Genetics and Genomics of the Triticeae (eBook)

Catherine Feuillet is research director and leader of the group "Structure, function and evolution of the wheat genomes" at the INRA, Clermont-Ferrand (France). She was educated as a geneticist and molecular biologist and worked for 10 years in Switzerland on the genomics of disease resistance in wheat and barley before moving to France. She is one of the co-chairs of the International Wheat Genome Sequencing Consortium (IWGSC), the International Triticeae Mapping Initiative (ITMI), and the European Triticeae Genomics Initiative (ETGI). Gary J. Muehlbauer is an Associate Professor and Endowed Chair in Molecular Genetics of Crop Improvement in the Department of Agronomy and Plant Genetics at the University of Minnesota. He studied maize genetics during his Ph.D. at the University of Minnesota and his postdoctoral work at the University of California at Berkeley. He has been on the faculty at the University of Minnesota for eleven years working on barley and wheat genomics. He is the vice chair of the International Barley Sequencing Consortium.

Foreword 6
Preface 9
Acknowledgments 11
Contents 12
Contributors 15
Part I: Genetics of the Triticeae 20
Scientific Names in the Triticeae 21
1.1 The Triticeae 21
1.2 Why so Many Names? 22
1.2.1 Impact of New Technologies on the Taxonomy of the Triticeae 23
1.2.2 Integrating New Information into the Taxonomy of the Triticeae 24
1.3 Interaction of Taxonomy and Nomenclature-Some Examples 25
1.3.1 Multiple Names at the Generic Level: Pseudoroegneria 25
1.3.2 Multiple Names at the Generic Level: Elymus 26
1.3.3 Additional Problems with Generic Changes 26
1.3.4 Multiple Names at the Species Level and Below: The Triticum monococcum Complex 27
1.4 Taxonomic Treatment in this Chapter 31
1.4.1 Taxonomic Treatment in this Chapter: The Genera 32
1.4.2 Taxonomic Treatment in this Chapter: The Species 40
1.5 Nomenclatural Web Sites 41
1.6 Appendix 42
References 44
Triticeae Genetic Resources in ex situ Genebank Collections 49
2.1 Introduction 49
2.2 Material and Methods 50
2.2.1 Information Sources: Online Databases and Reports 50
2.2.2 Information Extraction and Processing 51
2.2.3 Handling of Nomenclature 52
2.3 List of Cultivated and Useful Triticeae Species 53
2.3.1 Aegilops - Goat Grass 53
2.3.2 x Aegilotriticum 54
2.3.3 Agropyron - Wheatgrass 54
2.3.4 Amblyopyrum 55
2.3.5 Brachypodium - False Brome 55
2.3.6 Dasypyrum - Mosquitograss 55
2.3.7 Elymus - Wheatgrass, Wild Rye 55
2.3.8 Eremopyrum - False Wheatgrass 56
2.3.9 Heteranthelium 56
2.3.10 Hordeum - Barley 57
2.3.11 Kengyilia 57
2.3.12 Leymus - Wildrye 57
2.3.13 Pascopyrum - Wheatgrass 58
2.3.14 Psathyrostachys - Wildrye 58
2.3.15 Pseudoroegneria - Wheatgrass 59
2.3.16 Secale - Rye 59
2.3.17 Thinopyrum - Wheatgrass 60
2.3.18 x Triticosecale - Triticale 60
2.3.19 Triticum - Wheat 60
2.3.20 x Tritordeum 62
2.4 Overview of ex situ Collections of Triticeae 62
2.4.1 Overview by Countries and Institutions 62
2.4.2 Overviews by Genera and Species 64
2.4.3 Collections of Genetic Stocks and Mutants 64
2.4.4 Triticum 67
2.4.5 Hordeum 70
2.4.6 x Triticosecale 75
2.4.7 Aegilops 77
2.4.8 Secale 80
2.4.9 Elymus 82
2.4.10 Agropyron 84
