Plant Biotechnology and Genetics

C. Neal Stewart, PhD, 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.

• Foreword xviContributors xviiiPreface xx1. The Impact of Biotechnology on Plant Agriculture 1Graham Brookes1.0 Chapter Summary and Objectives 11.0.1 Summary 11.0.2 Discussion Questions 11.1 Introduction 11.2 Cultivation of Biotechnology (GM) Crops 21.3 Why Farmers Use Biotech Crops 41.4 GM’s Effects on Crop Production and Farming 71.5 How the Adoption of Plant Biotechnology has Impacted the Environment 81.5.1 Environmental Impacts from Changes in Insecticide and Herbicide Use 81.5.2 Impact on GHG Emissions 111.6 Conclusions 13Life Box 1.1 Norman E. Borlaug 14Life Box 1.2 Mary-Dell Chilton 15Life Box 1.3 Robert T. Fraley 17References 192. Mendelian Genetics and Plant Reproduction 20Matthew D. Halfhill and Suzanne I. Warwick2.0 Chapter Summary and Objectives 202.0.1 Summary 202.0.2 Discussion Questions 202.1 Overview of Genetics 202.2 Mendelian Genetics 232.2.1 Law of Segregation 262.2.2 Law of Independent Assortment 262.3 Mitosis and Meiosis 272.3.1 Mitosis 292.3.2 Meiosis 292.3.3 Recombination 302.3.4 Cytogenetic Analysis 312.3.5 Mendelian Genetics and Biotechnology Summary 322.4 Plant Reproductive Biology 322.4.1 History of Research in Plant Reproduction 322.4.2 Mating Systems 322.4.3 Hybridization and Polyploidy 362.4.4 Mating Systems and Biotechnology Summary 382.5 Conclusion 38Life Box 2.1 Richard A. Dixon 39Life Box 2.2 Michael L. Arnold 40References 423. Plant Breeding 43Nicholas A. Tinker and Elroy R. Cober3.0 Chapter Summary and Objectives 433.0.1 Summary 433.0.2 Discussion Questions 433.1 Introduction 443.2 Central Concepts in Plant Breeding 453.2.1 Simple vs. Complex Inheritance 453.2.2 Phenotype vs. Genotype 463.2.3 Mating Systems, Varieties, Landraces, and Pure Lines 473.2.4 Other Topics in Population and Quantitative Genetics 493.2.5 The Value of a Plant Variety Depends on Many Traits 513.2.6 A Plant Variety Must Be Environmentally Adapted 513.2.7 Plant Breeding is a Numbers Game 523.2.8 Plant Breeding is an Iterative and Collaborative Process 523.2.9 Diversity, Adaptation, and Ideotypes 533.2.10 Other Considerations 563.3 Objectives in Plant Breeding 563.4 Methods of Plant Breeding 573.4.1 Methods of Hybridization 583.4.2 Self‐Pollinated Species 583.4.3 Outcrossing Species 633.4.4 Clonally Propagated Species 673.5 Breeding Enhancements 683.5.1 Doubled Haploidy 683.5.2 Marker‐Assisted Selection 683.5.3 Mutation Breeding 703.5.4 Apomixis 713.6 Conclusions 71Life Box 3.1 Gurdev Singh Khush 72Life Box 3.2 P. Stephen Baenziger 74Life Box 3.3 Steven D. Tanksley 75References 774. Plant Development and Physiology 78Glenda E. Gillaspy4.0 Chapter Summary and Objectives 784.0.1 Summary 784.0.2 Discussion Questions 784.1 Plant Anatomy and Morphology 794.2 Embryogenesis and Seed Germination 804.2.1 Gametogenesis 804.2.2 Fertilization 824.2.3 Fruit Development 834.2.4 Embryogenesis 834.2.5 Seed Germination 854.2.6 Photomorphogenesis 854.3 Meristems 864.3.1 Shoot Apical Meristem 864.3.2 Root Apical Meristem and Root Development 884.4 Leaf Development 894.4.1 Leaf Structure 894.4.2 Leaf Development Patterns 914.5 Flower Development 924.5.1 Floral Evocation 924.5.2 Floral Organ Identity and the ABC Model 934.6 Hormone Physiology and Signal Transduction 944.6.1 Seven Plant Hormones and Their Actions 944.6.2 Plant Hormone Signal Transduction 964.7 Conclusions 100Life Box 4.1 Deborah Delmer 100Life Box 4.2 Natasha Raikhel 102Life Box 4.3 Brenda S.J. Winkel 103References 1055. Tissue Culture: The Manipulation of Plant Development 107Vinitha Cardoza5.0 Chapter Summary and Objectives 1075.0.1 Summary 1075.0.2 Discussion Questions 1075.1 Introduction 1075.2 History of Tissue Culture 1085.3 Media and Culture Conditions 1095.3.1 