Schmidt / Bancroft Genetics and Genomics of the Brassicaceae

1. Auflage 2010
ISBN: 978-1-4419-7118-0
Verlag: Springer US
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 9, 680 Seiten

Reihe: Plant Genetics and Genomics: Crops and Models

The Genetics and Genomics of the Brassicaceae provides a review of this important family (commonly termed the mustard family, or Cruciferae). The family contains several cultivated species, including radish, rocket, watercress, wasabi and horseradish, in addition to the vegetable and oil crops of the Brassica genus. There are numerous further species with great potential for exploitation in 21st century agriculture, particularly as sources of bioactive chemicals. These opportunities are reviewed, in the context of the Brassicaceae in agriculture. More detailed descriptions are provided of the genetics of the cultivated Brassica crops, including both the species producing most of the brassica vegetable crops (B. rapa and B. oleracea) and the principal species producing oilseed crops (B. napus and B. juncea). The Brassicaceae also include important 'model' plant species. Most prominent is Arabidopsis thaliana, the first plant species to have its genome sequenced. Natural genetic variation is reviewed for A. thaliana, as are the genetics of the closely related A. lyrata and of the genus Capsella. Self incompatibility is widespread in the Brassicaceae, and this subject is reviewed. Interest arising from both the commercial value of crop species of the Brassicaceae and the importance of Arabidopsis thaliana as a model species, has led to the development of numerous resources to support research. These are reviewed, including germplasm and genomic library resources, and resources for reverse genetics, metabolomics, bioinformatics and transformation. Molecular studies of the genomes of species of the Brassicaceae revealed extensive genome duplication, indicative of multiple polyploidy events during evolution. In some species, such as Brassica napus, there is evidence of multiple rounds of polyploidy during its relatively recent evolution, thus the Brassicaceae represent an excellent model system for the study of the impacts of polyploidy and the subsequent process of diploidisation, whereby the genome stabilises. Sequence-level characterization of the genomes of Arabidopsis thaliana and Brassica rapa are presented, along with summaries of comparative studies conducted at both linkage map and sequence level, and analysis of the structural and functional evolution of resynthesised polyploids, along with a description of the phylogeny and karyotype evolution of the Brassicaceae. Finally, some perspectives of the editors are presented. These focus upon the Brassicaceae species as models for studying genome evolution following polyploidy, the impact of advances in genome sequencing technology, prospects for future transcriptome analysis and upcoming model systems.

Professor Ian Bancroft completed his PhD at the University of Lancaster in 1986 and conducted his early postdoctoral research at Michigan State University, studying the genomes of cyanobacteria. He moved to the John Innes Centre in 1989 and has been expanding and applying his genomics expertise, initially in Arabidopsis thaliana, and since 1998 in the cultivated Brassica species. Renate Schmidt is leader of the group 'Genome plasticity' at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben (Germany). She was educated as a molecular geneticist, and her research interests center on comparative genome analysis in the Brassicaceae and transgene expression in plants.

Autoren/Hrsg.

