Feuillet / Muehlbauer Genetics and Genomics of the Triticeae

2009
ISBN: 978-0-387-77489-3
Verlag: Springer US
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 7, 700 Seiten

Reihe: Plant Genetics and Genomics: Crops and Models

Sequencing of the model plant genomes such as those of A. thaliana and rice has revolutionized our understanding of plant biology but it has yet to translate into the improvement of major crop species such as maize, wheat, or barley. Moreover, the comparative genomic studies in cereals that have been performed in the past decade have revealed the limits of conservation between rice and the other cereal genomes. This has necessitated the development of genomic resources and programs for maize, sorghum, wheat, and barley to serve as the foundation for future genome sequencing and the acceleration of genomic based improvement of these critically important crops. Cereals constitute over 50% of total crop production worldwide (http://www.fao.org/) and cereal seeds are one of the most important renewable resources for food, feed, and industrial raw materials. Crop species of the Triticeae tribe that comprise wheat, barley, and rye are essential components of human and domestic animal nutrition. With 17% of all crop area, wheat is the staple food for 40% of the world's population, while barley ranks fifth in the world production. Their domestication in the Fertile Crescent 10,000 years ago ushered in the beginning of agriculture and signified an important breakthrough in the advancement of civilization. Rye is second after wheat among grains most commonly used in the production of bread and is also very important for mixed animal feeds. It can be cultivated in poor soils and climates that are generally not suitable for other cereals. Extensive genetics and cytogenetics studies performed in the Triticeae species over the last 50 years have led to the characterization of their chromosomal composition and origins and have supported intensive work to create new genetic resources. Cytogenetic studies in wheat have allowed the identification and characterization of the different homoeologous genomes and have demonstrated the utility of studying wheat genome evolution as a model for the analysis of polyploidization, a major force in the evolution of the eukaryotic genomes. Barley with its diploid genome shows high collinearity with the other Triticeae genomes and therefore serves as a good template for supporting genomic analyses in the wheat and rye genomes. The knowledge gained from genetic studies in the Triticeae has also been used to produce Triticale, the first human made hybrid crop that results from a cross between wheat and rye and combines the nutrition quality and productivity of wheat with the ruggedness of rye. Despite the economic importance of the Triticeae species and the need for accelerated crop improvement based on genomics studies, the size (1.7 Gb for the bread wheat genome, i.e., 5x the human genome and 40 times the rice genome), high repeat content (>80%), and complexity (polyploidy in wheat) of their genomes often have been considered too challenging for efficient molecular analysis and genetic improvement in these species. Consequently, Triticeae genomics has lagged behind the genomic advances of other cereal crops for many years. Recently, however, the situation has changed dramatically and robust genomic programs can be established in the Triticeae as a result of the convergence of several technology developments that have led to new, more efficient scientific capabilities and resources such as whole-genome and chromosome-specific BAC libraries, extensive EST collections, transformation systems, wild germplasm and mutant collections, as well as DNA chips. Currently, the Triticeae genomics 'toolbox' is comprised of:- 9 publicly available BAC libraries from diploid (5), tetraploid (1) and hexaploid (3) wheat; 3 publicly available BAC libraries from barley and one BAC library from rye;- 3 wheat chromosome specific BAC libraries;- DNA chips including commercially available first generation chips from AFFYMETRIX containing 55'000 wheat and 22,000 barley genes;- A large number of wheat and barley genetic maps that are saturated by a significant number of markers;- The largest plant EST collection with 870'000 wheat ESTs, 