids 189
Identification of somatic hybrids 189
Factors affecting regeneration of hybrid plants 190
Screening and Development of Stress-Resistant Plants Using in vitro Selection Techniques 190
Introduction 190
General methods of screening and breeding using in vitro selection techniques 190
Biotic stress resistance 191
Abiotic stress tolerance 191
Future perspective of screening and breeding using in vitro selection techniques 194
Conclusions and Future Directions 194
Acknowledgments 194
11 Marker-assisted selection in plant breeding 202
Background 202
The concept of marker-assisted selection 202
Historical review 203
Plant Traits, DNA Markers, Technologies, and Applications 203
Genes controlling important traits 203
MAS for biotic stresses 203
MAS for abiotic stress 204
MAS for agronomic traits 204
DNA markers 204
Restriction fragment length polymorphism 205
Random amplified polymorphic DNA 206
Amplified fragment length polymorphism 206
Simple sequence repeats (also referred to as microsatellites) 206
Single nucleotide polymorphism 207
Modern genotyping technologies 207
Mass spectrometry 207
Diversity arrays technology 207
SNP arrays 207
Modern sequencing technologies 208
Solexa-Illumina 208
454 (now Roche) 209
Pacific biosciences 209
Identification of genes controlling commercially important traits 209
Classical methods of gene identification 209
Modern methods for gene identification 210
Targeting-induced local lesions in genomes 210
Genome-wide association 210
RNA interference 212
Expression QTLs 212
Chemical genetics 212
Application of DNA markers to breeding 212
Identification 212
Improving classical breeding projects 212
Conserving diversity 213
Selection of parents for the generation of heterosis 213
Introgression 213
Pyramiding 213
MAS in breeding programs 213
Discussion 215
Bottlenecks and difficulties in the application of MAS 215
Future prospects of application of genetic variations to breeding 216
Acknowledgment 217
12 Male sterility and hybrid seed production 224
Introduction 224
Male Gametogenesis 224
Pollen mitosis I 224
Pollen mitosis II 225
Male Sterility Mutants Elucidate Anther Development 226
Hormonal Influences on Male Reproduction in Plants 226
Gibberellic acid 226
GA regulates jasmonic acid biosynthesis 227
Brassinosteroids 227
Auxins 228
Cytoplasmic Male Sterility Systems in Agriculture 228
Plant mitochondrial mutations 228
Fertility restoration 228
Stability of the CMS trait 229
Male Sterility: Metabolic and Evolutionary Implications 229
CMS is a naturally found condition 229
Organelle metabolism influences pollen development 229
Genetic Engineering of Male Sterility 230
Implementation of Male Sterility in Agricultural Systems 230
13 Advances in identifying and exploiting natural genetic variation 234
Natural Genetic Variation in Crop Breeding: From Prehistory to the Green Revolution 234
The Genetic Limits of Evolving Domesticated Crops 235
Tapping the natural genetic variation present in wild ancestors 235
Natural Genetic Variation in Arabidopsis 236
QTL Analyses in Arabidopsis 236
Novel Arabidopsis genes isolated through the natural variation approach 237
What to Expect: Intraspecific Variation in Gene Structure and Content 237
Structural genome variation: Higher than expected? 237
QTL Analysis and Sequence Variation in Crops 238
Domestication genes of maize 238
Examples from rice 238
Examples from other cereals 239
Toward Prediction of Variation in Molecular Function: Why Model Organisms are here to Stay 239
Crucial support from model organism candidate genes 239
Model systems as references to characterize allele activities 240
Beyond Simple Traits: Epigenetics, Heterosis, Genetic Incompatibility, and Trade-offs 240
Incompatibility between natural accessions 240
Trade-offs between different beneficial traits 241
Extending the Toolbox: Genome-wide Association Mapping 241