Bancroft, Ian

Schmidt, Renate

Inhaltsverzeichnis

1;Preface;4
2;Contents;6
3;Contributors;8
4;1 Phylogeny, Genome, and Karyotype Evolution of Crucifers (Brassicaceae);12
4.1;1.1 General Introduction;13
4.2;1.2 Phylogenetic Position of Brassicaceae and Recognition of Infrafamiliar Taxa;16
4.3;1.3 Genome and Chromosomal Evolution;21
4.3.1;1.3.1 Prehistory of Crucifer Genomes: Whole-Genome Duplications and the Age of the Family;21
4.3.2;1.3.2 Genome Size Variation;23
4.3.3;1.3.3 Chromosomes and Chromosome Number Variation;24
4.3.4;1.3.4 Hybridization and Polyploidy;26
4.3.5;1.3.5 Genome and Chromosome Collinearity;29
4.3.6;1.3.6 Revealing Chromosome Homeology Through Comparative Chromosome Painting;29
4.3.7;1.3.7 Ancestral Crucifer Karyotype (ACK, n=8);31
4.3.8;1.3.8 Overview of Karyotype Evolution in Brassicaceae;33
4.4;References;35
5;2 Brassicaceae in Agriculture;43
5.1;2.1 Introduction;44
5.2;2.2 Taxonomy and Genetic Relationships of Brassica Crop Species;45
5.2.1;2.2.1 B. oleracea;46
5.2.2;2.2.2 B. rapa;47
5.2.3;2.2.3 B. nigra;48
5.2.4;2.2.4 B. napus;48
5.2.5;2.2.5 B. carinata;48
5.2.6;2.2.6 B. juncea;49
5.3;2.3 Other Crucifer Crops;49
5.3.1;2.3.1 Camelina;49
5.3.2;2.3.2 Crambe;49
5.3.3;2.3.3 Eruca;50
5.3.4;2.3.4 Raphanus;50
5.3.5;2.3.5 Sinapis;51
5.4;2.4 Underutilized Crucifer Crops;51
5.5;2.5 Brassicaceae as Sources of Agronomic and Economic Traits;52
5.5.1;2.5.1 Morphological Traits;52
5.5.2;2.5.2 Chemical Traits;53
5.5.3;2.5.3 C3--C4 Photosynthesis;54
5.5.4;2.5.4 Cytoplasmic Male Sterility;55
5.5.5;2.5.5 Breeding Systems and Apomixis;55
5.5.6;2.5.6 Plant Regeneration and Transformation;55
5.5.7;2.5.7 Salt and Heavy Metal Tolerances;56
5.5.8;2.5.8 Cold Tolerance;56
5.5.9;2.5.9 Drought Tolerance;57
5.5.10;2.5.10 Herbicide Resistance;57
5.5.11;2.5.11 Disease Resistance;58
5.5.12;2.5.12 Insect and Nematode Resistance;59
5.6;2.6 Conclusion;60
5.7;References;60
6;3 The Non-coding Landscape of the Genome of Arabidopsis thaliana;76
6.1;3.1 Introduction;77
6.1.1;3.1.1 An Introduction to Cis Elements;78
6.1.2;3.1.2 The Core Promoter;80
6.1.3;3.1.3 The Proximal and Distal Promoter;85
6.1.4;3.1.4 Detection of Cis-regulatory Elements;85
6.1.4.1;3.1.4.1 Experimental Approaches;85
6.1.4.2;3.1.4.2 Computational Approaches;88
6.1.5;3.1.5 Cis Elements: Conclusion and Outlook;96
6.1.6;3.1.6 The Arabidopsis Non-coding RNA Landscape;97
6.1.7;3.1.7 Long ncRNAs;99
6.1.7.1;3.1.7.1 Natural Antisense Transcripts;99
6.1.7.2;3.1.7.2 Transcripts Generated by RNA Polymerase V;99
6.1.8;3.1.8 Small RNAs;100
6.1.8.1;3.1.8.1 MicroRNAs;100
6.1.8.2;3.1.8.2 Small/Short Interfering RNAs;116
6.1.8.3;3.1.8.3 Repeat-Associated siRNAs;117
6.1.8.4;3.1.8.4 Natural Antisense siRNAs;119
6.1.8.5;3.1.8.5 Trans-acting siRNAs;119
6.1.9;3.1.9 Non-coding RNA: Conclusions;119
6.2;References;120
7;4 Natural Variation in Arabidopsis thaliana;131
7.1;4.1 Introduction;132
7.2;4.2 Geographical Distribution and Demographical History of A. thaliana;134
7.3;4.3 Genetic and Molecular Analysis of A. thaliana Natural Variation;135
7.4;4.4 Genetic Bases of Adaptation: QTL Underlying A. thaliana Natural Variation;138
7.5;4.5 Molecular Bases of Adaptation: Genes Underlying A. thaliana Natural Variation;145
