Model Plants And Crop Improvement

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ISBN: 9780849330636 | 0849330637
Cover: Hardcover
Copyright: 9/29/2006

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Within the past decade, there has been an explosion of research in both the public and private sectors regarding the use of plant genetic models to improve crop yield. Bringing together experts from across the globe, Model Plants and Crop Improvement provides a critical assessment of the potential of model plant species for crop improvement. The first comprehensive summary of the use of model plant systems, the book delineates the model species' contribution to understanding the genomes of crop species.The book provides an in-depth examination of the achievements and limitations of the model paradigm. It explores how continued research in models can contribute to the goal of delivering the outputs of molecular biology to crops. Covering the major genetic models such as Arabidopsis thaliana, Lotus japonicus, and Medigago, the book goes on to discuss applications to food plants of global importance including rice, canola, and legumes. The book introduces the evolutionary, genetic, genomic, and morphological attributes of B. distachyon that make it such an attractive new model plant system.As the post-genomic era dawns, a key question to address is how this growing body of genetic and biological information can be extended beyond the model to the modeled species. This book takes you one step closer to applying modeling results to crops in the field.

Chapter 1 Development and Application of Genomic Models for Large-Crop Plant Genomes

(10)

Robert M.D. Koebner and Rajeev K. Varshney

1.1 Introduction

(5)

1.1.1 Dicot Models

(1)

1.1.1.1 A rabidopsis thaliana (Thale Cress)

(1)

1.1.1.2 Lotus japonicus (Trefoil) and Medicago truncatula (Barrel Medic)

(1)

1.1.1.3 Populus trichocarpa (Poplar or Black Cottonwood)

(1)

1.1.2 Monocot Models

(31)

1.1.2.1 Oryza sativa (Rice)

(2)

1.1.2.2 Brachypodium spp. (False Bromes)

(1)

1.2 Harnessing Model Genomes for Crop Genetics and Improvement

(2)

1.3 Perspective

(1)

References

(2)

Chapter 2 Conserved Mechanisms of Dormancy and Germination as Targets for Manipulation of Agricultural Problems

(22)

Michael Holdsworth, Leónie Bentsink, and Maarten Koornneef

2.1 Dormancy and Germination of Seeds—Definitions and Ecological Significance

(3)

2.2 Dormancy as an Agricultural Problem

(2)

2.3 Role of the Model Organism Arabidopsis in Defining Genetic Control of Dormancy

(4)

2.4 Mechanism of Dormancy and Germination in Cereals

(1)

2.5 Potential for Information Transfer from Model Systems to Agronomically Important Systems

(5)

References

(7)

Chapter 3 Utilization of Arabidopsis and Brassica Genomic Resources to Underpin Genetic Analysis and Improvement of Brassica Crops

(38)

Graham King

3.1 Introduction

(1)

3.2 Comparative Genomics

(7)

3.2.1 Genome Organization

(5)

3.2.1.1 Collinearity and Chromosome Segmental Duplications

(2)

3.2.1.2 Genetic Markers

(1)

3.2.1.2.1 Marker Systems

(1)

3.2.1.2.2 Gene-Specific Markers and Comparative Genomics

(1)

3.2.1.3 Karyotype and Physical Map Analysis

(1)

3.2.2 Genome Rearrangements

(1)

3.2.2.1 Mechanisms

(1)

3.2.2.2 Timing

(1)

3.2.2.3 Recent Genome Rearrangements and Breeding Introgression

(1)

3.3 Gene Homology and Divergence of Function

(3)

3.3.1 Detecting Orthologous and Paralogous Gene Coding Sequences

(1)

3.3.2 Consequences of Genome Duplication

(2)

3.3.2.1 Redundancy of Gene Function

(1)

3.3.2.2 Divergence of Gene Function

(1)

3.4 Accounting for Trait Variation in Brassica Crops

(3)

3.4.1 QTL Analysis

(1)

3.4.2 Mutational Analysis

(1)

3.5 Characterizing Specific Gene Families

(10)

3.5.1 Development

(3)

3.5.1.1 Flowering

(1)

3.5.1.2 Vernalization

(1)

3.5.1.3 Floral Development

(1)

3.5.1.4 Gene Identification in Model and Crop

(1)

3.5.2 Oil and Fatty Acid Pathways

(2)