2.4.11 Other Triticeae Species 85
2.4.12 Brachypodium 89
2.5 Outlook and Conclusions 90
2.6 Appendix: Online Databases 92
References 92
Domestication of the Triticeae in the Fertile Crescent 98
3.1 Origins of Cultivated Plants and Agriculture - A Brief Historical Overview 99
3.2 Evolution and Domestication of Triticeae 100
3.2.1 Wheat Evolution and Domestication 101
3.2.1.1 Diploid Wheats 102
3.2.1.2 Tetraploid Wheats 105
3.2.1.3 Hexaploid Wheats - Bread Wheat 106
3.2.2 Barley Evolution and Domestication 107
3.2.3 Rye Evolution and Domestication 109
3.3 Traits Modified by Domestication 111
3.3.1 Free-Threshing 111
3.3.2 Brittle-Rachis 115
3.3.3 Seed Size and Grain Yield 115
3.3.4 Kernel Rows in the Ear 116
3.3.5 Plant Height 116
3.3.6 Grain Hardness 117
3.3.7 Tillering 118
3.3.8 Reduced Seed Dormancy 119
3.3.9 Control of Flowering Time 119
3.3.10 Photoperiod 119
3.3.11 Vernalization 120
3.3.12 Heading Time 121
3.3.13 Conclusions and Final Considerations 121
References 122
Cytogenetic Analysis of Wheat and Rye Genomes 137
4.1 Introduction 137
4.2 The Five Phases of Formal Wheat Cytogenetics Research 138
4.3 Wheat Anchor Karyotype 140
4.4 Wheat Chromosome Differentiation 142
4.5 Rye Anchor Karyotype 144
4.6 Future Prospects 146
References 147
Applying Cytogenetics and Genomics to Wide Hybridisations in the Genus Hordeum 152
5.1 Introduction 152
5.2 Cytological Characterisation and Chromosome Nomenclature of Barley Chromosomes 153
5.3 Cytogenetics and Species Relationships 157
5.4 Physical Mapping of the Barley Genome 160
5.5 Generation of Haploid Barley Through Wide Hybridisation and Uniparental Chromosome Elimination 162
5.6 Practical Breeding Applications of Cytogenetics 164
References 170
Methods for Genetic Analysis in the Triticeae 178
6.1 Construction of High Quality Dense Genetic Maps 178
6.1.1 Multilocus Ordering 179
6.1.2 Map Verification Procedures 180
6.1.3 Complication due to ‘Pseudo-Linkage’ and Negative Interference 181
6.1.4 Increasing the Stability of Multilocus Maps 185
6.1.5 Building Consensus Maps 186
6.2 QTL Mapping 189
6.2.1 Multiple Trait Analysis 190
6.2.2 Paradoxical Consequences of Variance-Covariance Effect 193
6.2.3 Multiple Environments 196
6.3 High-Resolution Mapping Based on Selective DNA Pooling 204
6.3.1 Standard Selective DNA Pooling Approach to QTL Mapping 204
6.3.2 Linkage Analysis (RIL) 206
6.3.3 Association Analysis 207
6.3.4 Simulations 208
6.3.5 Example of RIL Data Analysis by FPD 208
6.3.6 Example of Association Analysis by FPD 209
6.4 Final Comments 210
References 211
Genetic Mapping in the Triticeae 215
7.1 Introduction 216
7.2 Genetic Linkage Maps 217
7.2.1 Wheat Genetic Linkage Maps 222
7.2.2 Durum Genetic Linkage Maps 222
7.2.3 Barley Genetic Linkage Maps 222
7.2.4 Rye Genetic Linkage Maps 223
7.2.5 Triticale Genetic Linkage Maps 223
7.3 Physical Linkage Maps 224
7.4 Map Curation 225
7.5 Consensus Maps 227
7.6 QTL Mapping 231
7.6.1 Practical Considerations for QTL Mapping 231
7.7 High-Resolution Mapping 233
7.8 Future Directions 237
References 238
Early Stages of Meiosis in Wheat- and the Role of Ph1 250
8.1 The Introduction 250
8.2 Chromosome Sorting for Meiosis 251
8.3 Recombination- Factors Affecting its Distribution 252
