Altman / Hasegawa Plant Biotechnology and Agriculture

Prospects for the 21st Century
1. Auflage 2011
ISBN: 978-0-12-381467-8
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 624 Seiten

As the oldest and largest human intervention in nature, the science of agriculture is one of the most intensely studied practices. From manipulation of plant gene structure to the use of plants for bioenergy, biotechnology interventions in plant and agricultural science have been rapidly developing over the past ten years with immense forward leaps on an annual basis. This book begins by laying the foundations for plant biotechnology by outlining the biological aspects including gene structure and expression, and the basic procedures in plant biotechnology of genomics, metabolomics, transcriptomics and proteomics. It then focuses on a discussion of the impacts of biotechnology on plant breeding technologies and germplasm sustainability. The role of biotechnology in the improvement of agricultural traits, production of industrial products and pharmaceuticals as well as biomaterials and biomass provide a historical perspective and a look to the future. Sections addressing intellectual property rights and sociological and food safety issues round out the holistic discussion of this important topic. - Includes specific emphasis on the inter-relationships between basic plant biotechnologies and applied agricultural applications, and the way they contribute to each other - Provides an updated review of the major plant biotechnology procedures and techniques, their impact on novel agricultural development and crop plant improvement - Takes a broad view of the topic with discussions of practices in many countries

Autoren/Hrsg.

Altman, Arie

Hasegawa, Paul Michael

Inhaltsverzeichnis

1;Front cover;1
2;Plant biotechnology and agriculture;4
3;Copyright page;5
4;Contents;8
5;Contributors;22
6;Foreword;26
7;Preface;28
8;Introduction to plant biotechnology 2011: Basic aspects and agricultural implications;30
9;A. Introduction to basic procedures in plant biotechnology;40
9.1;1 Genetics and genomics of crop domestication;42
9.1.1;Plants and Domestication;42
9.1.1.1;Scope;42
9.1.1.2;Domesticated crops;42
9.1.1.3;Weeds;43
9.1.1.4;Invasive species;43
9.1.1.5;Model species and crop sciences;44
9.1.2;Understanding Domestication Processes;44
9.1.2.1;Evidence of relatives and processes of early domestication;44
9.1.2.2;Genes of domestication;45
9.1.2.3;Genetic variation and domestication;45
9.1.2.4;Genetic control related to diversity and speciation;45
9.1.2.5;Domestication of maize;46
9.1.2.6;Domestication of legumes;46
9.1.2.7;Yield traits;47
9.1.3;Hybrid Species and New Polyploids in Domestication;47
9.1.4;Post-Domestication Selection;47
9.1.4.1;Modifications in crop characteristics;47
9.1.5;New Domestication;48
9.1.5.1;Domesticated species;48
9.1.5.2;Lost crops;48
9.1.5.3;Trees and biofuels;48
9.1.5.4;Genetics and breeding for new uses: Ecosystem services;49
9.1.6;Features of Domesticated Genomes;50
9.1.7;Superdomestication;53
9.1.8;Acknowledgments;55
9.2;2 The scope of things to come: New paradigms in biotechnology;58
9.2.1;Introduction;58
9.2.2;Progress Enabled by Next-Generation DNA Sequencing;59
9.2.2.1;Mapping of comprehensive, genome-wide, treatment-specific transcript profiles;62
9.2.2.2;Current next-gen sequencing;62
9.2.2.3;Behold the third generation;62
9.2.3;The Elephant in the Laboratory: Data Handling;63
9.2.4;From Sequences to Comparative Genomics;63
9.2.4.1;Transcriptome profiling;64
9.2.5;Broadening the Genomics Toolbox: Proteins and Metabolites;65
9.2.5.1;Proteomics advances;65
9.2.5.2;Metabolomics highlights;65
9.2.6;Genomics Unlimited: Getting Beyond Mere Genes;66
9.2.7;Into the Future: Genomics-Based Biotechnology and Agriculture;67
9.2.7.1;From models to crops, from labs to fields;67
9.2.7.2;Genetic resources from extremophile species;68
9.2.7.3;Exploring “unknown unknowns”;68
9.2.7.4;The importance of stress “tolerance” engineering;68
9.2.8;Acknowledgments;69
9.3;3 Protein targeting: Strategic planning for optimizing protein products through plant biotechnology;74
9.3.1;Introduction: Strategic Decisions about How to Express an Output Trait;74
9.3.2;Approaches;76
9.3.2.1;Routing proteins to the endomembrane system;76
9.3.2.2;Accumulating proteins in the ER;77
9.3.2.3;Accumulating proteins in ER-derived protein bodies;78
9.3.2.4;Accumulating proteins in the vacuole or vacuolar protein bodies;78
9.3.2.5;Accumulating proteins in the apoplast;79
9.3.2.6;Accumulating proteins in the chloroplast;79
9.3.2.7;Accumulating proteins on the surface of oil bodies;80
9.3.3;Seed-Based Expression Systems;80
9.3.4;Leaf Systems;83
9.3.4.1;Stable versus transient leaf expression systems;83
9.3.4.2;Protein bodies in leaves;86
9.3.5;Hairy Root Cultures;86
9.3.5.1;Advantages of the hairy root culture system;87
9.3.5.2;Recombinant proteins expressed with hairy root cultures;87
9.3.5.3;Hairy root cultures in bioreactors and scale-up;87