7.6;4.6 The Use of A. thaliana Genetic Information in Brassica;147
7.7;References;149
8;5 Chasing Ghosts: Comparative Mapping in the Brassicaceae;160
8.1;5.1 Introduction;161
8.2;5.2 Common Terms Used in Comparative Mapping Studies;162
8.3;5.3 The Basics of Comparative Mapping;163
8.4;5.4 The Contribution of Polyploidy (Inter-specific Hybridization) to Brassica Genome Evolution;165
8.5;5.5 The Ghost of an Ancestral Hexaploid Genome;167
8.6;5.6 A. thaliana, a Model Genome for the Brassicaceae;167
8.6.1;5.6.1 Across the A, B, and C Genomes;169
8.6.2;5.6.2 Conserved Chromosome Landmarks;171
8.6.3;5.6.3 Rearrangement Hotspots;171
8.7;5.7 Exploiting Comparative Mapping for Trait Analysis;172
8.8;5.8 Extending the Comparisons to Related Species;173
8.9;5.9 The Promise of Sequenced Genomes;173
8.10;References;174
9;6 Comparative Genome Analysis at the Sequence Level in the Brassicaceae;178
9.1;6.1 Introduction/Overview;179
9.2;6.2 The A. thaliana Reference Genome;180
9.3;6.3 Comparative Analysis of A. thaliana Accessions;181
9.4;6.4 Sequence Comparisons Between A. thaliana and Near Relatives;183
9.5;6.5 Sequence Comparisons Between A. thaliana and Brassica Species;188
9.5.1;6.5.1 B. rapa;189
9.5.2;6.5.2 B. oleracea;191
9.5.3;6.5.3 B. napus;192
9.6;6.6 Sequence Relationships Between Brassica Genomes;195
9.6.1;6.6.1 Brassica A Genomes: B. rapa and B. napus;195
9.6.2;6.6.2 Brassica C Genomes: B. oleracea and B. napus;195
9.7;6.7 Comparative Analysis of B. napus Accessions;196
9.8;6.8 Summary;197
9.9;References;198
10;7 Structural and Functional Evolution of Resynthesized Polyploids;202
10.1;7.1 Polyploidy Is a Pervasive Phenomenon in Flowering Plants;203
10.2;7.2 Ancient Whole Genome Duplications in the Brassicaceae;204
10.3;7.3 Resynthesized Brassica and Arabidopsis Polyploids;206
10.3.1;7.3.1 Phenotypic Effects in Resynthesized Polyploids;207
10.3.2;7.3.2 Genetic and Epigenetic Changes in Resynthesized Polyploids ;208
10.3.2.1;7.3.2.1 Genetic Changes and Their Effects on Gene Expression and Phenotypes;208
10.3.2.2;7.3.2.2 Epigenetic Changes in Resynthesized Polyploids;211
10.3.2.3;7.3.2.3 Proteome Changes in Resynthesized Polyploids;211
10.4;7.4 Conclusions and Future Research in Resynthesized Polyploids;212
10.5;References;213
11;8 Genetics of Brassica rapa L.;222
11.1;8.1 Introduction;223
11.2;8.2 B. rapa Breeding and Trait Genetics;224
11.3;8.3 Molecular Markers;225
11.3.1;8.3.1 Molecular Markers in Diversity Studies;226
11.3.2;8.3.2 Molecular Markers and Development of Genetic Linkage Maps in B. rapa;226
11.3.3;8.3.3 Molecular Markers and Trait Genetics;240
11.3.3.1;8.3.3.1 Mapping of Bolting, Flowering, and Vernalizaton Requirement;240
11.3.3.2;8.3.3.2 Mapping of Plant Height;241
11.3.3.3;8.3.3.3 Mapping of Root Traits;242
11.3.3.4;8.3.3.4 Mapping of Agronomic and Morphological Traits;243
11.3.3.5;8.3.3.5 Genetics and Mapping of Seed Coat Color;244
11.3.3.6;8.3.3.6 Mapping of Anthocyanin Pigmentation;245
11.3.3.7;8.3.3.7 Mapping of Self-Incompatibility;246
11.3.3.8;8.3.3.8 Mapping of Embryogenic Ability in Microspore Culture;246
11.3.3.9;8.3.3.9 Mapping of Mineral Accumulation;247
11.3.3.10;8.3.3.10 Mapping of Fatty Acid Composition;248
