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The handbook of plant functional genomics : concepts and protocols / edited by Gunter Kahl and Khalid Meksem. — Weinheim : Wiley-VCH Verlag GmbH & Co. KGaA, c2008. – (58.8213/H236) |
Contents
Contents
Preface XIX
List of Contributors XXI
I Transcriptome Analysis 1
A Whole Genome Expression Analysis 1
1 Single Cell Expression Profiling: Transcript and Protein Analyses in Isolated Higher Plant Gametes and Zygotes 3
1.1 Introduction 3
1.2 Microdissection， Cell Isolation 6
1.3 In Vitro Fertilization 6
1.4 Techniques for Molecular Analyses of Single Cell Types 7
1.5 Analyses of Protein Expression 14
1.6 Prospects 15
2 AFLP-Based RNA Fingerprinting: Novel Variants and Applications
2.1 Introduction 21
2.2 Methods and Protocols 23
2.3 Applications of the Technology 31
2.4 Perspectives 34
3 SuperSAGE: The Most Advanced Transcriptome Technology for Functional Genomics 37
3.1 Introduction 37
3.2 Methods and Protocols 40
3.3 Applications of the Technology 47
3.4 Perspectives 49
4 From CAGE to DeepCAGE: High-Throughput Transcription Start Site and Promoter Identification for Gene Network Analysis 55
4.1 From Genomes to Transcriptomes 55
4.2 Addressing the Complexity of Transcriptomes 56
4.3 The Shift From CAGE to DeepCAGE 57
4.4 Applications of CAGE and DeepCAGE Libraries 58
4.5 Preparation of a DeepCAGE Library 59
4.6 CAGE Data Analysis and Genome Mapping Approaches 62
4.7 Expression Profiling: Putting CAGE Tags into a Biological Context 67
4.8 Perspectives 68
5 Gene Identification Signature-Paired End diTagging (GIS-PET): A Technology for Transcriptome Characterization 77
5.1 Introduction 77
5.2 Protocol 82
5.3 Data Analysis 103
5.4 Discussion 103
5.5 Perspectives 105
6 High-Throughput Functional Screening of Genes In Planta 113
6.1 Introduction 113
6.2 Methods and Protocols 115
6.3 Application of the Technology 131
6.4 Perspectives 133
7 Microarrays as Tools to Decipher Transcriptomes in Symbiotic Interactions 137
7.1 Introduction 137
7.2 Methods and Protocols 143
7.3 Applications of the Technology 151
7.4 Perspectives 156
B Gene-by-Gene Analysis 163
8 Genome-Wide Analysis of mRNA Expression by Fluorescent Differential Display 165
8.1 Introduction 165
8.2 Methods and Protocols 169
8.3 Applications of the Technology 183
8.4 Perspectives 184
9 Real-Time Quantitation of MicroRNAs by TaqMan MicroRNA Assays 187
9.1 Introduction 187
9.2 Methods and Protocols 190
9.3 Applications of the Technology 197
9.4 Perspectives 202
II Gene Silencing， Mutation Analysis and Functional Genomics 207
10 RNA Interference 209
10.1 Introduction 209
10.2 Methods and Protocols 213
10.3 Applications of the Technology 216
10.4 Perspectives 219
11 Extending Functional Genomics: VIGS for Model and Crop Plants 227
11.1 Introduction 227
11.2 Methods and Protocols 232
11.3 Applications of the Technology 241
11.4 Perspectives 242
12 TILLING: A Reverse Genetics and a Functional Genomics Tool in Soybean 251
12.1 Introduction 251
12.2 Methods and Protocols 252
12.3 Applications of TILLING to Soybean 258
12.4 Discussion and Perspectives 262
13 Transposon Taggingin Cereal Crops 267
13.1 Insertional Mutagenesis in Plants 268
13.2 Transposon Tagging in Maize 270
13.4 Ac/Ds Transposon Tagging in Barley 280
13.5 Future Direction of Tagging in Cereals 281
14 Fast Neutron Mutagenesis for Functional Genomics 291
14.1 Introduction 291
14.2 Methods and Protocols 294
14.3 Applications of the Technology 301
14.4 Perspectives 304
III Computational Analysis 307
15 Bioinformatics Tools to Discover Co-Expressed Genes in Plants 309
15.1 Introduction 309
15.2 The Expression Angler Tool of the Botany Array Resource 311
15.3 The CSB.DB Tool 320
15.4 The KaPPA-View 2: Co-Expression Analysis on the Plant Metabolic Pathway Maps 324
15.5 The KAGIANA Tool for Co-Expression Network Analysis of Arabidopsis Genes 328
16 AthaMap， a Database for the Identification and Analysis of Transcription Factor Binding Sites in the Arabidopsis thaliana Genome 337
16.1 Introduction 337
16.2 Methods and Applications 339
17 Structural Phylogenomic Inference of Plant Gene Function 347
17.1 Introduction 347
17.2 Challenges in Protein Function Prediction 349
17.3 The Nomenclature of Homology 352
17.4 Structural Phylogenomic Inference of Function 354
17.5 Recommended Protocols for a Structural Phylogenomic Pipeline 356
17.6 Web Servers and Databases useful in Phylogenomic Inference 362
17.7 Discussion 363
18 Structural， Functional， and Comparative Annotation of Plant Genomes 373
18.1 Introduction 373
18.2 Methods， Protocols， and Applications 374
18.3 Perspectives 387
19 Large-Scale Genomic Sequence Comparison and Gene Identification with ClustDB 397
19.1 Introduction 397
19.2 Methods and Protocols 401
19.3 Applications 410
19.4 Perspectives 413
IV Functional Genomics and Emerging Technologies 417
20 Nanotechnologies and Fluorescent Proteins for in planta Functional Genomics 419
20.1 Introduction 419
20.2 Green Fluorescent Protein 420
20.3 Protocol: Seeing GFP in Transgenic Plants 424
20.4 Nanotechnology for Monitoring Gene Expression 425
20.5 Barriers to Implementation 427
20.6 Conclusions 427
21 New Frontiers in Plant Functional Genomics Using Next Generation Sequencing Technologies 431
21.1 Introduction 431
21.2 Library Generation 434
21.3 Emulsion PCR 436
21.4 Sequencing by Ligation 437
21.5 Base Calling 439
21.6 Potential Applications 440
21.7 Conclusions 444
22 454 Sequencing: The Next Generation Tool for Functional Genomics 447
22.1 Introduction 448
22.2 Methods and Protocols 450
22.3 Applications of the Technology 470
Glossary 477
Index 537