440'000 barley ESTs and about 10'000 rye ESTs; - Established protocols for stable transformation by biolistic and agrobacterium as well as a transient expression system using VIGS in wheat and barley; and- Large collections of well characterized cultivated and wild genetic resources.International consortia, such as the International Triticeae Mapping Initiative (ITMI), have advanced synergies in the Triticeae genetics community in the development of additional mapping populations and markers that have led to a dramatic improvement in the resolution of the genetic maps and the amount of molecular markers in the three species resulting in the accelerated utilization of molecular markers in selection programs. Together, with the development of the genomic resources, the isolation of the first genes of agronomic interest by map-based cloning has been enabled and has proven the feasibility of forging the link between genotype and phenotype in the Triticeae species. Moreover, the first analyses of BAC sequences from wheat and barley have allowed preliminary characterizations of their genome organization and composition as well as the first inter- and intra-specific comparative genomic studies. These later have revealed important evolutionary mechanisms (e.g. unequal crossing over, illegitimate recombination) that have shaped the wheat and barley genomes during their evolution. These breakthroughs have demonstrated the feasibility of developing efficient genomic studies in the Triticeae and have led to the recent establishment of the International Wheat Genome Sequencing Consortium (IWGSC) (http//:www.wheatgenome.org) and the International Barley Sequencing Consortium (www.isbc.org) that aim to sequence, respectively, the hexaploid wheat and barley genomes to accelerate gene discovery and crop improvement in the next decade. Large projects aiming at the establishment of the physical maps as well as a better characterization of their composition and organization through large scale random sequencing projects have been initiated already. Concurrently, a number of projects have been launched to develop high throughput functional genomics in wheat and barley. Transcriptomics, proteomics, and metabolomics analyses of traits of agronomic importance, such as quality, disease resistance, drought, and salt tolerance, are underway in both species. Combined with the development of physical maps, efficient gene isolation will be enabled and improved sequencing technologies and reduced sequencing costs will permit ultimately genome sequencing and access to the entire wheat and barley gene regulatory elements repertoire. Because rye is closely related to wheat and barley in Triticeae evolution, the latest developments in wheat and barley genomics will be of great use for developing rye genomics and for providing tools for rye improvement. Finally, a new model for temperate grasses has emerged in the past year with the development of the genetics and genomics (including a 8x whole genome shotgun sequencing project) of Brachypodium, a member of the Poeae family that is more closely related to the Triticeae than rice and can provide valuable information for supporting Triticeae genomics in the near future. These recent breakthroughs have yet to be reviewed in a single source of literature and current handbooks on wheat, barley, or rye are dedicated mainly to progress in genetics. In 'Genetics and Genomics of the Triticeae', we will aim to comprehensively review the recent progress in the development of structural and functional genomics tools in the Triticeae species and review the understanding of wheat, barley, and rye biology that has resulted from these new resources as well as to illuminate how this new found knowledge can be applied for the improvement of these essential species. The book will be the seventh volume in the ambitious series of books, Plant Genetics and Genomics (Richard A. Jorgensen, series editor) that will attempt to bring the field up-to-date on the genetics and genomics of important crop plants and genetic models. It is our hope that the publication will be a useful and timely tool for researchers and students alike working with the Triticeae.

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.

Autoren/Hrsg.

Feuillet, Catherine

Muehlbauer, Gary J.