The Route to Effectively Exploit Natural Variation for Plant Biotechnology 241
14 From epigenetics to epigenomics and their implications in plant breeding 246
Mechanisms of Epigenetic Inheritance and their Interactions 246
Introduction 246
Epigenetic mechanisms and their interactions 247
DNA cytosine methylation 247
Histone modifications 248
Small RNAs 250
From Epigenetics to Epigenomics 251
Deciphering epigenomes: A matter of scale and complexity 251
Epigenomic methods and the type of data collected 251
ChIP-chip 251
ChIP-seq 252
Genome-wide DNA methylation profiling 252
Epigenomic resources 252
Transposable elements on the emerging epigenomic landscape(s) 255
An illustrative and practical example of data and resources integration 256
Epigenetic Phenomena and their Implications in Plant Breeding 256
Epigenetic controls during vegetative development and the role of the environment 256
Epigenetic control of flowering 258
Endosperm development and parental imprinting 259
Conclusions and Prospects 261
Acknowledgments 261
Abbreviations 261
C. Plant germplasm 266
15 An engineering view to micropropagation and generation of true to type and pathogen-free plants 268
Preface 268
Shoot Multiplication Through Meristem Culture 268
Stage 0: Disinfection and start of axenic culture 269
Stage I: Initiation of culture 269
Stage II: Multiplication 269
Stage III: Elongation and promotion of shoot and root development 270
Stage IV: Acclimatization and hardening 270
Automation 270
Energy and Lights 271
Photoautotrophic Cultures 271
Micropropagation in Liquid Media 272
Plant—Microbe Interaction During in vitro and ex vitro Stages of Micropropagation 272
Inoculation with Beneficial Microorganisms 273
Elimination of Viruses by in vitro Techniques 277
Concluding Remarks 277
Acknowledgments 277
16 Regulation of apomixis 282
Introduction 282
Overview of Ovule Development During Sexual Reproduction 283
Overview of Ovule Development During Apomictic Reproduction 283
Germline Specification 283
Apomeiosis 285
Megagametogenesis 286
Gamete Specification 286
Parthenogenesis 287
Endosperm Development 289
Chromatin Modification and Epigenetic Regulation 290
Conclusions and Future Prospects for Apomixis in Crops 290
17 Germplasm collection, storage, and conservation 294
Introduction 294
Strategies for conserving plant biodiversity 294
Ex situ conservation technologies 295
Applications of Biotechnologies for Conservation 296
In vitro collecting 296
Slow growth storage 297
Classical techniques 297
Alternative techniques 297
Current development and use of in vitro slow growth storage 297
Cryopreservation 298
Cryopreservation techniques 298
Classical cryopreservation techniques 298
New cryopreservation techniques 299
Cryopreservation of vegetatively propagated and recalcitrant seed species 299
Vegetatively propagated species 299
Recalcitrant seed species 300
Large-scale utilization of cryopreservation for germplasm conservation 301
Additional uses of cryopreservation 302
Cryopreservation: progress and prospects 302
Conclusions 303
D. Controlling plant response to the environment: Abiotic and biotic stress 308
18 Integrating genomics and genetics to accelerate development of drought and salinity tolerant crops 310
Impact of Abiotic Stresses on Crop Plant Productivity 310
Water Deficit: A Major Abiotic Stress Factor 311
Salinity 311
Plant Responses to Abiotic Stress 311
Breeding for Drought and Salinity Tolerance: “The Conventional Approach” 312
Germplasm resources for drought and salinity tolerance 313
Genetic dissection of plant responses to abiotic stress 313
Introducing new technologies for abiotic stress breeding 314
Engineering-Tolerant Crop Plants: The Transgenic Approach 314
Genes for osmoregulation 314
Dehydration-responsive element 317
NAC proteins 318
Genes for ionic balance 318
Genes for redox regulation 318
Aquaporins 319
Other transcription factors 319
Hormone Balance and Abiotic Stress 319