9.3.6;Summary and Conclusions;89
9.4;4 Proteomics and its application in plant biotechnology;94
9.4.1;Introduction;94
9.4.2;Mass Spectrometry-Based Proteomics;95
9.4.2.1;Sample preparation prior to mass spectrometry;95
9.4.2.1.1;Protein extraction and digestion;96
9.4.2.1.2;Protein and peptide fractionation;96
9.4.2.2;Mass spectrometry;96
9.4.2.3;Spectra assignment for peptide and protein identification;97
9.4.2.4;Quantitative proteomics;97
9.4.2.5;Post-translational modifications;97
9.4.3;Proteomics in Plant Biotechnology;98
9.4.3.1;What has been achieved so far in crop proteomics?;98
9.4.3.2;Arabidopsis thaliana as plant model organism;98
9.4.3.3;Crops and other economically relevant plant species;99
9.4.3.4;Future applications and perspectives;100
9.5;5 Plant metabolomics: Applications and opportunities for agricultural biotechnology;106
9.5.1;Introduction;106
9.5.2;Metabolite Networks: The Basics;107
9.5.3;Metabolomics: Technologies for Analyses;108
9.5.3.1;Analytical platforms;109
9.5.3.2;Data analysis and interpretation;110
9.5.3.2.1;Data pre-processing;111
9.5.3.2.2;Normalization and data transformation;111
9.5.3.2.3;Statistical analysis;111
9.5.3.2.4;Data visualization;112
9.5.4;Metabolomics: Applications in Agricultural Biotechnology;112
9.5.4.1;Metabolite profiling to test substantial equivalence;112
9.5.4.2;Phytochemical diversity, phenotyping, and classification;113
9.5.4.3;Postharvest quality of horticultural crops;113
9.5.4.4;Stress responses;113
9.5.4.5;Functional genomics;114
9.5.4.6;Breeding and metabolite quantitative trait loci;114
9.5.5;Metabolomics: Challenges and Future Perspectives;115
9.5.5.1;From model organisms to crop plants;115
9.5.5.2;Compartmentation of plant metabolism;115
9.5.5.3;High-resolution sampling;115
9.5.5.4;Primary and secondary metabolism pose different challenges;115
9.5.5.5;Identifying the metabolome;116
9.5.5.6;Measurements of metabolic flux;116
9.5.6;Outlook;117
9.5.7;Acknowledgments;117
9.6;6 Plant genome sequencing: Models for developing synteny maps and association mapping;122
9.6.1;Introduction;122
9.6.2;Genome Sequencing;123
9.6.2.1;Strategies for plant genome sequencing;123
9.6.2.2;High-throughput sequencing technologies;125
9.6.2.3;Single molecule and real-time sequencing;125
9.6.2.4;Assembly and alignment programs;125
9.6.2.5;Genome browsers;126
9.6.3;Models for Developing Syntenic Maps;127
9.6.3.1;Definitions;127
9.6.3.2;Intraspecies comparison;127
9.6.3.3;Cytogenetics for interspecies comparison;128
9.6.3.4;Sequence comparison;128
9.6.3.5;Macro- versus micro-synteny;128
9.6.3.6;Nature of the differences;128
9.6.3.7;Applications of syntenic maps;130
9.6.3.8;Tools and limitations;130
9.6.4;Association Mapping;130
9.6.4.1;Definitions;130
9.6.4.2;Population size and structure;131
9.6.4.3;Markers and marker density;132
9.6.5;Implications;133
9.7;7 Agrobacterium-mediated plant genetic transformation;138
9.7.1;Introduction;138
9.7.2;The Genetic Transformation Process;138
9.7.3;Agrobacterium as a Tool for Plant Transformation;143
9.7.4;Novel and Specialized Vectors for Plant Transformation;145
9.7.5;Manipulating the Plant Genome to Improve and Control Transformation;147
9.7.6;Using Novel Selection Methods and Restriction Enzymes to Control T-DNA Integration;148
9.7.7;Conclusions and Future Prospects;149
9.7.8;Acknowledgments;150
9.8;8 Biolistic and other non-Agrobacterium technologies of plant transformation;156
9.8.1;Introduction;156
9.8.2;Other Non-Agrobacterium Transformation;156
9.8.2.1;Electrophoretic transfection;156
9.8.2.2;Electroporation;157
9.8.2.3;Bioactive-beads-mediated gene transfer;157
9.8.2.4;Microinjection;157
9.8.2.5;Pollen-tube pathway;158
9.8.2.6;Silica carbide whisker-mediated transformation;158
9.8.3;Biolistic Transformation;159
9.8.3.1;The invention;159
9.8.3.2;Electric discharge particle acceleration;159
9.8.3.3;Current status of the “invention” hardware;160
9.8.4;Advantages of Biolistic Transformation;160
9.8.5;Implications of Biolistics in Agricultural Biotechnology;161
9.8.5.1;Application of biolistics in agriculture crops;161
9.8.5.2;Papaya: A case study of biolistic transformation;161
9.8.5.2.1;Papaya and papaya ringspot virus;161
9.8.5.2.2;Papaya and PRSV in Hawaii;164
9.8.5.2.3;Biolistic approach to transform papaya for resistance to PRSV;164
9.8.5.2.4;Testing, deregulation, commercialization, and impact of the transgenic papaya in Hawaii;166
9.8.5.2.5;Characteristics of transgene inserts in biolistically transformed line 55-1 and its derivatives;166
9.9;9 Plant tissue culture for biotechnology;170
9.9.1;Introduction;170
9.9.2;Plant Tissue Culture Technology;170
9.9.2.1;The basic laboratory setup;170
9.9.2.2;Preparation of tissue for culturing;171
9.9.2.3;Nutrient media;171
9.9.2.4;Types of culture;172
9.9.2.5;Environmental aspects of tissue culture;172
9.9.2.6;Modes of regeneration;173
9.9.3;Implications for Agricultural Biotechnology;173
9.9.3.1;Haploid tissue culture;174