Inhaltsverzeichnis

1;Foreword;6
2;Preface;9
3;Acknowledgments;11
4;Contents;12
5;Contributors;15
6;Part I: Genetics of the Triticeae;20
6.1;Scientific Names in the Triticeae;21
6.1.1;1.1 The Triticeae;21
6.1.2;1.2 Why so Many Names?;22
6.1.2.1;1.2.1 Impact of New Technologies on the Taxonomy of the Triticeae;23
6.1.2.2;1.2.2 Integrating New Information into the Taxonomy of the Triticeae;24
6.1.3;1.3 Interaction of Taxonomy and Nomenclature-Some Examples;25
6.1.3.1;1.3.1 Multiple Names at the Generic Level: Pseudoroegneria;25
6.1.3.2;1.3.2 Multiple Names at the Generic Level: Elymus;26
6.1.3.3;1.3.3 Additional Problems with Generic Changes;26
6.1.3.4;1.3.4 Multiple Names at the Species Level and Below: The Triticum monococcum Complex;27
6.1.4;1.4 Taxonomic Treatment in this Chapter;31
6.1.4.1;1.4.1 Taxonomic Treatment in this Chapter: The Genera;32
6.1.4.2;1.4.2 Taxonomic Treatment in this Chapter: The Species;40
6.1.5;1.5 Nomenclatural Web Sites;41
6.1.6;1.6 Appendix;42
6.1.7;References;44
6.2;Triticeae Genetic Resources in ex situ Genebank Collections;49
6.2.1;2.1 Introduction;49
6.2.2;2.2 Material and Methods;50
6.2.2.1;2.2.1 Information Sources: Online Databases and Reports;50
6.2.2.2;2.2.2 Information Extraction and Processing;51
6.2.2.3;2.2.3 Handling of Nomenclature;52
6.2.3;2.3 List of Cultivated and Useful Triticeae Species;53
6.2.3.1;2.3.1 Aegilops - Goat Grass;53
6.2.3.2;2.3.2 x Aegilotriticum;54
6.2.3.3;2.3.3 Agropyron - Wheatgrass;54
6.2.3.4;2.3.4 Amblyopyrum;55
6.2.3.5;2.3.5 Brachypodium - False Brome;55
6.2.3.6;2.3.6 Dasypyrum - Mosquitograss;55
6.2.3.7;2.3.7 Elymus - Wheatgrass, Wild Rye;55
6.2.3.8;2.3.8 Eremopyrum - False Wheatgrass;56
6.2.3.9;2.3.9 Heteranthelium;56
6.2.3.10;2.3.10 Hordeum - Barley;57
6.2.3.11;2.3.11 Kengyilia;57
6.2.3.12;2.3.12 Leymus - Wildrye;57
6.2.3.13;2.3.13 Pascopyrum - Wheatgrass;58
6.2.3.14;2.3.14 Psathyrostachys - Wildrye;58
6.2.3.15;2.3.15 Pseudoroegneria - Wheatgrass;59
6.2.3.16;2.3.16 Secale - Rye;59
6.2.3.17;2.3.17 Thinopyrum - Wheatgrass;60
6.2.3.18;2.3.18 x Triticosecale - Triticale;60
6.2.3.19;2.3.19 Triticum - Wheat;60
6.2.3.20;2.3.20 x Tritordeum;62
6.2.4;2.4 Overview of ex situ Collections of Triticeae;62
6.2.4.1;2.4.1 Overview by Countries and Institutions;62
6.2.4.2;2.4.2 Overviews by Genera and Species;64
6.2.4.3;2.4.3 Collections of Genetic Stocks and Mutants;64
6.2.4.4;2.4.4 Triticum;67
6.2.4.5;2.4.5 Hordeum;70
6.2.4.6;2.4.6 x Triticosecale;75
6.2.4.7;2.4.7 Aegilops;77
6.2.4.8;2.4.8 Secale;80
6.2.4.9;2.4.9 Elymus;82
6.2.4.10;2.4.10 Agropyron;84
6.2.4.11;2.4.11 Other Triticeae Species;85
6.2.4.12;2.4.12 Brachypodium;89
6.2.5;2.5 Outlook and Conclusions;90
6.2.6;2.6 Appendix: Online Databases;92
6.2.7;References;92
6.3;Domestication of the Triticeae in the Fertile Crescent;98