Challenges and Prospects 320
Acknowledgments 320
19 Molecular responses to extreme temperatures 326
Introduction 326
Plant Response to Low Temperature 326
Low temperature perception 327
Transducing the low-temperature signal 328
Ca2+ as a second messenger in low-temperature response 328
Other molecules involved in transducing the cold signal 329
Gene expression in response to low temperature 331
Transcriptional control of cold-regulated gene expression 331
Post-transcriptional control of cold-regulated gene expression 334
Translational and post-translational control of cold-regulated gene expression 334
Epigenetic regulation of low-temperature response 335
Cross-talk between Plant Responses to Extreme Temperatures 336
The membrane as a node in the perception of temperature oscillations 337
Transducing the signals initiated by temperature variations 337
Ca2+ is a versatile second messenger in plant responses to extreme temperatures 337
Hormones mediate extreme temperature signaling 337
Regulation of gene expression in response to extreme temperatures 338
Transcriptional regulation of gene expression in response to high and low temperatures 338
Post-transcriptional regulation of gene expression in response to high and low temperatures 338
Translational and post-translational regulation of gene expression in response to high and low temperatures 339
Conclusions 339
Acknowledgments 340
20 Biotechnological approaches for phytoremediation 348
Introduction 348
Overview of results from biotechnological approaches for different pollutants 350
Inorganic pollutants 350
Arsenic 350
Arsenic pollution and toxicity 350
Arsenic in foods and implications for human health 350
Mechanism of As uptake and detoxification in microbes and plants 351
Biotechnological approaches for As remediation and reducing As in food crops 351
Arsenic phytoremediation 351
Preventing arsenic uptake in food crops 352
Mercury 353
Mercury pollution and toxicity 353
Mercury detoxification in bacteria and plants 353
Biotechnological approaches for Hg transformation and phytoremediation 354
Mercury hyperaccumulation 355
Selenium 355
Overview of Se metabolism in plants 355
Biotechnological approaches to study and manipulate Se metabolism in plants 356
Selenium phytoremediation field studies 356
Organic pollutants 356
Solvents 357
Explosives 358
BTEX, PAHs, and PCBs 359
Pesticides 360
Future Prospects 362
Acknowledgments 362
21 Biotechnological strategies for engineering plants with durable resistance to fungal and bacterial pathogens 368
Introduction 368
Choosing the Target Gene for Transgenic Expression 369
Plant immune receptors mediating pathogen recognition 369
Elicitors of plant immunity 370
Plant genes involved in signaling networks of plant immunity 371
Antimicrobial genes 373
Genes targeting pathogen virulence determinants 374
How Many Transgenes Should be Expressed in a Single Plant for Efficient Disease Control? 374
When and Where Should the Transgene(s) be Expressed? 375
Pathogen-responsive and tissue-specific promoters 376
Pathogen-responsive elements and synthetic promoters 377
Conclusions and Prospects 378
Acknowledgments 378
22 Controlling plant response to the environment: Viral diseases 382
Introduction 382
Phytosanitation and Quarantine Regulation 383
Transmission of Plant Viruses 383
Cultural Strategies of Virus Control 383
Management of soil-borne viruses 383
Management of airborne viruses 384
Resistance to Virus Transmission by Insects 384
Pathogen-derived resistance 384
RNA-mediated resistance 385
Application of the PDR Concept for Developing Transgenic Virus Resistance to Horticultural Crops 385
RNA silencing-based applications for developing virus resistant plants 386
PDR stability and suppression of RNA silencing 387
Assessment of Risks Associated with Transgenic Virus Resistance in Plants 387
Conclusion 388