3.5.3 Glucosinol ate Pathways

(1)

3.5.4 Pollen—Stigma Interactions and Self-Incompatibility

(1)

3.5.5 Host Resistance to Pathogens

(3)

3.6 Understanding Gene Regulation

(2)

3.6.1 Gene Expression and Use of Transcriptional Arrays

(1)

3.6.2 Characterization of cis-Regulatory Regions

(2)

3.7 Future Developments and Applications

(2)

3.7.1 Assessing and Exploiting Genetic Diversity for Crop Improvement

(1)

3.7.2 Information Management and Bioinformatics

(1)

Acknowledgment

(1)

References

(9)

Chapter 4 Characterization of the Completed Rice Genome Sequence and Scope of Its Utilization in Cereal Improvement

(20)

Baltazar A. Antonio and Takuji Sasaki

4.1 Introduction

(1)

4.2 Mapping the Rice Genome

(3)

4.2.1 Genetic Mapping

(2)

4.2.2 Physical Mapping

(1)

4.2.3 Transcript Mapping

(1)

4.2.4 Sequence-Ready Physical Mapping

(1)

4.3 Sequencing the Genome

(1)

4.4 Characterization of the Completed Sequence

(4)

4.4.1 Genome Coverage

(1)

4.4.2 Gene Content

(1)

4.4.3 Gene Composition

(2)

4.4.4 Centromere Sequence

(1)

4.4.5 Complete versus Draft Sequence

(1)

4.4.6 Subspecies japonica versus indica Sequence

(1)

4.5 Utilization in Cereal Genomics

(4)

4.5.1 Marker-Assisted Approaches

(1)

4.5.2 Map-Based Cloning

(1)

4.5.3 QTL Approach

(1)

4.5.4 Synteny Approach

(1)

4.5.5 Functional Approach

(1)

4.6 Future Prospects

(1)

References

(5)

Chapter 5 Model Legume Medicago truncatula

(18)

Henk Franssen and René Geurts

5.1 Unique Features of Legumes

(1)

5.2 Medicago truncatula

(4)

5.3 The Medicago Genome as Reference for Legume Crop Species

(7)

5.3.1 Rhizobium–Legume Symbiosis

(36)

5.3.1.1 Non-Nodulators Enclose Nod Factor Signaling Genes

(3)

5.3.1.2 Supernodulators

102

(1)

5.4 Perspective

103

(1)

References

104

(5)

Chapter 6 Brachypodium distachyon: A New Model System for Structural and Functional Analysis of Grass Genomes

109

(16)

David F. Garvin

6.1 Introduction

109

(1)

6.2 Evolutionary Relationships between Brachypodium distachyon and Other Grass Crops

110

(2)

6.3 Structural Features of Brachypodium distachyon Genome

112

(1)

6.4 Genome Composition

113

(1)

6.5 Gene Content and Organization versus Those of Other Grasses

114

(1)

6.6 Functional Genomics

115

(1)

6.7 Transformation and Mutagenesis

116

(2)

6.8 Genetic Stocks and Genetic Variation

118

(1)

6.9 Growth Characteristics

119

(2)

6.10 Conclusions

121

(1)

References

121

(4)

Chapter 7 The Green Alga Chlamydomonas as a Tool to Study the Nitrate Assimilation Pathway in Plants

125

(34)

Aurora Galván, Vicente Mariscal, David Gonález-Ballester, and Emilio Fernández

7.1 Chlamydomonas as a Model Organism

126

(1)

7.2 The Nitrate Assimilation Pathway and Its Key Points

126

(5)

7.3 The Usefulness of Chlorate-Resistant Mutants to Study of Nitrate Assimilation

131

(1)

7.4 Nitrate and Nitrite Reduction and Its Regulation

131

(2)

7.5 Nitrate and Nitrite Transporters

133

(6)

7.5.1 Transport Systems

134

(1)

7.5.2 Functionality of NRT1 Transporters

135

(1)

7.5.3 Functionality of NRT2 Transporters

136

(2)

2.5.4 NAR1 Transporters

138

(1)

7.6 Ammonium Assimilation

139

(1)

7.7 Ammonium Transport Genes

140

(3)

7.8 Nitrate Assimilation and Light/Circadian Rhythm

143

(1)