11.3.3.11;8.3.3.11 Mapping of Glucosinolates Traits;249
11.3.3.12;8.3.3.12 Mapping of Abiotic Stress Tolerance;250
11.3.3.13;8.3.3.13 Genetics and Mapping of Disease Resistance;251
11.4;8.4 Comparative Mapping and Identification of Candidate Genes for Important Traits;256
11.5;8.5 Conclusions and Perspectives;258
11.6;References;259
12;9 The Genetics of Brassica oleracea;268
12.1;9.1 Importance of Brassica oleracea Crops;269
12.2;9.2 Origin, Distribution, and Domestication;270
12.3;9.3 Taxonomy of B. oleracea Crops: Coenospecies and Cytodemes;271
12.4;9.4 Interspecific and Intergeneric Hybridizations;273
12.5;9.5 Genetics of Main Crop Morphotypes;273
12.5.1;9.5.1 Cabbage Traits;274
12.5.2;9.5.2 Kohlrabi Traits;275
12.5.3;9.5.3 Kale Traits;275
12.5.4;9.5.4 Brussel Sprouts Traits;276
12.5.5;9.5.5 Cauliflower and Broccoli Traits;276
12.6;9.6 Flower Color and Bolting;278
12.7;9.7 Secondary Metabolites: Glucosinolates (GSL) and Carotenoids;279
12.8;9.8 Disease and Insect Resistance;282
12.9;9.9 Chromosome Number Variation;284
12.9.1;9.9.1 Polyploidy;284
12.9.2;9.9.2 Aneuploidy;285
12.10;9.10 Monoploids and Anther/Microspore Culture;285
12.11;9.11 Genomic Tools: Markers, Genetic and Physical Maps;286
12.12;9.12 Map Development in Brassica;286
12.13;9.13 Synteny Maps;287
12.14;9.14 Genomics;288
12.15;9.15 Outlook;289
12.16;References;289
13;10 The Genetics of Brassica napus;297
13.1;10.1 Brassica napus Origin and Domestication;299
13.2;10.2 B. napus and Its Importance as an Oilseed Crop;301
13.3;10.3 Status of the Genetics and Genomic Tools in Oil Rapeseed (B. napus);301
13.3.1;10.3.1 Genomic Tools I: Molecular Marker Technology in B. napus ;301
13.3.2;10.3.2 Genomic Tools II: Development of Genetic Linkage Maps;303
13.4;10.4 The Genetics of Specific Traits in Rapeseed B. napus;308
13.4.1;10.4.1 Modified FA and Specialty Oil and Meal Profiles;308
13.4.2;10.4.2 Oil Content;309
13.4.3;10.4.3 Flowering Time Variation: Winter vs. Spring;310
13.4.4;10.4.4 Hybrids, Population Development, and Seed Yield Improvement;312
13.4.5;10.4.5 Other Important Oil Quality-Related Traits;315
13.5;10.5 Conclusions;317
13.6;References;318
14;11 Genetics of Brassica juncea;329
14.1;11.1 Introduction;330
14.2;11.2 Available Variability;332
14.3;11.3 Genome Mapping in B. juncea;333
14.4;11.4 Genetics and Mapping of Important Traits;337
14.4.1;11.4.1 Erucic Acid Content and Oil Content;338
14.4.2;11.4.2 Glucosinolates and the Importance of Context;340
14.4.3;11.4.3 Seed Coat Colour;342
14.4.4;11.4.4 Agronomic and Yield Traits;343
14.4.5;11.4.5 Disease Resistance;344
14.5;11.5 Future Prospects;346
14.6;References;347
15;12 Arabidopsis lyrata Genetics;352
15.1;12.1 Introduction;353
15.2;12.2 Systematics and Distribution;353
15.3;12.3 A. lyrata Genome;355
15.4;12.4 A. lyrata Is Self-Incompatible and Has Inbreeding Depression;356
15.5;12.5 The Mating System Influences Genome Evolution;358
15.6;12.6 Population Genetic Diversity in Individual Populations;359
15.7;12.7 Disjunct Populations Are Highly Differentiated;363
15.8;12.8 Genetics of Local Adaptation;366
15.9;12.9 Perspectives for A. lyrata for Functional and Population Genomics;370
15.10;References;371
16;13 The Genetics of Capsella;378