8.4 Polyploids 253
8.5 Chromosome Pairing Loci 254
8.6 The Ph1 Locus 255
8.7 Exploitation of Chromosome Pairing Loci 261
References 262
Part 2: Tools, Resources and Approaches 266
A Toolbox for Triticeae Genomics 267
9.1 Introduction 267
9.2 Molecular Markers 268
9.2.1 Restriction Fragment Length Polymorphism (RFLP) Clones 268
9.2.2 Simple Sequence Repeat (SSR) Markers 270
9.2.3 Amplified Fragment Length Polymorphism (AFLP) Markers 272
9.2.4 Repeat-Based Markers 273
9.2.5 Diversity Array Technology (DArT) Markers 277
9.2.6 Single Nucleotide Polymorphism (SNP) Arrays 278
9.3 Expressed Sequence Tag (EST) Sequences and Microarrays 280
9.4 Bacterial Artificial Chromosome (BAC) Libraries 281
9.5 Outlook 284
References 285
Chromosome Genomics in the Triticeae 296
10.1 Introduction 296
10.2 Flow Cytogenetics 299
10.3 Applying Flow Cytogenetics to Triticeae Genomics 301
10.3.1 Hexaploid Wheat 302
10.3.2 Tetraploid Durum Wheat 305
10.3.3 Barley 306
10.3.4 Rye 308
10.3.5 A Toolkit for Triticeae Chromosome Sorting 310
10.4 Chromosome Genomics 312
10.4.1 Bacterial Artificial Chromosome (BAC) Libraries 312
10.4.2 BAC Contig Physical Maps and Positional Gene Cloning 313
10.4.3 Molecular Organization of Subgenomic Regions 316
10.4.4 Development of Molecular Markers 316
10.4.5 Physical and Genetic Mapping Using Flow-Sorted Chromosomes 318
10.4.6 Cytogenetic Mapping and Chromosome Structure 319
10.5 Conclusions 320
References 321
Physical Mapping in the Triticeae 328
11.1 Introduction 328
11.2 Generating a Physical Map - Basic Principles and Methods 329
11.2.1 Ordered-Marker Based Physical Mapping 329
11.2.1.1 Use of Cytogenetic Stocks and Chromosome-Microdissection 330
11.2.1.2 Fluorescence In Situ Hybridization (FISH) 332
11.2.1.3 Radiation Hybrid Mapping (RH) - HAPPY Mapping 333
11.2.2 Ordered-Clone Based Physical Mapping 335
11.2.2.1 Chromosome Walking 338
11.2.3 Optical Mapping 338
11.3 Physical Maps of Triticeae Genomes 339
11.3.1 Physical Maps of Diploid Triticeae Genomes 340
11.3.1.1 Aegilops Tauschii 340
11.3.1.2 Barley (Hordeum vulgare) 341
11.3.2 Physical Maps of Polyploid Triticeae Genomes 342
11.3.2.1 Bread wheat (Triticum aestivum) 342
11.4 Conclusion 342
References 343
Map-Based Cloning of Genes in Triticeae (Wheat and Barley) 347
12.1 Introduction 347
12.2 Genes Isolated from Wheat and Barley by Positional Cloning 348
12.3 Genetic Mapping 353
12.4 Physical Mapping for Map-Based Cloning 355
12.5 Application and Problems of Chromosome Walking in Triticeae 355
12.6 Problems Caused by Repetitive Elements 356
12.7 Aspects of Sequencing and Identification of Candidate Genes 357
12.8 The Use and Limits of Model Genomes for Marker Development and Map-Based Cloning in Triticeae 358
12.9 Validation of Candidate Genes 360
12.10 The Role of Bioinformatics in Map-Based Cloning 362
12.11 Outlook 363
References 364
Functional Validation in the Triticeae 368
13.1 Introduction 368
13.2 Targeted Induced Local Lesions in Genomes (TILLING) 369
13.2.1 Mutagens and Mutation Frequency 369
13.2.2 Mutation Spectrum Analysis 371
13.2.3 Web-Based Computational Tools for TILLING 371
13.2.4 Populations for Reverse Genetics 372
13.2.5 Mutation Detection and Validation 373