6.3.1;3.1 Origins of Cultivated Plants and Agriculture - A Brief Historical Overview;99
6.3.2;3.2 Evolution and Domestication of Triticeae;100
6.3.2.1;3.2.1 Wheat Evolution and Domestication;101
6.3.2.1.1;3.2.1.1 Diploid Wheats;102
6.3.2.1.2;3.2.1.2 Tetraploid Wheats;105
6.3.2.1.3;3.2.1.3 Hexaploid Wheats - Bread Wheat;106
6.3.2.2;3.2.2 Barley Evolution and Domestication;107
6.3.2.3;3.2.3 Rye Evolution and Domestication;109
6.3.3;3.3 Traits Modified by Domestication;111
6.3.3.1;3.3.1 Free-Threshing;111
6.3.3.2;3.3.2 Brittle-Rachis;115
6.3.3.3;3.3.3 Seed Size and Grain Yield;115
6.3.3.4;3.3.4 Kernel Rows in the Ear;116
6.3.3.5;3.3.5 Plant Height;116
6.3.3.6;3.3.6 Grain Hardness;117
6.3.3.7;3.3.7 Tillering;118
6.3.3.8;3.3.8 Reduced Seed Dormancy;119
6.3.3.9;3.3.9 Control of Flowering Time;119
6.3.3.10;3.3.10 Photoperiod;119
6.3.3.11;3.3.11 Vernalization;120
6.3.3.12;3.3.12 Heading Time;121
6.3.3.13;3.3.13 Conclusions and Final Considerations;121
6.3.4;References;122
6.4;Cytogenetic Analysis of Wheat and Rye Genomes;137
6.4.1;4.1 Introduction;137
6.4.2;4.2 The Five Phases of Formal Wheat Cytogenetics Research;138
6.4.3;4.3 Wheat Anchor Karyotype;140
6.4.4;4.4 Wheat Chromosome Differentiation;142
6.4.5;4.5 Rye Anchor Karyotype;144
6.4.6;4.6 Future Prospects;146
6.4.7;References;147
6.5;Applying Cytogenetics and Genomics to Wide Hybridisations in the Genus Hordeum;152
6.5.1;5.1 Introduction;152
6.5.2;5.2 Cytological Characterisation and Chromosome Nomenclature of Barley Chromosomes;153
6.5.3;5.3 Cytogenetics and Species Relationships;157
6.5.4;5.4 Physical Mapping of the Barley Genome;160
6.5.5;5.5 Generation of Haploid Barley Through Wide Hybridisation and Uniparental Chromosome Elimination;162
6.5.6;5.6 Practical Breeding Applications of Cytogenetics;164
6.5.7;References;170
6.6;Methods for Genetic Analysis in the Triticeae;178
6.6.1;6.1 Construction of High Quality Dense Genetic Maps;178
6.6.1.1;6.1.1 Multilocus Ordering;179
6.6.1.2;6.1.2 Map Verification Procedures;180
6.6.1.3;6.1.3 Complication due to ‘Pseudo-Linkage’ and Negative Interference;181
6.6.1.4;6.1.4 Increasing the Stability of Multilocus Maps;185
6.6.1.5;6.1.5 Building Consensus Maps;186
6.6.2;6.2 QTL Mapping;189
6.6.2.1;6.2.1 Multiple Trait Analysis;190
6.6.2.2;6.2.2 Paradoxical Consequences of Variance-Covariance Effect;193
6.6.2.3;6.2.3 Multiple Environments;196
6.6.3;6.3 High-Resolution Mapping Based on Selective DNA Pooling;204
6.6.3.1;6.3.1 Standard Selective DNA Pooling Approach to QTL Mapping;204
6.6.3.2;6.3.2 Linkage Analysis (RIL);206
6.6.3.3;6.3.3 Association Analysis;207
6.6.3.4;6.3.4 Simulations;208
6.6.3.5;6.3.5 Example of RIL Data Analysis by FPD;208
6.6.3.6;6.3.6 Example of Association Analysis by FPD;209
6.6.4;6.4 Final Comments;210
6.6.5;References;211
6.7;Genetic Mapping in the Triticeae;215
6.7.1;7.1 Introduction;216