7.9 Nitrate Assimilation and Redox Regulation

143

(3)

7.10 Regulatory Genes in Nitrate Assimilation

146

(2)

7.11 Conclusion

148

(1)

Acknowledgments

149

(1)

References

149

(10)

Chapter 8 Transcription Factors Regulating Plant Defense Responses

159

(48)

Pierre R. Fobert

8.1 Introduction

160

(3)

8.1.1 Transcriptional Regulation of Plant Defense Responses

160

(1)

8.1.2 Inducible Plant Defense Systems

161

(1)

8.1.3 Model Systems

162

(1)

8.2 Sequence-Specific Transcription Factors

163

(24)

8.2.1 Isolation

163

(3)

8.2.1.1 DNA Binding

164

(1)

8.2.1.2 Genetic Approaches

164

(1)

8.2.1.3 Protein–Protein Interaction

165

(1)

8.2.1.4 Gene Expression

165

(1)

8.2.1.5 Sequence Similarity

165

(1)

8.2.1.6 Genomic Approaches

165

(1)

8.2.2 Structure and Evolution of Transcription Factor Families Implicated in Mediating Defense Responses

166

(3)

8.2.2.1 The ERF Family

166

(1)

8.2.2.2 The WRKY Family

167

(1)

8.2.2.3 The Whiny Family

167

(1)

8.2.2.4 The TGA Factor Family

168

(1)

8.2.2.5 The R2R3MYB Family

168

(1)

8.2.2.6 Zinc Finger-Related Proteins

168

(1)

8.2.2.7 Others

169

(1)

8.2.3 Functional Characterization

169

(4)

8.2.3.1 DNA Binding Preferences

169

(1)

8.2.3.2 Transeffector Properties

170

(1)

8.2.3.3 Subcellular Localization

171

(1)

8.2.3.4 Gene Expression

172

(1)

8.2.4 Functional Analysis of Mutant and Transgenic Plants with Altered Levels of Transcription Factor Genes

173

(8)

8.2.4.1 Definitions and Limitations

173

(1)

8.2.4.2 ERFs

174

(3)

8.2.4.3 WKRY Factors

177

(1)

8.2.4.4 Whiny Factors

178

(1)

8.2.4.5 TGA Factors

178

(2)

8.2.4.6 R2R3 MYB Proteins

180

(1)

8.2.4.7 Zinc Finger-Related Proteins

180

(1)

8.2.4.8 MYC Proteins

181

(1)

8.2.5 Post-Translational Regulation

181

(4)

8.2.5.1 Post-Translational Modifications

181

(1)

8.2.5.1.1 Phosphorylation

182

(1)

8.2.5.1.2 Oxidoreduction

183

(1)

8.2.5.1.3. Protein Turnover/Proteolysis

184

(1)

8.2.5.2 Protein–Protein Interactions

184

(1)

8.2.6 Transcriptional Targets and Networks

185

(2)

8.3 NPR1

187

(8)

8.3.1 Genetic Analysis of NPR1

187

(4)

8.3.1.1 Isolation of nprl Mutants and Cloning of NPR1 Gene

187

(2)

8.3.1.2 nprl Suppressors

189

(1)

8.3.1.3 Other Genetic Interactions

189

(1)

8.3.1.3.1 SA-Dependent Signaling

189

(1)

8.3.1.3.2 JA/ET-Dependent Signaling

190

(1)

8.3.2 Biochemical Function of NPR1

191

(1)

8.3.3 Post-Translational Regulation of NPR1

192

(2)

8.3.4 Analysis of Transgenic Plants Overexpressing NPR1

194

(1)

8.3.5 NPR1 -Related Genes

194

(1)

8.4 ...To Crop Improvement

195

(1)

References

196

(11)

Chapter 9 Defense Signaling and Pathway Interactions Involved in Rice Disease Resistance

207

(20)

Xiangjun Zhou, Tameka Bailey:, and Yinong Yang

9.1 Introduction

207

(1)

9.2 Disease-Resistance Genes and Early Signal Perception

208

(2)

9.3 Major Signaling Pathways Involved in Rice Defense Response

210

(4)

9.3.1 Salicylic Acid Signaling Pathway

210

(1)

9.3.2 Jasmonate Signaling Pathway

211

(2)

9.3.3 Ethylene Signaling Pathway

213

(1)

