Kaynakça var.

180 Summary 181 Further reading 182 8 Reducing the effects of viral disease 184 Introduction 184 Types of plant virus 184 RNA viruses 186 Entry and replication: points of inhibition 188 How has the agricultural community dealt with viruses? 189 case study 8.1 Developments in the sugar beet industry 190 The transgenic approach: PDR 192 Interactions involving viral proteins 192 case study 8.2 Arabis mosaic virus 195 RNA effects 197 Some non-PDR approaches 202 case study 8.3 DNA viruses 203 What has been commercialized in Western agriculture? 204 Yellow squash and zucchini 204 Papaya 205 Potato 205 Risk 206 Summary 208 Further reading 209 9 Strategies for engineering stress tolerance 212 Introduction 212 The nature of abiotic stress 214 The nature of water-deficit stress 214 Different abiotic stresses create a water deficit 215 case study 9.1 Glycine betaine production 218 Targeted approaches to manipulating tolerance to specific water-deficit stresses 222 Alternative approaches to salt stress 222 case study 9.2 Na+/H+ antiporters improve salt tolerance in transgenic plants 223 Alternative approaches to cold stress 224 case study 9.3 The COR regulon 224 Tolerance to heat stress 228 Secondary effects of abiotic stress: the production of ROS 228 Strategy 1: Expression of enzymes involved in scavenging ROS 232 Strategy 2: Production of antioxidants 234 Summary 234 Further reading 234 10 The improvement of crop yield and quality 237 Introduction 237 The genetic manipulation of fruit ripening 238 case study 10.1 The genetic manipulation of fruit softening 240 case study 10.2 The genetic modification of ethylene biosynthesis 243 case study 10.3 Modification of colour 247 case study 10.4 Golden Rice 251 Engineering plant protein composition for improved nutrition 256 The genetic manipulation of crop yield by enhancement of photosynthesis 258 Manipulation of light harvesting and the assimilate distribution: phytochromes 258 Direct manipulation of photosynthesis: enhancement of dark reactions 261 Summary 263 Further reading 263 11 Molecular farming 267 Introduction 267 Carbohydrates and lipids 267 Carbohydrate production 267 case study 11.1 Starch 268 case study 11.2 Polyfructans 272 Metabolic engineering of lipids 276 case study 11.3 Bioplastics 282 Molecular farming of proteins 285 Production systems 286 case study 11.4 The oleosin system: hirudin and insulin production 289 Medically related proteins 296 case study 11.5 Custom-made antibodies 300 case study 11.6 Edible vaccines 304 Economic and regulatory considerations for molecular farming 307 Summary 311 Further reading 312 12 Science and society: public acceptance of genetically modified crops 316 Introduction 316 Public concerns 316 The current state of transgenic crops 318 Who has benefited from these first-generation GM crops? 318 What will drive the development of the future generations of GM crops? 322 Concerns about GM crops 323 Antibiotic-resistance genes 323 Herbicide resistance and super-weeds 324 Gene containment 325 Big business 328 Food safety 330 The regulation of GM crops and products 331 The EU 331 The USA 338 Summary 340 Further reading 340 13 Beyond genetically modified crops 343 Introduction 343 'Greener' genetic engineering 343 Genetic manipulation of complex agronomic traits 345 Identification of genes associated with desirable traits 348 Genetic mapping 348 Quantitative trait loci 352 Investigating gene function by reverse genetics 354 Insertional mutagenesis 354 TILLING 355 Understanding gene function within the genomic context: functional genomics 357 Transcriptomics 357 Proteomics 360 Interactomics 362 Metabolomics 362 Systems biology 363 Summary 363 Further reading 364 Index 367