6.7.2;7.2 Genetic Linkage Maps;217
6.7.2.1;7.2.1 Wheat Genetic Linkage Maps;222
6.7.2.2;7.2.2 Durum Genetic Linkage Maps;222
6.7.2.3;7.2.3 Barley Genetic Linkage Maps;222
6.7.2.4;7.2.4 Rye Genetic Linkage Maps;223
6.7.2.5;7.2.5 Triticale Genetic Linkage Maps;223
6.7.3;7.3 Physical Linkage Maps;224
6.7.4;7.4 Map Curation;225
6.7.5;7.5 Consensus Maps;227
6.7.6;7.6 QTL Mapping;231
6.7.6.1;7.6.1 Practical Considerations for QTL Mapping;231
6.7.7;7.7 High-Resolution Mapping;233
6.7.8;7.8 Future Directions;237
6.7.9;References;238
6.8;Early Stages of Meiosis in Wheat- and the Role of Ph1;250
6.8.1;8.1 The Introduction;250
6.8.2;8.2 Chromosome Sorting for Meiosis;251
6.8.3;8.3 Recombination- Factors Affecting its Distribution;252
6.8.4;8.4 Polyploids;253
6.8.5;8.5 Chromosome Pairing Loci;254
6.8.6;8.6 The Ph1 Locus;255
6.8.7;8.7 Exploitation of Chromosome Pairing Loci;261
6.8.8;References;262
7;Part 2: Tools, Resources and Approaches;266
7.1;A Toolbox for Triticeae Genomics;267
7.1.1;9.1 Introduction;267
7.1.2;9.2 Molecular Markers;268
7.1.2.1;9.2.1 Restriction Fragment Length Polymorphism (RFLP) Clones;268
7.1.2.2;9.2.2 Simple Sequence Repeat (SSR) Markers;270
7.1.2.3;9.2.3 Amplified Fragment Length Polymorphism (AFLP) Markers;272
7.1.2.4;9.2.4 Repeat-Based Markers;273
7.1.2.5;9.2.5 Diversity Array Technology (DArT) Markers;277
7.1.2.6;9.2.6 Single Nucleotide Polymorphism (SNP) Arrays;278
7.1.3;9.3 Expressed Sequence Tag (EST) Sequences and Microarrays;280
7.1.4;9.4 Bacterial Artificial Chromosome (BAC) Libraries;281
7.1.5;9.5 Outlook;284
7.1.6;References;285
7.2;Chromosome Genomics in the Triticeae;296
7.2.1;10.1 Introduction;296
7.2.2;10.2 Flow Cytogenetics;299
7.2.3;10.3 Applying Flow Cytogenetics to Triticeae Genomics;301
7.2.3.1;10.3.1 Hexaploid Wheat;302
7.2.3.2;10.3.2 Tetraploid Durum Wheat;305
7.2.3.3;10.3.3 Barley;306
7.2.3.4;10.3.4 Rye;308
7.2.3.5;10.3.5 A Toolkit for Triticeae Chromosome Sorting;310
7.2.4;10.4 Chromosome Genomics;312
7.2.4.1;10.4.1 Bacterial Artificial Chromosome (BAC) Libraries;312
7.2.4.2;10.4.2 BAC Contig Physical Maps and Positional Gene Cloning;313
7.2.4.3;10.4.3 Molecular Organization of Subgenomic Regions;316
7.2.4.4;10.4.4 Development of Molecular Markers;316
7.2.4.5;10.4.5 Physical and Genetic Mapping Using Flow-Sorted Chromosomes;318
7.2.4.6;10.4.6 Cytogenetic Mapping and Chromosome Structure;319
7.2.5;10.5 Conclusions;320
7.2.6;References;321
7.3;Physical Mapping in the Triticeae;328
7.3.1;11.1 Introduction;328
7.3.2;11.2 Generating a Physical Map - Basic Principles and Methods;329
7.3.2.1;11.2.1 Ordered-Marker Based Physical Mapping;329
7.3.2.1.1;11.2.1.1 Use of Cytogenetic Stocks and Chromosome-Microdissection;330
7.3.2.1.2;11.2.1.2 Fluorescence In Situ Hybridization (FISH);332
7.3.2.1.3;11.2.1.3 Radiation Hybrid Mapping (RH) - HAPPY Mapping;333