23 Insects, nematodes, and other pests 392
Introduction — Genetically Modified Crops for Insect Resistance 392
History of B. thuringiensis 392
Cry proteins 393
Commercially Available Insect Protected Crops 393
Bt maize 393
Bt cotton 395
Discontinued Bt crops 396
Bt Crops Under Development 396
Bt brinjal 396
Bt rice 397
Other Bt crops 397
Impact of Bt 398
Benefits of Bt crops 398
Concerns about Bt crops 398
Improving Bt 399
Cowpea Trypsin Inhibitor 399
Novel Insecticidal Protection 400
VIP genes 400
Microorganism-derived toxins 400
Plant-derived toxins 400
Secondary metabolites 401
Other toxins 402
RNAi 402
Nematode-Resistant Crops 403
Recombinant Insecticides 403
Conclusion 403
E. Biotechnology for improvement of yield and quality traits 410
24 Growth Control of Root Architecture 412
Introduction to Root System Architecture 412
Genetic and Developmental Aspects of Root Growth 412
Stereotypical organization of root tissues 413
Architectural possibilities 413
Signaling 414
Systems biology concept of cell identity 415
Plant–Environment Interactions 415
Environmental sensing and root exudation 415
Microbial interactions 416
Architectural responses to nutrient availability 417
Crop Root Systems 418
Types of root systems 418
Embryonic and post-embryonic root systems 418
Evolutionary strategies and trade-offs 419
Approaches to Study Root Architecture 419
Quantitative analysis 419
High-throughput sequencing 420
Phenomics 420
Concluding Remarks 421
25 Control of flowering 426
Introduction 426
A plant’s perspective 426
A farmer’s perspective 426
Proteins Controlling Flowering Time 427
Florigen and FLOWERING LOCUS T (FT) 427
Transcription factors regulating FT 428
FLOWERING LOCUS C (FLC) and MADS AFFECTING FLOWERING (MAF) proteins 428
SHORT VEGETATIVE PHASE (SVP) 428
CONSTANS (CO) 428
APETALA2-like flowering time repressors 428
TEMPRANILLO (TEM) 429
Proteins parallel or downstream of FT 429
SOC1 and FRUITFULL 429
APETALA1 and LEAFY 429
SEPALLATA3 (SEP3) 430
SQUAMOSA-PROMOTER BINDING PROTEIN LIKE (SPL) 430
PENNYWISE and PENNYFOOLISH 430
Processes Affecting Flowering Time Proteins 430
Histone modifications 430
Modifications associated with active genes 431
Modifications associated with inactive genes 431
Gibberellin 431
MicroRNAs 432
miR156 432
miR159 432
miR167 432
miR169 432
miR172 433
The circadian clock 433
Regulated proteolysis 433
Sugars 433
Developmental Decisions on Timing of Flowering 434
Juvenility 434
Seasonality 434
Photoperiod 434
Vernalization 434
Warm ambient temperatures 435
Reproductive cycles and alternate bearing 436
Summary 437
Acknowledgment 437
26 Fruit development and ripening: A molecular perspective 444
Fruit Classification 444
Fruit Development 445
Fruit shape, size, and mass 445
Fruit Ripening 448
Ripening mutations 448
Nutritional mutations 450
Shelf life mutations 451
Ethylene and Fruit Ripening 452
Ethylene biosynthesis 452
Ethylene perception and signal transduction 453
Genetic intervention in ethylene biosynthesis and perception 455
Fruit Texture 456
Cell wall depolymerizing enzymes 456
Expansins 457
Protein glycosylation 457
Future Perspectives 457
27 Potential application of biotechnology to maintain fresh produce postharvest quality and reduce losses during storage 464
Introduction 464
Ethylene Biosynthesis or Perception and Its Relation to Postharvest Quality of Fresh Produce 465
Senescence in Postharvest of Leafy Vegetables and Flowers 466
Background 466
Senescence regulatory genes 466
Senescence-associated hormone biosynthesis or perception 467
Oxidative stress involvement in senescence 468
Chlorophyll degradation 468
Abscission of Fruits, Flowers, and Leaves During Postharvest 468
Background 468
Development of the dedicated AZ tissue 469
Regulatory genes involved in abscission control or mediating hormonal signal transduction 469
Genes involved in actual execution of cell separation in the later stage of abscission 470