9.9.3.2;Somatic embryogenesis;174
9.9.3.3;Artificial seeds;174
9.9.3.4;In vitro flowering;175
9.9.4;Future Perspectives;175
9.9.5;Acknowledgments;175
10;B. Breeding biotechnologies;178
10.1;10 Somatic (asexual) procedures (haploids, protoplasts, cell selection) and their applications;180
10.1.1;General Introduction;180
10.1.2;Somatic Embryogenesis;180
10.1.2.1;Introduction;180
10.1.2.2;Patterns of somatic embryogenesis;181
10.1.2.3;Factors affecting somatic embryo induction;181
10.1.2.3.1;Explant and genotype;181
10.1.2.3.2;Chemical factors;181
10.1.2.3.3;Other inductive factors;182
10.1.2.3.4;Histodifferentiation;182
10.1.2.4;Plant maturation;182
10.1.2.5;Plant regeneration;183
10.1.2.6;Gene expression during somatic embryogenesis;183
10.1.2.7;Mass propagation and somaclonal variation;183
10.1.3;Haploid Technology;183
10.1.3.1;Introduction;183
10.1.3.2;Cytological basis underlying haploid plant induction;184
10.1.3.3;Factors affecting the induction of microspore embryos;185
10.1.3.3.1;Plant genotype;185
10.1.3.3.2;Developmental stage of the microspore;185
10.1.3.3.3;Stress pre-treatment;185
10.1.3.3.4;Culture medium;186
10.1.3.3.5;Growth regulators;186
10.1.3.4;Haploid induction via ovary and ovule cultures;186
10.1.4;Protoplast and Somatic Hybridization;187
10.1.4.1;Introduction;187
10.1.4.2;Types of somatic hybrids;187
10.1.4.3;Protoplast fusion methods;187
10.1.4.4;Selection of somatic hybrids;189
10.1.4.5;Identification of somatic hybrids;189
10.1.4.6;Factors affecting regeneration of hybrid plants;190
10.1.5;Screening and Development of Stress-Resistant Plants Using in vitro Selection Techniques;190
10.1.5.1;Introduction;190
10.1.5.2;General methods of screening and breeding using in vitro selection techniques;190
10.1.5.3;Biotic stress resistance;191
10.1.5.4;Abiotic stress tolerance;191
10.1.5.5;Future perspective of screening and breeding using in vitro selection techniques;194
10.1.6;Conclusions and Future Directions;194
10.1.7;Acknowledgments;194
10.2;11 Marker-assisted selection in plant breeding;202
10.2.1;Background;202
10.2.1.1;The concept of marker-assisted selection;202
10.2.1.2;Historical review;203
10.2.2;Plant Traits, DNA Markers, Technologies, and Applications;203
10.2.2.1;Genes controlling important traits;203
10.2.2.1.1;MAS for biotic stresses;203
10.2.2.1.2;MAS for abiotic stress;204
10.2.2.1.3;MAS for agronomic traits;204
10.2.2.2;DNA markers;204
10.2.2.2.1;Restriction fragment length polymorphism;205
10.2.2.2.2;Random amplified polymorphic DNA;206
10.2.2.2.3;Amplified fragment length polymorphism;206
10.2.2.2.4;Simple sequence repeats (also referred to as microsatellites);206
10.2.2.2.5;Single nucleotide polymorphism;207
10.2.2.3;Modern genotyping technologies;207
10.2.2.3.1;Mass spectrometry;207
10.2.2.3.2;Diversity arrays technology;207
10.2.2.3.3;SNP arrays;207
10.2.2.3.4;Modern sequencing technologies;208
10.2.2.3.4.1;Solexa-Illumina;208
10.2.2.3.4.2;454 (now Roche);209
10.2.2.3.4.3;Pacific biosciences;209
10.2.2.4;Identification of genes controlling commercially important traits;209
10.2.2.4.1;Classical methods of gene identification;209
10.2.2.4.2;Modern methods for gene identification;210
10.2.2.4.2.1;Targeting-induced local lesions in genomes;210
10.2.2.4.2.2;Genome-wide association;210
10.2.2.4.2.3;RNA interference;212
10.2.2.4.2.4;Expression QTLs;212
10.2.2.4.2.5;Chemical genetics;212
10.2.2.5;Application of DNA markers to breeding;212
10.2.2.5.1;Identification;212
10.2.2.5.2;Improving classical breeding projects;212
10.2.2.5.2.1;Conserving diversity;213
10.2.2.5.2.2;Selection of parents for the generation of heterosis;213
10.2.2.5.2.3;Introgression;213
10.2.2.5.2.4;Pyramiding;213
10.2.2.6;MAS in breeding programs;213
10.2.3;Discussion;215
10.2.3.1;Bottlenecks and difficulties in the application of MAS;215
10.2.3.2;Future prospects of application of genetic variations to breeding;216
10.2.4;Acknowledgment;217
10.3;12 Male sterility and hybrid seed production;224
10.3.1;Introduction;224
10.3.2;Male Gametogenesis;224
10.3.2.1;Pollen mitosis I;224
10.3.2.2;Pollen mitosis II;225
10.3.3;Male Sterility Mutants Elucidate Anther Development;226
10.3.4;Hormonal Influences on Male Reproduction in Plants;226
10.3.4.1;Gibberellic acid;226
10.3.4.2;GA regulates jasmonic acid biosynthesis;227
10.3.4.3;Brassinosteroids;227
10.3.4.4;Auxins;228
10.3.5;Cytoplasmic Male Sterility Systems in Agriculture;228
10.3.5.1;Plant mitochondrial mutations;228
10.3.5.2;Fertility restoration;228
10.3.5.3;Stability of the CMS trait;229
10.3.6;Male Sterility: Metabolic and Evolutionary Implications;229
10.3.6.1;CMS is a naturally found condition;229
10.3.6.2;Organelle metabolism influences pollen development;229
10.3.7;Genetic Engineering of Male Sterility;230
10.3.8;Implementation of Male Sterility in Agricultural Systems;230
10.4;13 Advances in identifying and exploiting natural genetic variation;234
10.4.1;Natural Genetic Variation in Crop Breeding: From Prehistory to the Green Revolution;234