Basal Media 1095.3.2 Growth Regulators 1105.4 Sterile Technique 1115.4.1 Clean Equipment 1115.4.2 Surface Sterilization of Explants 1125.5 Culture Conditions and Vessels 1135.6 Culture Types and Their Uses 1135.6.1 Callus and Somatic Embryo Culture 1135.6.2 Cell Suspension Cultures 1175.6.3 Anther/Microspore Culture 1195.6.4 Protoplast Culture 1195.6.5 Somatic Hybridization 1205.6.6 Embryo Culture 1205.6.7 Meristem Culture 1215.7 Regeneration Methods of Plants in Culture 1215.7.1 Organogenesis 1215.7.2 Somatic Embryogenesis 1235.7.3 Synthetic Seeds 1235.8 Rooting of Shoots 1235.9 Acclimation 1245.10 Problems that can Occur in Tissue Culture 1245.10.1 Culture Contamination 1245.10.2 Hyperhydricity 1245.10.3 Browning of Explants 1245.11 Conclusions 125Acknowledgments 125Life Box 5.1 Glenn Burton Collins 125Life Box 5.2 Martha S. Wright 127Life Box 5.3 Vinitha Cardoza 128References 1296. Molecular Genetics of Gene Expression 133Maria Gallo and Alison K. Flynn6.0 Chapter Summary and Objectives 1336.0.1 Summary 1336.0.2 Discussion Questions 1336.1 The Gene 1336.1.1 DNA Coding for a Protein via the Gene 1336.1.2 DNA as a Polynucleotide 1346.2 DNA Packaging into Eukaryotic Chromosomes 1346.3 Transcription 1356.3.1 Transcription of DNA to Produce Messenger Ribonucleic Acid 1356.3.2 Transcription Factors 1406.3.3 Coordinated Regulation of Gene Expression 1406.3.4 Chromatin as an Important Regulator of Transcription 1416.3.5 Regulation of Gene Expression by DNA Methylation 1426.3.6 RNA‐Directed Gene Silencing by Small RNAs 1436.3.7 Processing to Produce Mature mRNA 1436.4 Translation 1446.4.1 Initiation of Translation 1476.4.2 Elongation Phase of Translation 1476.4.3 Translation Termination 1476.5 Protein Postranslational Modification 147Life Box 6.1 Maarten Chrispeels 150Life Box 6.2 David W. Ow 152References 1547. Plant Systems Biology 155Wusheng Liu and C. Neal Stewart, Jr.7.0 Chapter Summary and Objectives 1557.0.1 Summary 1557.0.2 Discussion Questions 1557.1 Introduction 1557.2 Defining Plant Systems Biology 1577.3 Properties of Plant Systems 1587.4 A Framework of Plant Systems Biology 1597.4.1 Comprehensive Quantitative Data Sets 1607.4.2 Network Analysis 1617.4.3 Dynamic Modeling 1617.4.4 Exploring Systems and Models Toward Refinement 1617.5 Disciplines and Enabling Tools of Plant Systems Biology 1627.5.1 Plant Genomics 1627.5.2 Plant Transcriptomics 1667.5.3 Plant Proteomics 1687.5.4 Plant Metabolomics 1707.5.5 Bioinformatics 1727.6 Conclusions 176Life Box 7.1 C. Robin Buell 177Life Box 7.2 Zhenbiao Yang 178References 1798. Recombinant DNA, Vector Design, and Construction 181Mark D. Curtis and David G.J. Mann8.0 Chapter Summary and Objectives 1818.0.1 Summary 1818.0.2 Discussion Questions 1818.1 DNA Modification 1818.2 DNA Vectors 1868.2.1 DNA Vectors for Plant Transformation 1888.2.2 Components for Efficient Gene Expression in Plants 1908.3 Greater Demands Lead to Innovation 1928.3.1 “Modern” Cloning Strategies 1928.4 Vector Design 1978.4.1 Vectors for High‐Throughput Functional Analysis 1978.4.2 Vectors for Gene Down‐Regulation Using RNA Interference (RNAi) 1998.4.3 Expression Vectors 1998.4.4 Vectors for Promoter Analysis 2008.4.5 Vectors Derived from Plant Sequences 2018.4.6 Vectors for Multigenic Traits 2038.5 Targeted Transgene Insertions 2048.6 Prospects 205Life Box 8.1 Wayne Parrott 206Life Box 8.2 David Mann 207References 2089. Genes and Traits of Interest 211Kenneth L. Korth9.0 Chapter Summary and Objectives 2119.0.1 Summary 2119.0.2 Discussion Questions 2119.1 Introduction 2129.2 Identifying Genes of Interest via Genomics and other Omics Technologies 2129.3 Traits for Improved Crop Production Using Transgenics 2149.3.1 Herbicide Resistance 2159.3.2 Insect Resistance 2189.3.3 Pathogen Resistance 2209.3.4 Traits for