Rice Functional Genomics: Challenges, Progress and Prospects

Rice Functional Genomics......Page 3
ISBN 9780387489032......Page 4
Foreword......Page 5
Preface......Page 7
Contents......Page 9
Contributors......Page 19
1 Introduction......Page 34
2.1 The Importance of the Accurate Genome Sequence of Rice......Page 38
2.2 Construction of the Sequence-Ready Physical Maps.......Page 40
2.3 Two-Step Strategy for Completion of Rice Genome Sequencing......Page 43
2.4.3 Cf. Sequences from Whole Genome Shotgun, & Clone-by-Clone Shotgun Sequencing (IRGSP)......Page 46
2.5 Initial Analysis of the Rice Genome......Page 47
2.6 Current Status and Future Developments......Page 49
References.......Page 50
3.1 Introduction.......Page 54
3.2 Computational Methods of Annotation.......Page 55
3.3 Automated Annotation System.......Page 57
3.4 Comprehensive Genome Annotation and Curation......Page 58
3.5 From Annotations to Functional Genomics......Page 59
References.......Page 60
4.1 Introduction......Page 64
4.2.1 Rice EST Collection & First cDNA Microarray System Based on the EST Clones......Page 65
4.2.2 Full-Length cDNA Project......Page 68
4.2.3 Oligoarray Systems......Page 70
4.3 Deep Transcriptome Analysis of the Rice Genome.......Page 71
4.3.1 Principles of Different SAGE Techniques......Page 73
4.3.2 Development of the Robust-LongSAGE (RL-SAGE) Method......Page 75
4.3.3 Application of RL-SAGE for Defense Transcriptome Analysis in Rice......Page 76
4.3.5 Deep Transcriptome Analysis Using MPSS.......Page 77
4.4 Transcriptional Analysis Using Genome Tiling Microarrays......Page 78
4.4.1 Principle of Genome Tiling Microarrays.......Page 79
4.4.2 Application of Genome Tiling Microarray Analysis in Rice.......Page 80
4.5 Perspective.......Page 85
Acknowledgments.......Page 86
References.......Page 87
5.1 Significance......Page 94
5.2.1 Strategy to Determine Amino Acid Sequences for Rice Proteome Database.......Page 96
5.2.2 Format and Content of the Rice Proteome Database.......Page 98
5.2.3 How to Use the Rice Proteome Database......Page 99
5.2.5 Future Prospects of the Rice Proteome Database......Page 100
5.3.1 Stresses......Page 101
5.3.2 Hormones......Page 107
5.4.1 Two-Dimensional Liquid Chromatography and Fluorescence 2-Dim. Difference Gel Electrophoresis.......Page 110
5.4.2 Identification of Protein Modification for Functional Analysis......Page 112
5.4.3 Protein-Protein Interaction Analyses for Functional Prediction.......Page 114
References.......Page 116
6.1 Significance......Page 124
6.2 Plant Sampling and Chemical Analysis......Page 125
6.3 Case Studies in Rice Metabolomics.......Page 127
6.4 Case Studies Integrating Functional Genomic Levels......Page 129
6.5 Time and Space Limitations in Integrated Functional-Genomic Analyses......Page 131
6.7 Databases and Resources......Page 132
6.8 Data Analysis.......Page 135
6.9 Summary.......Page 137
References.......Page 138
7 Use of Naturally Occurring Alleles for Crop Improvement......Page 142
7.1.1 Why Study Natural Variation?.......Page 143
7.2.1 Importance of Germplasm Conservation for Crop Improvement......Page 144
7.3.1 Origins of Natural Variation: A Short History of Orzya sativa......Page 146
7.3.2 Genetic Markers: Assessing Diversity, Population Structure in O. sativa......Page 147
7.4.2 Mapping Populations.......Page 149
7.4.3 Association Mapping.......Page 161
7.4.4 Gene Identification & Development of Perfect Markers for Appls. in Breeding.......Page 163
7.5 Natural Variation and Epistasis......Page 165
7.6 Natural Variation or Mutant Analysis?.......Page 166
7.7 Natural Variation versus Transgenic Approaches for Crop Improvement.......Page 168
References.......Page 170
8 Chemical- and Irradiation-Induced Mutants and TILLING......Page 182
8.1 Introduction......Page 183