16.1;13.1 Introduction;379
16.2;13.2 Speciation;380
16.2.1;13.2.1 On the Ancestry of C. grandiflora;380
16.2.2;13.2.2 On the Origin of C. rubella;381
16.2.3;13.2.3 On the Origin of C. bursa-pastoris;381
16.3;13.3 Genome and Chromosome Evolution;382
16.4;13.4 Evolution and Development of Phenotypic Traits;383
16.4.1;13.4.1 Leaf Development;383
16.4.2;13.4.2 Flowering Time;383
16.4.3;13.4.3 Floral Structure and Function;384
16.4.3.1;13.4.3.1 Floral Size;384
16.4.3.2;13.4.3.2 Saltational Change in Floral Architecture;385
16.4.3.3;13.4.3.3 Self-Incompatibility;387
16.4.4;13.4.4 Fruit Structure;388
16.5;13.5 Outlook;389
16.6;References;389
17;14 Self-Incompatibility in the Brassicaceae;393
17.1;14.1 Introduction;394
17.2;14.2 Genetics of Self-Incompatibility;395
17.3;14.3 Mechanism of Recognition and Inhibition of Self Pollen;396
17.3.1;14.3.1 Cytological Responses;396
17.3.2;14.3.2 Molecular Studies;397
17.3.2.1;14.3.2.1 Identification of the Stigma and Pollen Determinants of SI: From Immunogenetics, Protein Electrophoresis, to Molecular Cloning;397
17.3.2.2;14.3.2.2 The S Haplotype and Control of Recognition Specificity;400
17.3.2.3;14.3.2.3 Signal Transduction;402
17.4;14.4 S haplotype Structure, Suppressed Recombination, and Diversification;404
17.4.1;14.4.1 Diversification of SRK and SCR;404
17.5;14.5 Mating-Type Dimorphism in the Brassicaceae: Loss of SI and the Switch From an Outbreeding to a Self-Fertile Mode of Mating;407
17.5.1;14.5.1 Analysis of Self-Fertility in Non-model Members of the Brassicaceae;407
17.5.2;14.5.2 Analysis of Self-Fertility in the Model Plant A. thaliana;408
17.6;14.6 Future Prospects;409
17.7;References;410
18;15 Sequencing the Gene Space of Brassica rapa;416
18.1;15.1 B. rapa as a Reference for the Brassica A Genome;417
18.2;15.2 Genome Structure of B. rapa ;418
18.2.1;15.2.1 Cytogenetic Study of the B. rapa Genome;418
18.2.2;15.2.2 Repetitive Sequences of B. rapa;419
18.2.3;15.2.3 Triplicated Nature of the B. rapa Genome;422
18.3;15.3 Genomic Resources for B. rapa;423
18.3.1;15.3.1 BAC Libraries and BAC-end Sequences;423
18.3.2;15.3.2 Genetic Map;425
18.3.3;15.3.3 Physical Map;425
18.3.4;15.3.4 Expressed Sequence Tags and Transcriptome Analysis;427
18.3.5;15.3.5 Information Resources;430
18.4;15.4 Progress of Genome Sequencing;430
18.4.1;15.4.1 Sequencing of Euchromatic Regions Based on the Clone-by-Clone Strategy;430
18.4.2;15.4.2 Seed BAC Selection;431
18.4.3;15.4.3 Characteristics of the Seed BAC Sequences;433
18.4.4;15.4.4 Sequencing Process;435
18.5;15.5 Perspective;436
18.6;References;437
19;16 Germplasm and Molecular Resources;439
19.1;16.1 Introduction;441
19.2;16.2 Germplasm Resources;442
19.2.1;16.2.1 A. thaliana ;447
19.2.2;16.2.2 Brassica Species;449
19.2.2.1;16.2.2.1 Diversity Fixed Foundation Sets (DFFS);452
19.2.2.2;16.2.2.2 Mapping Populations;452
19.2.2.3;16.2.2.3 Emerging Resources;453
19.2.2.4;16.2.2.4 Educational Resources;453
19.3;16.3 Molecular Resources;453
19.3.1;16.3.1 Genomic Library/Clone Resources for A. thaliana;458
19.3.1.1;16.3.1.1 Resources Utilized by the Arabidopsis Genome Initiative;458
19.3.1.2;16.3.1.2 Bacterial Artificial Chromosome and P1 Libraries and Clones Used to Generate Genome Sequence;458