Improved Products and Food Quality 2229.4 Conclusion 227Life Box 9.1 Dennis Gonsalves 227Life Box 9.2 Ingo Potrykus 229References 23110. Promoters and Marker Genes 233Wusheng Liu, Brian Miki and C. Neal Stewart, Jr.10.0 Chapter Summary and Objectives 23310.0.1 Summary 23310.0.2 Discussion Questions 23310.1 Introduction 23410.2 Promoters 23410.2.1 Constitutive Promoters 23510.2.2 Tissue‐Specific Promoters 23610.2.3 Inducible Promoters 23710.2.4 Synthetic Promoters 23910.3 Marker Genes 23910.3.1 Selectable Marker Genes 24210.3.2 Reporter Genes 24610.4 Marker‐Free Strategies 25010.5 Conclusions 254Life Box 10.1 Fredy Altpeter 255Life Box 10.2 Taniya Dhillon 257References 25911. Transgenic Plant Production 262John J. Finer11.0 Chapter Summary and Objectives 26211.0.1 Summary 26211.0.2 Discussion Questions 26211.1 Overview of Plant Transformation 26311.1.1 Introduction 26311.1.2 Basic Components for Successful Gene Transfer to Plant Cells 26311.2 Agrobacterium Tumefaciens 26511.2.1 History of Agrobacterium Research 26611.2.2 Use of the T‐DNA Transfer Process for Transformation 26811.2.3 Optimizing Delivery and Broadening the Taxonomical Range of Targets 26911.2.4 Strain and Cultivar Compatibility 27011.2.5 Agroinfiltration 27111.2.6 Arabidopsis Floral Dip (Clough and Bent 1998) 27111.3 Particle Bombardment 27211.3.1 History of Particle Bombardment 27211.3.2 The Fate of the Introduced DNA into Plant Cells 27411.3.3 The Power and Problems of Direct DNA Introduction 27511.3.4 Improvements in the Control of Transgene Expression 27611.4 Other Methods of Transformation 27611.4.1 The Need for Additional Technologies 27611.4.2 Protoplasts 27711.4.3 Whole Tissue Electroporation 27811.4.4 Silicon Carbide Whiskers 27811.4.5 Viral Vectors 27811.4.6 Laser Micropuncture 27911.4.7 Nanofiber Arrays 27911.5 The Rush to Publish 28011.5.1 Controversial Reports of Plant Transformation 28011.5.2 Criteria to Consider in Judging Novel Plant Transformation Methods 28411.6 A Look to the Future 286Life Box 11.1 Ted Klein 286Life Box 11.2 John Finer 287Life Box 11.3 Kan Wang 289References 29112. Analysis of Transgenic Plants 293C. Neal Stewart, Jr.12.0 Chapter Summary and Objectives 29312.0.1 Summary 29312.0.2 Discussion Questions 29312.1 Essential Elements of Transgenic Plant Analysis 29312.2 Assays for Transgenicity, Insert Copy Number, and Segregation 29512.2.1 Polymerase Chain Reaction 29512.2.2 Quantitative PCR 29512.2.3 Southern (DNA) Blot Analysis 29612.2.4 Segregation Analysis of Progeny 30012.3 Transgene Expression 30112.3.1 Transcript Abundance 30112.3.2 Protein Abundance 30212.4 Knockdown or Knockout Analysis Rather than Overexpression Analysis 30412.5 The Relationship Between Molecular Analyses and Phenotype 305Life Box 12.1 Hong S. Moon 305Life Box 12.2 Neal Stewart 306Life Box 12.3 Nancy A. Reichert 308References 31013. Regulations and Biosafety 311Alan McHughen13.0 Chapter Summary and Objectives 31113.0.1 Summary 31113.0.2 Discussion Questions 31113.1 Introduction 31113.2 History of Genetic Engineering and Its Regulation 31313.3 Regulation of GM Plants 31513.3.1 New Technologies 31613.3.2 US Regulatory Agencies and Regulations 31713.3.3 European Union 31913.3.4 Canada 32113.3.5 International Perspectives 32113.4 Regulatory Flaws and Invalid Assumptions 32313.4.1 Conventional Plant Breeding has Higher Safety than Biotechnology‐Derived GM 32413.4.2 GMOs Should Be Regulated Because They’re GMOs and Un‐natural 32413.4.3 Even though Product Risk is Important, It is Reasonable that Process (GMO) Should Trigger Regulation 32413.4.4 Since GM Technology is New, It Might Be Hazardous and Should Be Regulated 32513.4.5 If We Have a Valid Scientific Test, Then It Should Be Used in Regulations 32613.4.6 Better Safe than Sorry: Overregulation is Better than