7.3.2.2;11.2.2 Ordered-Clone Based Physical Mapping;335
7.3.2.2.1;11.2.2.1 Chromosome Walking;338
7.3.2.3;11.2.3 Optical Mapping;338
7.3.3;11.3 Physical Maps of Triticeae Genomes;339
7.3.3.1;11.3.1 Physical Maps of Diploid Triticeae Genomes;340
7.3.3.1.1;11.3.1.1 Aegilops Tauschii;340
7.3.3.1.2;11.3.1.2 Barley (Hordeum vulgare);341
7.3.3.2;11.3.2 Physical Maps of Polyploid Triticeae Genomes;342
7.3.3.2.1;11.3.2.1 Bread wheat (Triticum aestivum);342
7.3.4;11.4 Conclusion;342
7.3.5;References;343
7.4;Map-Based Cloning of Genes in Triticeae (Wheat and Barley);347
7.4.1;12.1 Introduction;347
7.4.2;12.2 Genes Isolated from Wheat and Barley by Positional Cloning;348
7.4.3;12.3 Genetic Mapping;353
7.4.4;12.4 Physical Mapping for Map-Based Cloning;355
7.4.5;12.5 Application and Problems of Chromosome Walking in Triticeae;355
7.4.6;12.6 Problems Caused by Repetitive Elements;356
7.4.7;12.7 Aspects of Sequencing and Identification of Candidate Genes;357
7.4.8;12.8 The Use and Limits of Model Genomes for Marker Development and Map-Based Cloning in Triticeae;358
7.4.9;12.9 Validation of Candidate Genes;360
7.4.10;12.10 The Role of Bioinformatics in Map-Based Cloning;362
7.4.11;12.11 Outlook;363
7.4.12;References;364
7.5;Functional Validation in the Triticeae;368
7.5.1;13.1 Introduction;368
7.5.2;13.2 Targeted Induced Local Lesions in Genomes (TILLING);369
7.5.2.1;13.2.1 Mutagens and Mutation Frequency;369
7.5.2.2;13.2.2 Mutation Spectrum Analysis;371
7.5.2.3;13.2.3 Web-Based Computational Tools for TILLING;371
7.5.2.4;13.2.4 Populations for Reverse Genetics;372
7.5.2.5;13.2.5 Mutation Detection and Validation;373
7.5.2.6;13.2.6 Mutation Confirmation and Functional Validation;374
7.5.3;13.3 Transient Gene Validation Assays;375
7.5.3.1;13.3.1 Virus Induced Gene Silencing (VIGS);375
7.5.3.2;13.3.2 Biolistic Approaches;377
7.5.3.3;13.3.3 Antisense Oligodeoxynucleotide;378
7.5.4;13.4 Stable Genetic Transformation;380
7.5.4.1;13.4.1 Transfer of Recombinant DNA into Plant Cells;380
7.5.4.2;13.4.2 Patterns of DNA-Integration;382
7.5.4.3;13.4.3 The Design of Transformation Vectors;383
7.5.4.4;13.4.4 Insertional Mutagenesis;385
7.5.4.5;13.4.5 Linking Manipulated Gene Expression with Gene Function;385
7.5.5;13.5 Final Remarks;387
7.5.6;References;387
7.6;Genomics of Transposable Elements in the Triticeae;395
7.6.1;14.1 Introduction;396
7.6.2;14.2 Structural Genomics;398
7.6.3;14.3 Functional Genomics;403
7.6.3.1;14.3.1 Direct Effects;403
7.6.3.2;14.3.2 Effects on Genes, Sequence Chimeras, and Gene Regulation;406
7.6.4;14.4 Comparative Genomics;407
7.6.5;14.5 Exploitation as Molecular Markers;407
7.6.6;14.6 Conclusions;409
7.6.7;References;409
7.7;Gene and Repetitive Sequence Annotation in the Triticeae;414
7.7.1;15.1 Triticeae Genomics;415
7.7.2;15.2 Triticeae Genome Sequence and Annotation Data;416