19.3.1.3;16.3.1.3 Sources of Agi BAC and P1 Libraries, Filters, and Clones;459
19.3.1.4;16.3.1.4 Other Arabidopsis Genomic Clone Resources;459
19.3.1.5;16.3.1.5 Utilization of Large Insert Genomic Libraries;460
19.3.2;16.3.2 Genomic Library/Clone Resources for Members of the Brassicaceae;461
19.3.2.1;16.3.2.1 Resources Associated with Brassica Sequencing Projects;461
19.3.3;16.3.3 Other Molecular Resources for Arabidopsis;462
19.3.3.1;16.3.3.1 Expressed Sequence Tags and cDNA Clones;462
19.3.3.2;16.3.3.2 Sequenced Full-Length cDNA and ORF Clones in Entry Vectors;464
19.3.3.3;16.3.3.3 Gene-Specific Tag and RNA Interference Clones;464
19.3.3.4;16.3.3.4 Multifunctional Vectors;465
19.3.4;16.3.4 New Resources for the Brassicaceae;465
19.4;16.4 Conclusions;465
19.5;References ;468
20;17 Resources for Metabolomics;470
20.1;17.1 Introduction;471
20.2;17.2 Non-targeted Profiling of Semi-polar Plant Metabolites Using UPLC/ESI-QTOF-MS;473
20.2.1;17.2.1 Experimental Design and Sampling -- General Considerations;473
20.2.2;17.2.2 Sample Preparation;474
20.2.2.1;17.2.2.1 Extraction;474
20.2.2.2;17.2.2.2 Fractionation;475
20.2.2.3;17.2.2.3 Derivatization;477
20.2.3;17.2.3 Data Acquisition;477
20.2.4;17.2.4 Data Extraction in Non-targeted Analysis of Metabolite Profiles;482
20.2.5;17.2.5 Elucidation of Molecular Structures;484
20.3;17.3 Compound Classes Amenable for LC/API-MS-Based Profiling Approaches;489
20.3.1;17.3.1 Secondary Metabolites in Arabidopsis;489
20.3.2;17.3.2 Lipids;494
20.4;17.4 Conclusion and Outlook;496
20.5;References;497
21;18 Transformation Technology in the Brassicaceae;505
21.1;18.1 Introduction;506
21.2;18.2 Agrobacterium Transformation Methods;508
21.2.1;18.2.1 Agrobacterium tumefaciens;508
21.2.2;18.2.2 Agrobacterium rhizogenes;510
21.3;18.3 Direct Uptake Transformation Methods;511
21.4;18.4 Chloroplast Transformation;511
21.5;18.5 Bacterial Strains and Plasmids;511
21.6;18.6 Shoot Regeneration;512
21.6.1;18.6.1 The Genetic Basis of In Vitro Shoot Regeneration;512
21.6.2;18.6.2 Intolerance to In Vitro Conditions;513
21.6.3;18.6.3 Choice of Explant and Tissue Culture Media;513
21.6.4;18.6.4 Shoot Elongation and Rooting In Vitro;514
21.7;18.7 Hyperhydricity and Tissue Necrosis: Use of Ethylene Inhibitors;514
21.8;18.8 Floral Dipping/Microinjection;515
21.9;18.9 Selection of Transgenics;516
21.10;18.10 Transformation as a Research Tool;517
21.11;18.11 Concluding Remarks;518
21.12;References;518
22;19 Resources for Reverse Genetics Approaches in Arabidopsis thaliana;526
22.1;19.1 Introduction;528
22.2;19.2 Gene Function Analyses;528
22.2.1;19.2.1 Similarity to Other Known Proteins;529
22.2.2;19.2.2 Expression Analyses;530
22.2.2.1;19.2.2.1 Array-Related Expression Data (Microarrays);530
22.2.2.2;19.2.2.2 Expression Analyses Using Promoter:Reporter Gene Fusions and Promoter, Gene, and Enhancer Trap Lines;531
22.2.3;19.2.3 Mutation Analyses;532
22.2.3.1;19.2.3.1 Chemically Generated Mutants;532
22.2.3.2;19.2.3.2 Mutants Generated by Physical Agents;538
22.2.3.3;19.2.3.3 Biologically Generated Insertional Mutants;538
22.2.3.4;19.2.3.4 Targeted (Homologous Recombination Induced) Mutations;545
22.2.4;19.2.4 Over-Expression/Activation-Mediated Functional Assays;546