8.2 Mutagens and Mutagenesis.......Page 184
8.2.1 Chemical Mutagens.......Page 185
8.2.2 Irradiation Mutagens......Page 188
8.2.3 Raising Mutant Populations......Page 190
8.3 Rice Mutant Stocks and Databases.......Page 191
8.3.2 IRRI Mutant Stocks and Database.......Page 192
8.3.4 Taiwan Mutant Stock......Page 193
8.4.1 Phenotyping.......Page 194
8.4.2 Map-Based Cloning.......Page 195
8.4.3 Detecting Genomic Changes Using Genome-Wide Chips......Page 196
8.5 Reverse Genetics with Mutants......Page 197
8.5.2 TILLING......Page 198
8.6.1 Seattle TILLING Project......Page 199
8.6.3 TILLING Case Studies for Specific Traits.......Page 201
8.7 Future Prospects......Page 205
Acknowledgments.......Page 206
References.......Page 207
9 T-DNA Insertion Mutants as a Resource for Rice Functional Genomics.......Page 214
9.1 Introduction.......Page 215
9.2 Agrobacterium-Mediated Transformation of Rice.......Page 216
9.3 T-DNA as an Insertional Mutagen.......Page 218
9.4.1 Korea......Page 221
9.4.2 China......Page 223
9.4.3 France......Page 225
9.4.5 Current Collection of T-DNA Insertion Lines and FSTs.......Page 227
9.5 Current Knowledge on T-DNA Integration in Rice.......Page 228
9.6.1 Preference Among and Along Rice Chromosomes......Page 231
9.6.2 Preference for Integration into Intergenic vs Genic Regions, Regulatory vs Coding Regions.......Page 234
9.6.4 Preference for GC Content and DNA Structure......Page 236
9.7 Gene and Enhancer Trapping with T-DNA in Rice.......Page 237
9.8 Forward Genetics Screens and Gene Isolation Using T-DNA Insertion Lines......Page 241
9.8.1 Gene Trapping......Page 242
9.8.2 Activation Tagging......Page 244
9.9 Reverse Genetics with T-DNA Mutants in Rice.......Page 245
9.10 Conclusion and Prospects......Page 246
References.......Page 248
Functional Genomics......Page 256
10.1 Introduction.......Page 257
10.2.1 Activity of Transposons in Rice.......Page 258
10.2.2 One-Element System versus Two-Element System......Page 262
10.2.3 Design of Constructs......Page 265
10.2.4 Gene and Enhancer Traps......Page 269
10.2.6 A High-Throughput System to Index Transposants.......Page 271
10.2.7 Using Endogenous Transposons......Page 273
10.2.8 Inducible Transposition.......Page 276
10.3.1 Random or Non-targeted Mutagenesis.......Page 278
10.3.2 Localized or Targeted Mutagenesis......Page 279
10.4 Transposon Insertional Mutant Populations......Page 280
10.4.1 CSIRO Plant Industry Population......Page 281
10.4.2 EU (Wageningen) Population......Page 282
10.4.3 National University of Singapore Population......Page 283
10.4.4 Korea Population......Page 284
10.4.5 UC Davis Population......Page 287
10.5.1 Forward and Reverse Genetics Strategies.......Page 289
10.5.2 Other Approaches for Mutation Identification.......Page 292
10.5.3 Tagging Efficiency.......Page 293
10.6 Future Prospects......Page 294
References.......Page 295
11.1 Introduction......Page 306
11.2 Gene Targeting by Homologous Recombination.......Page 311
11.2.1 Gene-Specific Selection and Gene-Specific Screening.......Page 312
11.2.2 Strong Positive-Negative Selection for Enriching Targeted Homologous Recombinants......Page 313
11.3 Potential Approaches for Homologous Recombination-Dependent Gene Targeting.......Page 315
11.4 Concluding Remarks......Page 318
References.......Page 319
12.1 Introduction......Page 324
12.2 Discovery of RNA Silencing......Page 325
12.3 RNA Silencing Pathways.......Page 328
12.3.2 Repeat-Associated Small Interfering RNA and RNA-Directed DNA Methylation......Page 329
12.4.1 The Dicer-Like Proteins.......Page 332
12.4.2 Hua Enhancer 1.......Page 336
12.4.4 The Argonaute Protein Family.......Page 338
12.5 RNA Silencing and Anti-Viral Defense.......Page 340
12.6 Gene Silencing Platforms in Plants.......Page 343