10.4.2;The Genetic Limits of Evolving Domesticated Crops;235
10.4.2.1;Tapping the natural genetic variation present in wild ancestors;235
10.4.3;Natural Genetic Variation in Arabidopsis;236
10.4.4;QTL Analyses in Arabidopsis;236
10.4.4.1;Novel Arabidopsis genes isolated through the natural variation approach;237
10.4.5;What to Expect: Intraspecific Variation in Gene Structure and Content;237
10.4.5.1;Structural genome variation: Higher than expected?;237
10.4.6;QTL Analysis and Sequence Variation in Crops;238
10.4.6.1;Domestication genes of maize;238
10.4.6.2;Examples from rice;238
10.4.6.3;Examples from other cereals;239
10.4.7;Toward Prediction of Variation in Molecular Function: Why Model Organisms are here to Stay;239
10.4.7.1;Crucial support from model organism candidate genes;239
10.4.7.2;Model systems as references to characterize allele activities;240
10.4.8;Beyond Simple Traits: Epigenetics, Heterosis, Genetic Incompatibility, and Trade-offs;240
10.4.8.1;Incompatibility between natural accessions;240
10.4.8.2;Trade-offs between different beneficial traits;241
10.4.9;Extending the Toolbox: Genome-wide Association Mapping;241
10.4.10;The Route to Effectively Exploit Natural Variation for Plant Biotechnology;241
10.5;14 From epigenetics to epigenomics and their implications in plant breeding;246
10.5.1;Mechanisms of Epigenetic Inheritance and their Interactions;246
10.5.1.1;Introduction;246
10.5.1.2;Epigenetic mechanisms and their interactions;247
10.5.1.2.1;DNA cytosine methylation;247
10.5.1.2.2;Histone modifications;248
10.5.1.2.3;Small RNAs;250
10.5.2;From Epigenetics to Epigenomics;251
10.5.2.1;Deciphering epigenomes: A matter of scale and complexity;251
10.5.2.2;Epigenomic methods and the type of data collected;251
10.5.2.2.1;ChIP-chip;251
10.5.2.2.2;ChIP-seq;252
10.5.2.2.3;Genome-wide DNA methylation profiling;252
10.5.2.3;Epigenomic resources;252
10.5.2.4;Transposable elements on the emerging epigenomic landscape(s);255
10.5.2.5;An illustrative and practical example of data and resources integration;256
10.5.3;Epigenetic Phenomena and their Implications in Plant Breeding;256
10.5.3.1;Epigenetic controls during vegetative development and the role of the environment;256
10.5.3.2;Epigenetic control of flowering;258
10.5.3.3;Endosperm development and parental imprinting;259
10.5.4;Conclusions and Prospects;261
10.5.5;Acknowledgments;261
10.5.6;Abbreviations;261
11;C. Plant germplasm;266
11.1;15 An engineering view to micropropagation and generation of true to type and pathogen-free plants;268
11.1.1;Preface;268
11.1.2;Shoot Multiplication Through Meristem Culture;268
11.1.2.1;Stage 0: Disinfection and start of axenic culture;269
11.1.2.2;Stage I: Initiation of culture;269
11.1.2.3;Stage II: Multiplication;269
11.1.2.4;Stage III: Elongation and promotion of shoot and root development;270
11.1.2.5;Stage IV: Acclimatization and hardening;270
11.1.3;Automation;270
11.1.4;Energy and Lights;271
11.1.5;Photoautotrophic Cultures;271
11.1.6;Micropropagation in Liquid Media;272
11.1.7;Plant—Microbe Interaction During in vitro and ex vitro Stages of Micropropagation;272
11.1.8;Inoculation with Beneficial Microorganisms;273
11.1.9;Elimination of Viruses by in vitro Techniques;277
11.1.10;Concluding Remarks;277
11.1.11;Acknowledgments;277
11.2;16 Regulation of apomixis;282
11.2.1;Introduction;282
11.2.2;Overview of Ovule Development During Sexual Reproduction;283
11.2.3;Overview of Ovule Development During Apomictic Reproduction;283
11.2.4;Germline Specification;283
11.2.5;Apomeiosis;285
11.2.6;Megagametogenesis;286
11.2.7;Gamete Specification;286
11.2.8;Parthenogenesis;287
11.2.9;Endosperm Development;289
11.2.10;Chromatin Modification and Epigenetic Regulation;290
11.2.11;Conclusions and Future Prospects for Apomixis in Crops;290
11.3;17 Germplasm collection, storage, and conservation;294
11.3.1;Introduction;294
11.3.1.1;Strategies for conserving plant biodiversity;294
11.3.1.2;Ex situ conservation technologies;295
11.3.2;Applications of Biotechnologies for Conservation;296
11.3.2.1;In vitro collecting;296
11.3.2.2;Slow growth storage;297
11.3.2.2.1;Classical techniques;297
11.3.2.2.2;Alternative techniques;297
11.3.2.2.3;Current development and use of in vitro slow growth storage;297
11.3.2.3;Cryopreservation;298
11.3.2.3.1;Cryopreservation techniques;298
11.3.2.3.1.1;Classical cryopreservation techniques;298
11.3.2.3.1.2;New cryopreservation techniques;299
11.3.2.3.2;Cryopreservation of vegetatively propagated and recalcitrant seed species;299
11.3.2.3.2.1;Vegetatively propagated species;299
11.3.2.3.2.2;Recalcitrant seed species;300
11.3.2.3.3;Large-scale utilization of cryopreservation for germplasm conservation;301
11.3.2.3.4;Additional uses of cryopreservation;302
11.3.2.3.5;Cryopreservation: progress and prospects;302
11.3.3;Conclusions;303
12;D. Controlling plant response to the environment: Abiotic and biotic stress;308