Underregulation 32613.5 Conclusion 327Life Box 13.1 Alan McHughen 328Life Box 13.2 Raymond D. Shillito 329References 33114. Field Testing of Transgenic Plants 333Detlef Bartsch, Achim Gathmann, Christiane Saeglitz and Arti Sinha14.0 Chapter Summary and Objectives 33314.0.1 Summary 33314.0.2 Discussion Questions 33314.1 Introduction 33414.2 Environmental Risk Assessment Process 33414.2.1 Initial Evaluation (Era Step 1) 33414.2.2 Problem Formulation (ERA Step 2) 33514.2.3 Controlled Experiments and Gathering of Information (ERA Step 3) 33514.2.4 Risk Evaluation (ERA Step 4) 33514.2.5 Progression through a Tiered Risk Assessment 33514.3 An Example Risk Assessment: The Case of Bt Maize 33614.3.1 Effect of Bt Maize Pollen on Nontarget Caterpillars 33714.3.2 Statistical Analysis and Relevance for Predicting Potential Adverse Effects on Butterflies 33914.4 Proof of Safety Versus Proof of Hazard 34014.5 Modeling the Risk Effects on a Greater Scale 34014.6 Proof of Benefits: Agronomic Performance 34114.7 Conclusions 342Life Box 14.1 Tony Shelton 343Life Box 14.2 Detlef Bartsch 344References 34615. Intellectual Property in Agricultural Biotechnology: Strategies for Open Access 347Monica Alandete‐Saez, Cecilia Chi‐Ham, Gregory Graff, Sara Boettiger and Alan B. Bennett15.0 Chapter Summary and Objectives 34715.0.1 Summary 34715.0.2 Discussion Questions 34715.1 Intellectual Property and Agricultural Biotechnology 34815.1.1 What is Intellectual Property? 34915.1.2 What is a Patent? 34915.2 The Relationship Between Intellectual Property and Agricultural Research 35115.3 Patenting Plant Biotechnology: Has an Anti‐Commons Developed? 35215.3.1 Transformation Methods 35215.3.2 Selectable Markers 35315.3.3 Promoters 35415.3.4 Subcellular Localization 35415.3.5 The Importance of Combining IP‐Protected Components in Transgenic Crops 35515.4 What is Freedom to Operate (FTO)? 35515.4.1 The Importance of FTO 35515.4.2 FTO Case Study: the Tomato E8 Promoter 35615.5 Strategies for Open Access 35815.6 Conclusions 359Life Box 15.1 Alan Bennett 360Life Box 15.2 Maud Hinchee 361References 36316. Why Transgenic Plants Are So Controversial 366Jennifer Trumbo and Douglas Powell16.0 Chapter Summary and Objectives 36616.0.1 Summary 36616.0.2 Discussion Questions 36616.1 Introduction 36716.1.1 The Frankenstein Backdrop 36716.1.2 Agricultural Innovations and Questions 36716.2 Perceptions of Risk 36816.3 Responses of Fear 37016.4 Feeding Fear: Case Studies 37216.4.1 Pusztai’s Potatoes 37216.4.2 Monarch Butterfly Flap 37316.5 How Many Benefits are Enough? 37316.6 Continuing Debates 37516.6.1 Process vs. Product 37516.6.2 Health Concerns 37516.6.3 Environmental Concerns 37616.6.4 Consumer Choice 37616.7 Business and Control 37616.8 Conclusions 377Life Box 16.1 Tony Conner 378Life Box 16.2 Channapatna S. Prakash 379References 38117. The Future: Advanced Plant Biotechnology, Genome Editing, and Synthetic Biology 383Wusheng Liu and C. Neal Stewart, Jr.17.0 Chapter Summary and Objectives 38317.0.1 Summary 38317.0.2 Discussion Questions 38317.1 Introduction: The Birth of Synthetic Biology 38417.2 Defining Synthetic Biology for Plants 38517.2.1 Design Cycles of Synthetic Biology 38517.2.2 Foundations of Synthetic Biology 38717.2.3 Components of Plant Synthetic Biology 38817.3 Enabling Tools for Plant Synthetic Biology 38917.3.1 Computer‐Aided Design 38917.3.2 Synthetic Promoters 38917.3.3 Precise Genome Editing 38917.4 Synthetic Biology Applications in Plants 39317.4.1 Synthetic Inducible Promoters 39417.4.2 A Device for Monitoring Auxin‐Induced Plant IAA Degradation in Yeast 39517.4.3 Circuits for Phytosensing of Explosives or Bacterial Pathogens in Transgenic Plants 39517.5 Conclusions 397Life Box 17.1 Joshua Yuan 397Life Box 17.2 Wusheng Liu 398References 399Index 402