12.6.1 Delivery by Transgenes.......Page 346
12.6.2 Transient Delivery by Viral Vectors — Virus-Induced Gene Silencing......Page 354
12.7 Future Prospects of Gene Silencing Technology in Plants......Page 356
References.......Page 357
13.1 Introduction.......Page 366
13.2.1 Classical Activation Tagging in Plants......Page 368
13.2.2 Structure and Function of the CaMV 35S Activation Tagging System.......Page 369
13.2.3 Variations to the CaMV 35S Activation Tagging System......Page 371
13.2.4 CaMV 35S Activation Tagging Resources in Rice.......Page 372
13.3.1 Gene Expression at the Cell Type–Specific Level......Page 374
13.3.2 Origin of the GAL4 Enhancer Trapping System.......Page 375
13.3.3 GAL4 Enhancer Trapping in Plants......Page 376
13.3.4 Cell Type–Specific Activation of Target Genes Using GAL4 Transactivation.......Page 377
13.3.5 Cell Type–Specific Activation Tagging Using GAL4 Transactivation.......Page 379
13.4 Future Perspectives......Page 381
References.......Page 382
14 Informatics Resources for Rice Functional Genomics......Page 388
14.1 Introduction......Page 389
14.2.1 INtegrated Rice Genome Explorer.......Page 392
14.2.2 RGP Annotation Databases.......Page 394
14.2.4 Rice PIPELINE.......Page 395
14.3 TIGR Informatics Resources......Page 396
14.4.1 Database Contents.......Page 399
14.4.3 Comparative Genomics Resources......Page 401
14.5 Gramene.......Page 402
14.5.2 Maps and Markers.......Page 403
14.5.3 QTL, Genes, and Proteins......Page 404
14.5.5 Database Availability.......Page 405
14.6.1 OryGenesDB.......Page 406
14.6.2 Oryza Tag Line......Page 408
14.6.3 Greenphyl.......Page 409
14.7 IRRI Informatics Resources.......Page 410
14.7.1 The International Rice Information System......Page 411
14.7.2 Current Developments......Page 412
14.8.1 Tos17 Insertion Mutant Database.......Page 413
14.8.3 Rice Ds Tagging Lines.......Page 414
14.8.4 Taiwan Rice Insertional Mutants Database.......Page 415
14.8.6 Rice T-DNA Insertion Sequence Database.......Page 416
14.8.8 CSIRO Rice FST Database and RGMIMS......Page 417
14.8.9 RiceGE: Rice Functional Genomic Browser......Page 418
14.9.1 High-Speed Networks......Page 419
14.9.3 Web Integration......Page 420
14.10 Rice Functional Genomics Network.......Page 421
References.......Page 422
15.1 Introduction.......Page 428
15.2 Development of the OMAP BAC Library Resource......Page 430
15.3.2 BAC Fingerprinting......Page 432
15.3.3 Analysis of Structural Variation Between O. sativa and the 3 AA Genome OMAP Accessions......Page 434
15.4 Summary, Conclusions, and Future Research.......Page 437
References.......Page 440
16.1 Rice Genomics.......Page 444
16.2 Molecular Markers for Improved Breeding Efficiency.......Page 445
16.3 QTL Analysis.......Page 446
16.3.1 Genetic and Molecular Dissection of QTLs.......Page 448
16.3.4 QTL Pyramiding for Breeding......Page 451
16.3.5 QTL Detection Using Chromosome Segment Substitution Lines.......Page 453
16.6 Outlook......Page 455
References.......Page 456
17.1 Introduction.......Page 462
17.2 Origin and Evolution of Cereals......Page 464
17.3 Use of Comparative Genomics to Improve Genome Sequence Annotation......Page 466
17.4 Comparative Genomics & Conserved Noncoding Sequences: Discovery of New Genes & Signals......Page 469
17.5 Comparative Phylogeny of Multigene Families......Page 470
17.6 Revised “Circle Diagram” Model and Synteny Disruption......Page 476
17.7 The Rice Genome as a Model for Map-Based Cloning in Cereals......Page 483
17.8 Comparative QTL Mapping and Meta-Analysis of QTL......Page 487
17.9 Comparative Expression Profiling.......Page 490
17.10 Comparative Biology in the Era of Genomics......Page 491
17.11 Genome Sequencing in Grasses: Beyond the Model......Page 494
References.......Page 497
Index.......Page 514