12.1;18 Integrating genomics and genetics to accelerate development of drought and salinity tolerant crops;310
12.1.1;Impact of Abiotic Stresses on Crop Plant Productivity;310
12.1.2;Water Deficit: A Major Abiotic Stress Factor;311
12.1.3;Salinity;311
12.1.4;Plant Responses to Abiotic Stress;311
12.1.5;Breeding for Drought and Salinity Tolerance: “The Conventional Approach”;312
12.1.5.1;Germplasm resources for drought and salinity tolerance;313
12.1.5.2;Genetic dissection of plant responses to abiotic stress;313
12.1.5.3;Introducing new technologies for abiotic stress breeding;314
12.1.6;Engineering-Tolerant Crop Plants: The Transgenic Approach;314
12.1.6.1;Genes for osmoregulation;314
12.1.6.2;Dehydration-responsive element;317
12.1.6.3;NAC proteins;318
12.1.6.4;Genes for ionic balance;318
12.1.6.5;Genes for redox regulation;318
12.1.6.5.1;Aquaporins;319
12.1.6.6;Other transcription factors;319
12.1.7;Hormone Balance and Abiotic Stress;319
12.1.8;Challenges and Prospects;320
12.1.9;Acknowledgments;320
12.2;19 Molecular responses to extreme temperatures;326
12.2.1;Introduction;326
12.2.2;Plant Response to Low Temperature;326
12.2.2.1;Low temperature perception;327
12.2.2.2;Transducing the low-temperature signal;328
12.2.2.2.1;Ca2+ as a second messenger in low-temperature response;328
12.2.2.2.2;Other molecules involved in transducing the cold signal;329
12.2.2.2.3;Gene expression in response to low temperature;331
12.2.2.2.3.1;Transcriptional control of cold-regulated gene expression;331
12.2.2.2.3.2;Post-transcriptional control of cold-regulated gene expression;334
12.2.2.2.3.3;Translational and post-translational control of cold-regulated gene expression;334
12.2.2.2.4;Epigenetic regulation of low-temperature response;335
12.2.3;Cross-talk between Plant Responses to Extreme Temperatures;336
12.2.3.1;The membrane as a node in the perception of temperature oscillations;337
12.2.3.2;Transducing the signals initiated by temperature variations;337
12.2.3.2.1;Ca2+ is a versatile second messenger in plant responses to extreme temperatures;337
12.2.3.2.2;Hormones mediate extreme temperature signaling;337
12.2.3.2.3;Regulation of gene expression in response to extreme temperatures;338
12.2.3.2.3.1;Transcriptional regulation of gene expression in response to high and low temperatures;338
12.2.3.2.3.2;Post-transcriptional regulation of gene expression in response to high and low temperatures;338
12.2.3.2.3.3;Translational and post-translational regulation of gene expression in response to high and low temperatures;339
12.2.4;Conclusions;339
12.2.5;Acknowledgments;340
12.3;20 Biotechnological approaches for phytoremediation;348
12.3.1;Introduction;348
12.3.1.1;Overview of results from biotechnological approaches for different pollutants;350
12.3.1.1.1;Inorganic pollutants;350
12.3.1.1.2;Arsenic;350
12.3.1.1.2.1;Arsenic pollution and toxicity;350
12.3.1.1.2.2;Arsenic in foods and implications for human health;350
12.3.1.1.2.3;Mechanism of As uptake and detoxification in microbes and plants;351
12.3.1.1.2.4;Biotechnological approaches for As remediation and reducing As in food crops;351
12.3.1.1.2.4.1;Arsenic phytoremediation;351
12.3.1.1.2.4.2;Preventing arsenic uptake in food crops;352
12.3.1.1.3;Mercury;353
12.3.1.1.3.1;Mercury pollution and toxicity;353
12.3.1.1.3.2;Mercury detoxification in bacteria and plants;353
12.3.1.1.3.3;Biotechnological approaches for Hg transformation and phytoremediation;354
12.3.1.1.3.4;Mercury hyperaccumulation;355
12.3.1.1.4;Selenium;355
12.3.1.1.4.1;Overview of Se metabolism in plants;355
12.3.1.1.4.2;Biotechnological approaches to study and manipulate Se metabolism in plants;356
12.3.1.1.4.3;Selenium phytoremediation field studies;356
12.3.1.2;Organic pollutants;356
12.3.1.2.1;Solvents;357
12.3.1.2.2;Explosives;358
12.3.1.2.3;BTEX, PAHs, and PCBs;359
12.3.1.2.4;Pesticides;360
12.3.2;Future Prospects;362
12.3.3;Acknowledgments;362
12.4;21 Biotechnological strategies for engineering plants with durable resistance to fungal and bacterial pathogens;368
12.4.1;Introduction;368
12.4.2;Choosing the Target Gene for Transgenic Expression;369
12.4.2.1;Plant immune receptors mediating pathogen recognition;369
12.4.2.2;Elicitors of plant immunity;370
12.4.2.3;Plant genes involved in signaling networks of plant immunity;371
12.4.2.4;Antimicrobial genes;373
12.4.2.5;Genes targeting pathogen virulence determinants;374
12.4.3;How Many Transgenes Should be Expressed in a Single Plant for Efficient Disease Control?;374
12.4.4;When and Where Should the Transgene(s) be Expressed?;375
12.4.4.1;Pathogen-responsive and tissue-specific promoters;376
12.4.4.2;Pathogen-responsive elements and synthetic promoters;377
12.4.5;Conclusions and Prospects;378
12.4.6;Acknowledgments;378
12.5;22 Controlling plant response to the environment: Viral diseases;382
12.5.1;Introduction;382
12.5.2;Phytosanitation and Quarantine Regulation;383
12.5.3;Transmission of Plant Viruses;383
12.5.4;Cultural Strategies of Virus Control;383
