Genetics and Genomics of the Brassicaceae (eBook)

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.

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