Contents List of Abbreviations xvii 1 Plant genomes: the organization and expression of plant genes 1 Introduction 1 DNA, chromatin, and chromosome structure 1 Chromatin 4 An introduction to gene structure and gene expression 6 Gene structure and expression in a eukaryotic protein-coding gene 9 Translation 11 Regulation of gene expression 16 Chromatin conformation 16 Gene transcription 16 RNA modification, splicing, turnover, and transport 18 Translation 20 Post-translational modification 21 Localization 21 Protein turnover 21 Conclusions 22 Implications for plant transformation 22 Examples of promoter elements used to drive transgene expression 26 Protein targeting 26 Heterologous promoters 26 Genome size and organization 27 Arabidopsis and the new technologies 28 Genome-sequencing projects-technology, findings, and applications 28 Biotechnological implications of the AGI 31 Crop plant genome sequencing 31 Summary 33 Further reading 34 2 Plant tissue culture 37 Introduction 37 Plant tissue culture 37 Plasticity and totipotency 37 The culture environment 38 Plant cell culture media 39 Plant growth regulators 41 Culture types 44 Callus 44 Cell-suspension cultures 45 Protoplasts 46 Root cultures 46 Shoot tip and meristem culture 46 Embryo culture 46 Microspore culture 47 Plant regeneration 48 Somatic embryogenesis 48 case study 2.1 Cereal regeneration via somatic embryogenesis from immature or mature embryos 50 Organogenesis 51 Integration of plant tissue culture into plant transformation protocols 51 Summary 52 Further reading 53 3 Techniques for plant transformation 54 Introduction 54 Agrobacterium-mediated gene transfer 54 The biology of Agrobacterium 54 The Ti plasmid 56 Ti-plasmid features 56 The process of T-DNA transfer and integration 59 Step 1. Signal recognition by Agrobacterium 60 Step 2. Attachment to plant cells 60 Step 3. Induction of vir genes 60 Step 4. T-strand production 60 Step 5. Transfer of T-DNA out of the bacterial cell 60 Step 6. Transfer of the T-DNA and Vir proteins into the plant cell and nuclear localization 60 Practical applications of Agrobacterium-mediated plant transformation 61 case study 3.1 Agrobacterium-mediated transformation of tobacco 62 Transformation 64 Direct gene-transfer methods 66 Particle bombardment 67 case study 3.2 Biolistic transformation of rice 68 Polyethylene glycol-mediated transformation 72 Electroporation 73 Silicon carbide fibres: WHISKERSTM 73 Summary 74 Further reading 74 4 Vectors for plant transformation 77 Introduction 77 Desirable features of any plasmid vector 77 Development of plant transformation vectors 79 Basic features of vectors for plant transformation 79 Promoters and terminators 79 Selectable markers 86 Reporter genes 87 Origins of replication 91 Co-integrative and binary vectors 91 Families of binary vectors 91 Optimization 92 Arrangement of genes in the vector 95 Transgene copy number 98 Transgene position 98 Transgene features 98 Clean-gene technology 100 Summary 100 Further reading 101 5 The genetic manipulation of herbicide tolerance 105 Introduction 105 The use of herbicides in modern agriculture 106 What types of compounds are herbicides? 107 Strategies for engineering herbicide tolerance 111 case study 5.1 Glyphosate tolerance 111 case study 5.2 Phosphinothricin 121 Prospects for plant detoxification systems 123 Commercialization of herbicide-tolerant plants to date 124 case study 5.3 Engineering imidazolinone tolerance by targeted modification of endogenous plant genes 126 The environmental impact of herbicide-tolerant crops 127 The development of super-weeds 129 Summary 130 Further reading 131 6 The genetic manipulation of pest resistance 133 Introduction 133 The nature and scale of insect pest damage to crops 134 GM strategies for insect resistance: the Bacillus thuringiensis approach 134 The use of B. thuringiensis as a biopesticide 138 Bt-based genetic modification of plants 138 case study 6.1 Resistance of Bt maize to the European corn borer and other pests 140 The problem of insect resistance to Bt 141 The environmental impact of Bt crops 145 The Copy Nature strategy 146 case study 6.2 Cowpea trypsin inhibitor 149 Insect-resistant crops and food safety 153 Summary 153 Further reading 153 7 Plant disease resistance 156 Introduction 156 Plant-pathogen interactions 157 Prokaryotes 158 Fungi and water moulds 158 Viruses 160 Existing approaches to combating disease 160 Natural disease-resistance pathways: overlap between pests and diseases 162 Anatomical defences 162 Pre-existing protein and chemical protection 162 Inducible systems 163 Systemic responses 170 Biotechnological approaches to disease resistance 172 Protection against pathogens 173 Antimicrobial proteins 174 Transgenic crops for food safety 176 Induction of HR and SAR in transgenic plants 177 case study 7.1 The BASF potato 178 Developments for the future 179 Other transgenic approaches 179 Future prospects for breeding 179 case study 7.2 Xanthomonas spp.