12.5.4.1;Management of soil-borne viruses;383
12.5.4.2;Management of airborne viruses;384
12.5.5;Resistance to Virus Transmission by Insects;384
12.5.5.1;Pathogen-derived resistance;384
12.5.5.2;RNA-mediated resistance;385
12.5.6;Application of the PDR Concept for Developing Transgenic Virus Resistance to Horticultural Crops;385
12.5.6.1;RNA silencing-based applications for developing virus resistant plants;386
12.5.6.2;PDR stability and suppression of RNA silencing;387
12.5.7;Assessment of Risks Associated with Transgenic Virus Resistance in Plants;387
12.5.8;Conclusion;388
12.6;23 Insects, nematodes, and other pests;392
12.6.1;Introduction — Genetically Modified Crops for Insect Resistance;392
12.6.1.1;History of B. thuringiensis;392
12.6.1.2;Cry proteins;393
12.6.2;Commercially Available Insect Protected Crops;393
12.6.2.1;Bt maize;393
12.6.2.2;Bt cotton;395
12.6.2.3;Discontinued Bt crops;396
12.6.3;Bt Crops Under Development;396
12.6.3.1;Bt brinjal;396
12.6.3.2;Bt rice;397
12.6.3.3;Other Bt crops;397
12.6.4;Impact of Bt;398
12.6.4.1;Benefits of Bt crops;398
12.6.4.2;Concerns about Bt crops;398
12.6.4.3;Improving Bt;399
12.6.5;Cowpea Trypsin Inhibitor;399
12.6.6;Novel Insecticidal Protection;400
12.6.6.1;VIP genes;400
12.6.6.2;Microorganism-derived toxins;400
12.6.6.3;Plant-derived toxins;400
12.6.6.4;Secondary metabolites;401
12.6.6.5;Other toxins;402
12.6.6.6;RNAi;402
12.6.7;Nematode-Resistant Crops;403
12.6.8;Recombinant Insecticides;403
12.6.9;Conclusion;403
13;E. Biotechnology for improvement of yield and quality traits;410
13.1;24 Growth Control of Root Architecture;412
13.1.1;Introduction to Root System Architecture;412
13.1.2;Genetic and Developmental Aspects of Root Growth;412
13.1.2.1;Stereotypical organization of root tissues;413
13.1.2.2;Architectural possibilities;413
13.1.2.3;Signaling;414
13.1.2.4;Systems biology concept of cell identity;415
13.1.3;Plant–Environment Interactions;415
13.1.3.1;Environmental sensing and root exudation;415
13.1.3.2;Microbial interactions;416
13.1.3.3;Architectural responses to nutrient availability;417
13.1.4;Crop Root Systems;418
13.1.4.1;Types of root systems;418
13.1.4.2;Embryonic and post-embryonic root systems;418
13.1.4.3;Evolutionary strategies and trade-offs;419
13.1.5;Approaches to Study Root Architecture;419
13.1.5.1;Quantitative analysis;419
13.1.5.2;High-throughput sequencing;420
13.1.5.3;Phenomics;420
13.1.6;Concluding Remarks;421
13.2;25 Control of flowering;426
13.2.1;Introduction;426
13.2.1.1;A plant’s perspective;426
13.2.1.2;A farmer’s perspective;426
13.2.2;Proteins Controlling Flowering Time;427
13.2.2.1;Florigen and FLOWERING LOCUS T (FT);427
13.2.2.2;Transcription factors regulating FT;428
13.2.2.2.1;FLOWERING LOCUS C (FLC) and MADS AFFECTING FLOWERING (MAF) proteins;428
13.2.2.2.2;SHORT VEGETATIVE PHASE (SVP);428
13.2.2.2.3;CONSTANS (CO);428
13.2.2.2.4;APETALA2-like flowering time repressors;428
13.2.2.2.5;TEMPRANILLO (TEM);429
13.2.2.3;Proteins parallel or downstream of FT;429
13.2.2.3.1;SOC1 and FRUITFULL;429
13.2.2.3.2;APETALA1 and LEAFY;429
13.2.2.3.3;SEPALLATA3 (SEP3);430
13.2.2.3.4;SQUAMOSA-PROMOTER BINDING PROTEIN LIKE (SPL);430
13.2.2.3.5;PENNYWISE and PENNYFOOLISH;430
13.2.3;Processes Affecting Flowering Time Proteins;430
13.2.3.1;Histone modifications;430
13.2.3.1.1;Modifications associated with active genes;431
13.2.3.1.2;Modifications associated with inactive genes;431
13.2.3.2;Gibberellin;431
13.2.3.3;MicroRNAs;432
13.2.3.3.1;miR156;432
13.2.3.3.2;miR159;432
13.2.3.3.3;miR167;432
13.2.3.3.4;miR169;432
13.2.3.3.5;miR172;433
13.2.3.4;The circadian clock;433
13.2.3.5;Regulated proteolysis;433
13.2.3.6;Sugars;433
13.2.4;Developmental Decisions on Timing of Flowering;434
13.2.4.1;Juvenility;434
13.2.4.2;Seasonality;434
13.2.4.2.1;Photoperiod;434
13.2.4.2.2;Vernalization;434
13.2.4.2.3;Warm ambient temperatures;435
13.2.4.3;Reproductive cycles and alternate bearing;436
13.2.5;Summary;437
13.2.6;Acknowledgment;437
13.3;26 Fruit development and ripening: A molecular perspective;444
13.3.1;Fruit Classification;444
13.3.2;Fruit Development;445
13.3.2.1;Fruit shape, size, and mass;445
13.3.3;Fruit Ripening;448
13.3.3.1;Ripening mutations;448
13.3.3.2;Nutritional mutations;450
13.3.3.3;Shelf life mutations;451
13.3.4;Ethylene and Fruit Ripening;452
13.3.4.1;Ethylene biosynthesis;452
13.3.4.2;Ethylene perception and signal transduction;453
13.3.4.3;Genetic intervention in ethylene biosynthesis and perception;455
13.3.5;Fruit Texture;456
13.3.5.1;Cell wall depolymerizing enzymes;456
13.3.5.2;Expansins;457
13.3.5.3;Protein glycosylation;457
13.3.6;Future Perspectives;457
13.4;27 Potential application of biotechnology to maintain fresh produce postharvest quality and reduce losses during storage;464
13.4.1;Introduction;464
13.4.2;Ethylene Biosynthesis or Perception and Its Relation to Postharvest Quality of Fresh Produce;465
13.4.3;Senescence in Postharvest of Leafy Vegetables and Flowers;466
13.4.3.1;Background;466