22.2.4.1;19.2.4.1 Collections of Transgenic Lines that Over-Express Plant Genes;546
22.2.4.2;19.2.4.2 Activation Tagging Lines;546
22.2.5;19.2.5 Gene Silencing-Mediated Functional Analysis;547
22.2.5.1;19.2.5.1 Antisense Lines;548
22.2.5.2;19.2.5.2 RNAi Lines;548
22.2.5.3;19.2.5.3 MicroRNAs and Targeted miRNA Lines;551
22.3;19.3 Outlook;551
22.4;References;552
23;20 Resources for Reverse Genetics Approaches in Brassica Species;560
23.1;20.1 Introduction;561
23.2;20.2 TILLING;561
23.2.1;20.2.1 EMS;561
23.2.2;20.2.2 EMS-Induced Mutations and the Genetic Code;562
23.2.3;20.2.3 Mutation Load;563
23.2.4;20.2.4 TILLING in Brassica Step by Step;564
23.2.4.1;20.2.4.1 Optimising Mutagen Dosage;564
23.2.4.2;20.2.4.2 M1 and M2 Population Structure;565
23.2.4.3;20.2.4.3 Setting up the TILLING Platform;566
23.2.4.4;20.2.4.4 Choosing the Amplicon;566
23.2.4.5;20.2.4.5 Linking Mutation to Phenotype;567
23.3;20.3 RNA Interference;567
23.3.1;20.3.1 Background;567
23.3.2;20.3.2 Classes of sRNA Associated with PTGS;568
23.3.3;20.3.3 RNAi/PTGS Mechanisms: Gene Silencing Approaches in Brassicaceae;569
23.3.3.1;20.3.3.1 Virally Induced Gene Silencing;569
23.3.3.2;20.3.3.2 Co-suppression and Antisense RNA;571
23.3.3.3;20.3.3.3 IR-PTGS: siRNA-Directed Gene Silencing Using hpRNA Constructs ;572
23.3.3.4;20.3.3.4 hpRNA;572
23.3.4;20.3.4 Examples of RNAi in Brassica Species;576
23.3.4.1;20.3.4.1 Metabolic Engineering and Manipulation of Biosynthetic Pathways Using RNAi;576
23.3.4.2;20.3.4.2 Studying Gene Function Throughout Brassica Development;577
23.3.4.3;20.3.4.3 Conferring Tissue Specificity in RNAi Approaches in Brassica Species;577
23.4;20.4 Concluding Remarks;578
23.5;References;578
24;21 Bioinformatics Resources for Arabidopsis thaliana;583
24.1;21.1 Background to Arabidopsis thaliana;584
24.2;21.2 Genome Browsers;584
24.3;21.3 Transcriptomics Data;586
24.4;21.4 Gene and Protein Analysis Resources;588
24.5;21.5 Gene Interactions and Pathways;590
24.6;21.6 Small RNA Databases;591
24.7;21.7 Metabolomic Data;592
24.8;21.8 Integration of Data;592
24.9;References;593
25;22 Bioinformatics Resources for the Brassica Species;595
25.1;22.1 Introduction;596
25.2;22.2 First Steps in Brassica Bioinformatics;596
25.3;22.3 A Directory of Current Web Resources;597
25.4;22.4 EST Resources, Transcript Assemblies, and Microarrays;597
25.5;22.5 The B. rapa Genome Sequencing Project;601
25.5.1;22.5.1 Methodology;601
25.5.2;22.5.2 BAC End Sequencing;601
25.5.3;22.5.3 Physical Maps and Informatics;601
25.5.4;22.5.4 Bioinformatic Selection of Seed BACs;603
25.5.5;22.5.5 Coordination of Sequencing Programme;605
25.5.6;22.5.6 Automated Annotation;606
25.6;22.6 Next Generation Sequencing and the Re-sequencing of Brassica Genomes;609
25.7;22.7 Future Developments;611
25.8;References;612
26;23 Perspectives on Genetics and Genomics of the Brassicaceae;614
26.1;23.1 Brassicaceae Species as Models for Studying Genome Evolution Following Polyploidy;615
26.2;23.2 The Impact of Advances in Genome Sequencing Technology;618
26.3;23.3 Prospects for Transcriptome Analysis in the Brassicaceae;620
26.4;23.4 Upcoming Model Systems in the Brassicaceae;623
26.5;References;625
27;Index;630