13.2.6 Mutation Confirmation and Functional Validation 374
13.3 Transient Gene Validation Assays 375
13.3.1 Virus Induced Gene Silencing (VIGS) 375
13.3.2 Biolistic Approaches 377
13.3.3 Antisense Oligodeoxynucleotide 378
13.4 Stable Genetic Transformation 380
13.4.1 Transfer of Recombinant DNA into Plant Cells 380
13.4.2 Patterns of DNA-Integration 382
13.4.3 The Design of Transformation Vectors 383
13.4.4 Insertional Mutagenesis 385
13.4.5 Linking Manipulated Gene Expression with Gene Function 385
13.5 Final Remarks 387
References 387
Genomics of Transposable Elements in the Triticeae 395
14.1 Introduction 396
14.2 Structural Genomics 398
14.3 Functional Genomics 403
14.3.1 Direct Effects 403
14.3.2 Effects on Genes, Sequence Chimeras, and Gene Regulation 406
14.4 Comparative Genomics 407
14.5 Exploitation as Molecular Markers 407
14.6 Conclusions 409
References 409
Gene and Repetitive Sequence Annotation in the Triticeae 414
15.1 Triticeae Genomics 415
15.2 Triticeae Genome Sequence and Annotation Data 416
15.2.1 The Triticeae Transcriptome 416
15.2.2 The Triticeae Genomes 417
15.2.3 Genome Annotation: Structural and Functional Annotation 418
15.2.4 Comparative Genome Annotation 420
15.3 Repetitive Sequences in the Triticeae 421
15.3.1 Methods for the Identification of Transposable Elements 421
15.3.2 Problems with Transposable Elements in Triticeae Sequencing 423
15.3.3 Software for Repeat Recognition and Isolation 425
15.3.4 The Challenge of the Large Number: Quality in Quantity is Needed 426
References 427
Brachypodium distachyon, a New Model for the Triticeae 433
16.1 Model Systems in Biology 433
16.2 Introduction to Brachypodium distachyon 434
16.2.1 Genome Size and Polyploidy 436
16.2.2 Relationship to Other Grasses 437
16.3 Brachypodium as An Experimental System 437
16.3.1 Growth Requirements and Flowering Triggers 438
16.3.2 Germplasm Resources and Natural Diversity 440
16.3.3 Chemical and Radiation Mutagenesis 441
16.3.4 Transformation and T-DNA Tagging 441
16.3.5 Related Species 444
16.4 Genomic Resources 445
16.4.1 ESTs 445
16.4.2 BAC Library Resources 446
16.4.3 Physical and Genetic Maps 447
16.4.4 Whole Genome Sequencing 448
16.4.5 Bioinformatic Resources 448
16.5 Applications of Brachypodium as a Model for Grass Research 448
16.5.1 Brachypodium as Structural Model for Wheat and Barley Genomics 449
16.5.2 Brachypodium as a Functional Model 450
16.6 Future Prospects and Directions 452
References 453
Comparative Genomics in the Triticeae 456
17.1 Introduction 456
17.2 Comparative Genomics at the Genome Scale: Macrocolinearity 458
17.2.1 Marker Based Macrocolinearity Studies 459
17.2.2 Sequence Based Macrocolinearity Studies 460
17.3 Comparative Genomics at the ‘‘Locus-Based’’ Level: Microcolinearity 463
17.3.1 Interspecific Comparative Studies: Looking at 50-70 MY of Speciation 463
17.3.2 Intraspecific Comparisons: Microcolinearity Studies Within Few MY of Speciation 465
17.3.3 Intravarietal Comparisons: Microcolinearity Studies Within Few 10,000 Years of Speciation 467
17.4 Duplications in the Triticeae Genomes 469
17.5 Comparative Genomics as Tool for Gene Discovery and Marker Development 472
17.5.1 Colinearity-Based Gene Cloning in Triticeae 472