13.4.3.2;Senescence regulatory genes;466
13.4.3.3;Senescence-associated hormone biosynthesis or perception;467
13.4.3.4;Oxidative stress involvement in senescence;468
13.4.3.5;Chlorophyll degradation;468
13.4.4;Abscission of Fruits, Flowers, and Leaves During Postharvest;468
13.4.4.1;Background;468
13.4.4.2;Development of the dedicated AZ tissue;469
13.4.4.3;Regulatory genes involved in abscission control or mediating hormonal signal transduction;469
13.4.4.4;Genes involved in actual execution of cell separation in the later stage of abscission;470
13.4.4.5;Ethylene and abscission;470
13.4.4.6;Regulated manipulation of abscission;470
13.4.5;Reducing Postharvest Chilling Sensitivity;470
13.4.5.1;Background;470
13.4.5.2;Membrane structure and chilling sensitivity;471
13.4.5.3;Oxidative stress and chilling sensitivity or tolerance;472
13.4.5.4;Regulation of low-temperature responses;472
13.4.5.5;Molecules with protective functions during cold stress;473
13.4.6;Affecting Postharvest Texture and Appearance Qualities;474
13.4.6.1;Background;474
13.4.6.2;Softening and cell wall hydrolysis;474
13.4.6.3;Softening and turgor;474
13.4.6.4;Tissue lignifications;474
13.4.7;Implications for Plant and Agricultural Biotechnology;475
13.5;28 Engineering the biosynthesis of low molecular weight metabolites for quality traits (essential nutrients, health-promoting phytochemicals, volatiles, and aroma compounds);482
13.5.1;General Introduction;482
13.5.2;Lessons from Essential Nutrients;483
13.5.2.1;Essential amino acids;483
13.5.2.2;Fatty acids;485
13.5.2.3;Vitamins;485
13.5.2.3.1;Vitamin A;485
13.5.2.3.2;Vitamin E;486
13.5.2.3.3;Folate;486
13.5.2.3.4;Vitamin C;487
13.5.2.4;Improvement of the bioavailability of minerals through metabolic engineering;488
13.5.2.5;Multigene transfer for improved food quality;488
13.5.3;General Strategy for the Engineering of Secondary Metabolites with Nutritional Value;488
13.5.3.1;Identification of biosynthetic genes;488
13.5.3.2;Identification of transcription factors and engineering through integrated “omics”;489
13.5.3.3;Modulation of organelle development;489
13.5.4;Quality Improvement of Plants as Functional or Medicinal Food;490
13.5.4.1;Resveratrol;490
13.5.4.2;Anthocyanins and flavonoids;491
13.5.4.3;Catechins and proanthocyanidins;491
13.5.4.4;Sesamins;491
13.5.5;Beloved Metabolites: Plant Volatiles;491
13.5.5.1;Biochemistry of plant volatile secondary metabolites;492
13.5.5.2;Flavor compounds in fruits;493
13.5.5.3;Scent/aroma of flowers;494
13.5.5.4;Volatile organic chemicals in vegetative organs of plants;494
13.5.6;Perspectives;495
13.5.7;Conclusion;497
13.5.8;Acknowledgments;497
14;F. Plants as factories for industrial products, pharmaceuticals, biomaterials, and bioenergy;502
14.1;29 Vaccines, antibodies, and pharmaceutical proteins;504
14.1.1;Introduction;504
14.1.2;Expression Technologies: Nuclear Transformation;505
14.1.3;Expression Technologies: Plastid Transformation;508
14.1.4;Expression Technologies: Transient Expression Systems;508
14.1.4.1;“Full virus” vectors;509
14.1.4.2;Magnifection;509
14.1.4.3;Derisking the new manufacturing process;510
14.1.5;Plant-Made Pharmaceuticals: A Unique Selling Proposition?;510
14.1.6;Plant-Based Manufacturing, Post-Translational Modifications, and Plant-Specific Sugars;511
14.1.7;Plant-Based Manufacturing and Downstream Issues;512
14.1.8;Plant-Based Expression Systems: Advantages and Limitations;513
14.1.8.1;Nuclear transformation;514
14.1.8.2;Plastid transformation;514
14.1.8.3;Transient expression;515
14.1.9;Conclusions and Outlook;515
14.1.10;Acknowledgments;515
14.2;30 Plants as factories for bioplastics and other novel biomaterials;520
14.2.1;Introduction;520
14.2.2;Major Natural Plant Biopolymers;521
14.2.2.1;Starch;521
14.2.2.2;Cellulose;521
14.2.2.3;Rubber;522
14.2.2.4;Proteins;524
14.2.3;Novel Polymers Produced in Transgenic Plants;524
14.2.3.1;A role for transgenic crops in the production of biopolymers?;524
14.2.3.2;Which biopolymers should be targeted for production in transgenic crops?;525
14.2.3.3;Which crops should be targeted?;526
14.2.3.4;Fibrous proteins;526
14.2.3.5;Cyanophycin;527
14.2.3.6;Polyhydroxyalkanoate;528
14.2.4;Conclusion and Prospects;530
14.3;31 Bioenergy from plants and plant residues;534
14.3.1;Introduction;534
14.3.2;Biochemical Conversion;536
14.3.2.1;Comminution;537
14.3.2.2;Pre-treatment;538
14.3.2.3;Saccharification;539
14.3.2.4;Fuel synthesis;539
14.3.3;Thermochemical Conversion;540
14.3.3.1;Pyrolysis;540
14.3.3.2;Gasification;541
14.3.4;Concluding Remarks;542
14.3.5;Acknowledgment;542
15;G. Commercial, legal, sociological, and public aspects of agricultural plant biotechnologies;546
15.1;32 Containing and mitigating transgene flow from crops to weeds, to wild species, and to crops;548
15.1.1;Introduction: Does Transgene Flow Matter?;548
15.1.1.1;Transgene flow: To what ecosystem?;549
15.1.1.2;Thresholds matter;550
15.1.1.3;Gene containment and/or mitigation is often necessary;550