Ethylene and abscission 470
Regulated manipulation of abscission 470
Reducing Postharvest Chilling Sensitivity 470
Background 470
Membrane structure and chilling sensitivity 471
Oxidative stress and chilling sensitivity or tolerance 472
Regulation of low-temperature responses 472
Molecules with protective functions during cold stress 473
Affecting Postharvest Texture and Appearance Qualities 474
Background 474
Softening and cell wall hydrolysis 474
Softening and turgor 474
Tissue lignifications 474
Implications for Plant and Agricultural Biotechnology 475
28 Engineering the biosynthesis of low molecular weight metabolites for quality traits (essential nutrients, health-promoting phytochemicals, volatiles, and aroma compounds) 482
General Introduction 482
Lessons from Essential Nutrients 483
Essential amino acids 483
Fatty acids 485
Vitamins 485
Vitamin A 485
Vitamin E 486
Folate 486
Vitamin C 487
Improvement of the bioavailability of minerals through metabolic engineering 488
Multigene transfer for improved food quality 488
General Strategy for the Engineering of Secondary Metabolites with Nutritional Value 488
Identification of biosynthetic genes 488
Identification of transcription factors and engineering through integrated “omics” 489
Modulation of organelle development 489
Quality Improvement of Plants as Functional or Medicinal Food 490
Resveratrol 490
Anthocyanins and flavonoids 491
Catechins and proanthocyanidins 491
Sesamins 491
Beloved Metabolites: Plant Volatiles 491
Biochemistry of plant volatile secondary metabolites 492
Flavor compounds in fruits 493
Scent/aroma of flowers 494
Volatile organic chemicals in vegetative organs of plants 494
Perspectives 495
Conclusion 497
Acknowledgments 497
F. Plants as factories for industrial products, pharmaceuticals, biomaterials, and bioenergy 502
29 Vaccines, antibodies, and pharmaceutical proteins 504
Introduction 504
Expression Technologies: Nuclear Transformation 505
Expression Technologies: Plastid Transformation 508
Expression Technologies: Transient Expression Systems 508
“Full virus” vectors 509
Magnifection 509
Derisking the new manufacturing process 510
Plant-Made Pharmaceuticals: A Unique Selling Proposition? 510
Plant-Based Manufacturing, Post-Translational Modifications, and Plant-Specific Sugars 511
Plant-Based Manufacturing and Downstream Issues 512
Plant-Based Expression Systems: Advantages and Limitations 513
Nuclear transformation 514
Plastid transformation 514
Transient expression 515
Conclusions and Outlook 515
Acknowledgments 515
30 Plants as factories for bioplastics and other novel biomaterials 520
Introduction 520
Major Natural Plant Biopolymers 521
Starch 521
Cellulose 521
Rubber 522
Proteins 524
Novel Polymers Produced in Transgenic Plants 524
A role for transgenic crops in the production of biopolymers? 524
Which biopolymers should be targeted for production in transgenic crops? 525
Which crops should be targeted? 526
Fibrous proteins 526
Cyanophycin 527
Polyhydroxyalkanoate 528
Conclusion and Prospects 530
31 Bioenergy from plants and plant residues 534
Introduction 534
Biochemical Conversion 536
Comminution 537
Pre-treatment 538
Saccharification 539
Fuel synthesis 539
Thermochemical Conversion 540
Pyrolysis 540
Gasification 541
Concluding Remarks 542
Acknowledgment 542
G. Commercial, legal, sociological, and public aspects of agricultural plant biotechnologies 546
32 Containing and mitigating transgene flow from crops to weeds, to wild species, and to crops 548
Introduction: Does Transgene Flow Matter? 548
Transgene flow: To what ecosystem? 549
Thresholds matter 550
Gene containment and/or mitigation is often necessary 550
Methods of Containment 550
Containment by targeting genes to a cytoplasmic genome 551
Male sterility 551
Rendering crops asexual 552
Genetic use restriction technologies: Alias “terminators” 552
Chemically induced promoters for containment 552