17.5.2 Comparative Genomics Supports Gene Annotation and Marker Development 474
17.6 Summary and Outlook 475
References 476
Part III: Genetics and Genomics of Triticeae Biology 483
Genomics of Tolerance to Abiotic Stress in the Triticeae 484
18.1 Introduction 484
18.2 Searching QTLs and Genes for Tolerance to Abiotic Stress 485
18.2.1 Candidate Gene Approach 515
18.2.2 Exploiting the ‘‘-omics’’ Platforms 516
18.3 QTLs and Genes for Tolerance to Abiotic Stress 518
18.3.1 Tolerance to Drought 519
18.3.1.1 Barley 520
18.3.1.2 Wheat 522
18.3.2 Tolerance to Salinity 524
18.3.3 Tolerance to Low Nutrients 525
18.3.3.1 Nitrogen 526
18.3.3.2 Phosphorus 528
18.3.4 Tolerance to Aluminium Toxicity 529
18.3.5 Tolerance to Boron Toxicity 531
18.3.6 Tolerance to Zinc and Manganese Deficiency 532
18.3.7 Tolerance to Waterlogging 533
18.3.8 Tolerance to Low Temperature 534
18.3.9 Tolerance to High Temperature 536
18.4 Genomics of Genotype x Environment Interaction Under Conditions of Abiotic Stress 537
18.5 Prospects of Genomics-Assisted Improvement of Tolerance to Abiotic Stress 538
References 540
Genomics of Biotic Interactions in the Triticeae 562
19.1 Disease Epidemics and Current Threats 562
19.1.1 Plant Defenses Employed in Response to Biotic Stress 563
19.1.2 Integrative Genomics Holds the Keys to Durable Resistance 564
19.2 The Toolbox for Investigating Biotic Interactions 565
19.2.1 Molecule Profiling Approaches 565
19.2.2 Integration of Phenotypic, Genetic and Physical-Map Data 566
19.2.3 High-Throughput Functional Analysis 568
19.3 Triticeae-Fungal ‘‘Host’’ Interactions 572
19.4 Triticeae-Fungal ‘‘Nonhost’’ Interactions 574
19.5 Triticeae Interactions with Insects, Viruses, Worms and Bacteria 576
19.6 Pathogen Genomics 577
19.6.1 Fusarium graminearum (Fusarium Head Blight) 577
19.6.2 Puccinia graminis (Stem Rust) 578
19.6.3 Mycosphaerella graminicola (Septoria Tritici Blotch) 579
19.6.4 Stagonospora nodorum (Stagonospora Nodorum Blotch) 580
19.6.5 Blumeria graminis (Powdery Mildew) 580
19.6.6 Barley Yellow Dwarf Virus (BYDV) 581
19.7 Synthesis 582
References 583
Developmental and Reproductive Traits in the Triticeae 593
20.1 Introduction 593
20.2 Gene Catalogues 596
20.3 Identifying Flowering Time Genes in the Triticeae 597
20.3.1 The Candidate Gene Method 597
20.3.2 The Positional Cloning Method 598
20.3.3 The Positional Cloning/Candidate Gene Hybrid Method 599
20.4 Identifying Inflorescence Development Genes in the Triticeae 601
20.4.1 The Candidate Gene Method 601
20.4.2 The Positional Cloning Method 601
20.5 Understanding Gene Function 602
20.5.1 The Analysis of Genetic Pathways 602
20.5.2 Validation of Candidate Flowering Genes 604
20.6 Advances in Triticeae Genomics and Gene Identification 605
20.7 Using Flowering and Inflorescence Genes in Triticeae Breeding 607
References 607
Genomics of Quality Traits 612
21.1 Introduction 612
21.2 Genomics of Barley Quality 613
21.2.1 Human Food 613
21.2.2 Malting and Brewing 615
21.2.2.1 beta-amylase 616
21.2.3 QTL associated with malting quality 617
21.2.4 Germination as a Key Variable in Barley Quality 620
21.3 Genomics of Wheat Quality 622
21.3.1 The Wheat Flour Proteins 623
21.3.1.1 High Molecular Weight Glutenin Subunits (HMWGS) 626