15.1.2;Methods of Containment;550
15.1.2.1;Containment by targeting genes to a cytoplasmic genome;551
15.1.2.2;Male sterility;551
15.1.2.3;Rendering crops asexual;552
15.1.2.4;Genetic use restriction technologies: Alias “terminators”;552
15.1.2.5;Chemically induced promoters for containment;552
15.1.2.6;Recoverable block of function;553
15.1.2.7;Repressible seed-lethal technologies;553
15.1.2.8;Trans-splicing to prevent movement;553
15.1.2.9;A genetic chaperon to prevent promiscuous transgene flow from wheat to its wild and weedy relatives;554
15.1.2.10;Transiently transgenic crops;554
15.1.3;Mitigating Transgene Flow;555
15.1.3.1;Demonstration of transgenic mitigation;555
15.1.3.2;Will transgenic mitigation traits adversely affect wild relatives of the crop? Models that suggest that mitigation is deleterious;556
15.1.4;Traits that can be Used in Tandem Transgenic Mitigation Constructs;557
15.1.4.1;Morphological traits and genes for mitigation;557
15.1.4.1.1;Secondary dormancy;557
15.1.4.1.2;Seed shattering;557
15.1.4.1.3;Dwarfing;557
15.1.4.1.4;Shade avoidance;558
15.1.4.2;Chemical mitigation of transgene flow;558
15.1.4.2.1;Activatable genes for susceptibility to chemicals;558
15.1.4.2.2;Hypersensitivity to herbicides as transgenic mitigation;558
15.1.4.3;Special cases where transgenic mitigation is needed;559
15.1.4.3.1;Mitigation for biennial and annual “root” crops;559
15.1.4.3.2;Transgenically mitigated genes for crop-produced pharmaceuticals and industrial products;559
15.1.4.3.3;Mitigation in species used for phytoremediation;559
15.1.5;Concluding Remarks;560
15.2;33 Intellectual property rights of biotechnologically improved plants;564
15.2.1;Introduction: Capitalizing on Research and Development in Agricultural Biotechnology with Intellectual Property Protection;564
15.2.2;Intellectual Property Protection of Biotechnologically Improved Plants;565
15.2.2.1;International intellectual property protection agreements;565
15.2.2.1.1;Union International pour la Protection des Obtentions Végétales;565
15.2.2.1.2;Trade-related Intellectual Property Rights;566
15.2.2.1.3;International Treaty on Plant Genetic Resources;566
15.2.2.2;Types of intellectual property protection in plant biotechnology;567
15.2.2.2.1;Plant variety protection;567
15.2.2.2.2;U.S. plant patents;567
15.2.2.2.3;Utility patents applied to plant biotechnology;568
15.2.2.2.4;Gene patenting;569
15.2.2.2.5;Material transfer agreements;570
15.2.2.2.6;Trademarks, trade secrets, know-how, and geographical designations;571
15.2.3;Freedom-to-Operate in Agricultural Biotechnology: The Road from a Research Idea to Commercialization of a Biotechnologically Improved Plant Product;571
15.2.4;Technology Transfer as a Means to Facilitate the Development of Biotechnology-Based Agriculture;573
15.2.5;Conclusion and Future Needs;575
15.2.6;Acknowledgments;576
15.3;34 Regulatory issues of biotechnologically improved plants;580
15.3.1;Introduction;580
15.3.2;Commercializing an Agricultural Biotechnology Product;581
15.3.3;The Regulatory Framework;582
15.3.3.1;The U.S. Coordinated Framework;584
15.3.3.1.1;USDA–APHIS;584
15.3.3.1.2;EPA;585
15.3.3.1.3;FDA;586
15.3.4;Perspectives;586
15.3.4.1;Specialty crops regulatory assistance: A new paradigm;586
15.3.4.2;Standardization;587
15.3.5;Conclusions;587
15.4;35 Prospects for increased food production and poverty alleviation: What plant biotechnology can practically deliver and what it cannot;590
15.4.1;Introduction;590
15.4.2;Progress to Date;591
15.4.3;The Next Generation;593
15.4.4;Barriers to Introduction;596
15.5;36 Crop biotechnology in developing countries;602
15.5.1;Introduction;602
15.5.2;Agriculture and Food in Developing Countries: The Needs;603
15.5.2.1;Feeding a growing world population;603
15.5.2.2;Undernutrition and poverty;603
15.5.2.3;Technology;604
15.5.3;Current State of GM Crops;604
15.5.3.1;Geographic distribution;604
15.5.3.2;Crops, traits, and farmers;604
15.5.3.3;Future and trends;604
15.5.4;Economic Impact of Transgenic Crops in Developing Countries;606
15.5.4.1;Main effects of current GM crops;606
15.5.4.2;Empirical evidence of farm level benefits;606
15.5.4.2.1;Bt cotton;606
15.5.4.2.2;Bt maize;607
15.5.4.2.3;HT crops;607
15.5.4.3;Effect of GM crops on poverty and inequality;607
15.5.4.4;Combined effects on farmer income;607
15.5.4.5;Macro level impacts;608
15.5.5;Health Impact;608
15.5.5.1;Safety concerns;608
15.5.5.2;Nutritional benefits of biofortification;609
15.5.5.3;Nutritional impact of GM biofortification;609
15.5.5.4;Reduced exposure to toxins, pesticides, and anti-nutrients;610
15.5.6;The Environment;610
15.5.7;Consumer Acceptance of GM Food;611
15.5.7.1;Regional differences;611
15.5.7.2;Factors influencing acceptance;611
15.5.8;Regulatory Systems;612
15.5.8.1;Importance of regulatory systems;612
15.5.8.2;Regional differences;612
15.5.8.3;Economics of regulation;612
15.5.8.4;The way forward;613
15.5.9;Conclusions;613
15.5.10;Acknowledgments;613
16;Index;616