9.3.4 Abscisic Acid Signaling Pathway

213

(1)

9.3.5 Brassinosteroid Signaling Pathway

214

(1)

9.4 Defense-Related Map Kinases and Transcription Factors

214

(4)

9.4.1 Mitogen-Activated Protein Kinase Cascade in Rice

214

(2)

9.4.2 Transcription Factors and Defense Gene Activation

216

(2)

9.5 Interactions among Various Defense Signal Pathways

218

(1)

9.5.1 Cross-Talk between SA and JA Signaling Pathways

218

(1)

9.5.2 Cross-Talk between ET and ABA Signaling Pathways

218

(1)

9.5.3 Cross-Talk between JA and ABA Pathways

218

(1)

9.5.4 Cross-Talk between MAP Kinase and Other Signaling Pathways

219

(1)

9.6 Conclusions and Prospects

219

(1)

References

220

(7)

Chapter 10 Identification of Heat-Shock Factor Regulated Genes and Pathways

227

(20)

Friedrich Schöffl, Wolfgang Busch, Mukesh Kumar, and Tressa J. Panikulangara

10.1 Introduction

228

(1)

10.2 Transgenic HSF Loss-of-Function Mutants of Arabidopsis

229

(2)

10.2.1 Loss of Function by Overexpression of Heat-Shock Factor Constructs

229

(1)

10.2.2 Functional Analysis of EN-Hsf Lines in Arabidopsis

229

(2)

10.3 Arabidopsis Heat-Shock Factor Knockout Mutants

231

(3)

10.3.1 Gene Knockout Mutants in Early Active Heat-Shock Factors

231

(2)

10.3.2 Heat Shock and Heat-Shock Factor-Dependent Transcriptome of Arabidopsis

233

(1)

10.4 Identification of Heat-Shock Factor Target Genes

234

(3)

10.4.1 AtHsfA1a/1b-Dependent Genes

234

(1)

10.4.2 AtHsfA1a/1b-Regulated Expression of Other Transcription Factors during Heat Stress

235

(1)

10.4.3 AtHsfA1a/1b-Controlled Pathway for Raffinose Family Oligosaccharides

236

(1)

10.5 General Aspects of Expression Profiling for Identification of Target Genes

237

(3)

10.5.1 Experimental Design Affecting Detected Target Gene Expression

237

(3)

10.5.2 AtHsfA1a/1b Target Genes Exhibit Two Different Expression Profiles

240

(1)

10.6 General Conclusions

240

(2)

References

242

(5)

Chapter 11 Improving Low-Temperature Tolerance in Plants

247

(44)

Markku K. Aalto, Pekka Heino, and E. Tapio Palva

11.1 Introduction

248

(2)

11.1.1 Freezing Stress

248

(1)

11.1.2 Cold Acclimation

249

(1)

11.2 Cold Signaling in Plants

250

(4)

11.2.1 Signal Transduction at Low Temperature

250

(1)

11.2.2 Cold-Regulated Gene Expression

251

(1)

11.2.3 The CBF/DREB1 Regulon

252

(1)

11.2.4 ABA-Mediated Gene Expression

253

(1)

11.3 Engineering Tolerance

254

(6)

11.3.1 Target Genes

254

(1)

11.3.2 LEA Proteins

255

(1)

11.3.3 LEA Proteins and Yeast

256

(1)

11.3.4 Functional Divergence of LEA Proteins

256

(1)

11.3.5 Membrane-Binding Proteins

257

(1)

11.3.6 Antifreeze Proteins

258

(1)

11.3.7 Antioxidants and Detoxification

258

(1)

11.3.8 Membranes

259

(1)

11.3.9 Enzyme Engineering

260

(1)

11.4 Metabolic Engineering

260

(7)

11.4.1 Betaines

261

(4)

11.4.2 Amino Acids

265

(1)

11.4.3 Sugars

265

(2)

11.4.4 Other Metabolites

267

(1)

11.5 Regulon Engineering

267

(1)

11.5.1 Stress Signaling

267

(1)

11.5.2 Cold-Tolerant Mutations

268

(1)

11.6 Conclusions

268

(1)

11.7 Perspective

269

(1)

Acknowledgments

270

(1)

References

270

(21)

Index

291

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Model Plants And Crop Improvement

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