Recoverable block of function 553
Repressible seed-lethal technologies 553
Trans-splicing to prevent movement 553
A genetic chaperon to prevent promiscuous transgene flow from wheat to its wild and weedy relatives 554
Transiently transgenic crops 554
Mitigating Transgene Flow 555
Demonstration of transgenic mitigation 555
Will transgenic mitigation traits adversely affect wild relatives of the crop? Models that suggest that mitigation is deleterious 556
Traits that can be Used in Tandem Transgenic Mitigation Constructs 557
Morphological traits and genes for mitigation 557
Secondary dormancy 557
Seed shattering 557
Dwarfing 557
Shade avoidance 558
Chemical mitigation of transgene flow 558
Activatable genes for susceptibility to chemicals 558
Hypersensitivity to herbicides as transgenic mitigation 558
Special cases where transgenic mitigation is needed 559
Mitigation for biennial and annual “root” crops 559
Transgenically mitigated genes for crop-produced pharmaceuticals and industrial products 559
Mitigation in species used for phytoremediation 559
Concluding Remarks 560
33 Intellectual property rights of biotechnologically improved plants 564
Introduction: Capitalizing on Research and Development in Agricultural Biotechnology with Intellectual Property Protection 564
Intellectual Property Protection of Biotechnologically Improved Plants 565
International intellectual property protection agreements 565
Union International pour la Protection des Obtentions Végétales 565
Trade-related Intellectual Property Rights 566
International Treaty on Plant Genetic Resources 566
Types of intellectual property protection in plant biotechnology 567
Plant variety protection 567
U.S. plant patents 567
Utility patents applied to plant biotechnology 568
Gene patenting 569
Material transfer agreements 570
Trademarks, trade secrets, know-how, and geographical designations 571
Freedom-to-Operate in Agricultural Biotechnology: The Road from a Research Idea to Commercialization of a Biotechnologically Improved Plant Product 571
Technology Transfer as a Means to Facilitate the Development of Biotechnology-Based Agriculture 573
Conclusion and Future Needs 575
Acknowledgments 576
34 Regulatory issues of biotechnologically improved plants 580
Introduction 580
Commercializing an Agricultural Biotechnology Product 581
The Regulatory Framework 582
The U.S. Coordinated Framework 584
USDA–APHIS 584
EPA 585
FDA 586
Perspectives 586
Specialty crops regulatory assistance: A new paradigm 586
Standardization 587
Conclusions 587
35 Prospects for increased food production and poverty alleviation: What plant biotechnology can practically deliver and what it cannot 590
Introduction 590
Progress to Date 591
The Next Generation 593
Barriers to Introduction 596
36 Crop biotechnology in developing countries 602
Introduction 602
Agriculture and Food in Developing Countries: The Needs 603
Feeding a growing world population 603
Undernutrition and poverty 603
Technology 604
Current State of GM Crops 604
Geographic distribution 604
Crops, traits, and farmers 604
Future and trends 604
Economic Impact of Transgenic Crops in Developing Countries 606
Main effects of current GM crops 606
Empirical evidence of farm level benefits 606
Bt cotton 606
Bt maize 607
HT crops 607
Effect of GM crops on poverty and inequality 607
Combined effects on farmer income 607
Macro level impacts 608
Health Impact 608
Safety concerns 608
Nutritional benefits of biofortification 609
Nutritional impact of GM biofortification 609
Reduced exposure to toxins, pesticides, and anti-nutrients 610
The Environment 610
Consumer Acceptance of GM Food 611
Regional differences 611
Factors influencing acceptance 611
Regulatory Systems 612
Importance of regulatory systems 612
Regional differences 612
Economics of regulation 612
The way forward 613
Conclusions 613
Acknowledgments 613
Index 616