21.3.1.2 Low Molecular Weight Glutenin Subunits (LMWGS) 627
21.3.2 Seed Storage Protein Gene Structure and Variation 628
21.3.2.1 Assaying Variation in Seed Storage Proteins 630
21.3.3 Flour Color 631
21.3.3.1 The Yellowness of Flour and Its End Products 632
21.3.3.2 The Finely Divided Bran Specks in Flour 632
21.3.4 Flour Paste Viscosity 634
21.4 Grain Hardness and Carbohydrates in Wheat and Barley 634
21.4.1 Starch Content 634
21.4.2 Starch Composition 635
21.4.3 Non-Starch Polysaccharides 636
21.4.4 Grain Hardness 636
21.5 Traits that Are Not Analysed at the Genomic Level to Date 637
21.5.1 Milling Yield 637
21.5.2 Water Absorption 638
21.5.3 Grain Protein Content 638
21.6 Impact of New Technologies 639
21.7 Conclusions 640
References 641
Part IV: Early Messages 654
Linkage Disequilibrium and Association Mapping in the Triticeae 655
22.1 Introduction 655
22.2 Linkage Disequilibrium 656
22.2.1 Measurement and Interpretation of Linkage Disequilibrium 656
22.2.2 LD Estimates for the Triticeae 658
22.3 Association Analysis 662
22.3.1 Population Structure 662
22.3.2 Association Mapping Strategies 663
22.3.3 Association Mapping in the Triticeae 665
22.3.4 Germplasm Panels 667
22.3.5 Simulations 669
22.4 Future Needs and Directions 671
22.4.1 Fine-Mapping 671
22.4.2 Breeding Applications 672
22.4.3 Association Breeding 673
22.4.4 Marker Assisted Recurrent Selection 676
22.4.5 Genomic Selection 677
References 677
Triticeae Genome Structure and Evolution 684
23.1 Structure of Triticeae Genomes 684
23.1.1 Genome Size 684
23.1.2 Overall Structure 685
23.1.3 Tandem Repeated Sequences 686
23.1.3.1 Centromeric Regions 687
23.1.3.2 Telomeric Region 689
23.1.3.3 Interstitial Sites 691
23.1.3.4 rRNA Genes 692
23.1.4 Interspersed Repeated Sequences 694
23.2 Genome Evolution 695
23.2.1 TEs and Triticeae Genome Evolution 695
23.2.2 Gene Order Paradox 696
23.2.3 Conservative and Dynamic Strata of Triticeae Genomes 697
23.2.4 Recombination and Gene Content Evolution Along the Centromere-Telomere Axis of Triticeae Chromosomes 698
23.2.4.1 Variation in Gene Density Along Chromosomes 699
23.2.4.2 The Cause of Correlation Between Gene Density and Recombination Rate 700
23.2.5 The Evolutionary Significance of Repeated DNA 701
23.3 Conclusions 702
References 702
Wheat and Barley Genome Sequencing 711
24.1 Introduction 711
24.2 History of Sequencing in Higher Plants 714
24.2.1 The First Plant Genome Model - Arabidopsis thaliana 718
24.2.2 The First Economically Important Plant Genome - Rice 718
24.2.3 The First Tree Genome - Poplar Genome Sequence 720
24.2.4 Two Grapevine Sequences 721
24.2.5 The First Moderately-Sized Plant Genome Sequence - Maize 721
24.2.6 Other Plant Genome Projects 722
24.3 Current Status of Triticeae Genome Sequencing 723
24.3.1 EST Sequencing 723
24.3.2 GSS 724
24.3.3 Contiguous Genomic DNA Sequences 725
24.4 Next Generation Sequencing (NGS) Technologies 726
24.4.1 Roche-454 GSFLX 727
24.4.2 Illumina Genome Analyzer 728
24.4.3 Applied Biosystems SOLiD (Sequencing by Oligo Ligation and Detection) 728
24.4.4 HeliScope, Helicos 729
24.4.5 Impact on Triticeae Genome Sequencing 729
24.5 The Future of Triticeae Genome Sequencing 731
24.6 Outlook 733
References 734
Index 741