7.7.2.1;15.2.1 The Triticeae Transcriptome;416
7.7.2.2;15.2.2 The Triticeae Genomes;417
7.7.2.3;15.2.3 Genome Annotation: Structural and Functional Annotation;418
7.7.2.4;15.2.4 Comparative Genome Annotation;420
7.7.3;15.3 Repetitive Sequences in the Triticeae;421
7.7.3.1;15.3.1 Methods for the Identification of Transposable Elements;421
7.7.3.2;15.3.2 Problems with Transposable Elements in Triticeae Sequencing;423
7.7.3.3;15.3.3 Software for Repeat Recognition and Isolation;425
7.7.3.4;15.3.4 The Challenge of the Large Number: Quality in Quantity is Needed;426
7.7.4;References;427
7.8;Brachypodium distachyon, a New Model for the Triticeae;433
7.8.1;16.1 Model Systems in Biology;433
7.8.2;16.2 Introduction to Brachypodium distachyon;434
7.8.2.1;16.2.1 Genome Size and Polyploidy;436
7.8.2.2;16.2.2 Relationship to Other Grasses;437
7.8.3;16.3 Brachypodium as An Experimental System;437
7.8.3.1;16.3.1 Growth Requirements and Flowering Triggers;438
7.8.3.2;16.3.2 Germplasm Resources and Natural Diversity;440
7.8.3.3;16.3.3 Chemical and Radiation Mutagenesis;441
7.8.3.4;16.3.4 Transformation and T-DNA Tagging;441
7.8.3.5;16.3.5 Related Species;444
7.8.4;16.4 Genomic Resources;445
7.8.4.1;16.4.1 ESTs;445
7.8.4.2;16.4.2 BAC Library Resources;446
7.8.4.3;16.4.3 Physical and Genetic Maps;447
7.8.4.4;16.4.4 Whole Genome Sequencing;448
7.8.4.5;16.4.5 Bioinformatic Resources;448
7.8.5;16.5 Applications of Brachypodium as a Model for Grass Research;448
7.8.5.1;16.5.1 Brachypodium as Structural Model for Wheat and Barley Genomics;449
7.8.5.2;16.5.2 Brachypodium as a Functional Model;450
7.8.6;16.6 Future Prospects and Directions;452
7.8.7;References;453
7.9;Comparative Genomics in the Triticeae;456
7.9.1;17.1 Introduction;456
7.9.2;17.2 Comparative Genomics at the Genome Scale: Macrocolinearity;458
7.9.2.1;17.2.1 Marker Based Macrocolinearity Studies;459
7.9.2.2;17.2.2 Sequence Based Macrocolinearity Studies;460
7.9.3;17.3 Comparative Genomics at the ‘‘Locus-Based’’ Level: Microcolinearity;463
7.9.3.1;17.3.1 Interspecific Comparative Studies: Looking at 50-70 MY of Speciation;463
7.9.3.2;17.3.2 Intraspecific Comparisons: Microcolinearity Studies Within Few MY of Speciation;465
7.9.3.3;17.3.3 Intravarietal Comparisons: Microcolinearity Studies Within Few 10,000 Years of Speciation;467
7.9.4;17.4 Duplications in the Triticeae Genomes;469
7.9.5;17.5 Comparative Genomics as Tool for Gene Discovery and Marker Development;472
7.9.5.1;17.5.1 Colinearity-Based Gene Cloning in Triticeae;472
7.9.5.2;17.5.2 Comparative Genomics Supports Gene Annotation and Marker Development;474
7.9.6;17.6 Summary and Outlook;475
7.9.7;References;476
8;Part III: Genetics and Genomics of Triticeae Biology;483
8.1;Genomics of Tolerance to Abiotic Stress in the Triticeae;484
8.1.1;18.1 Introduction;484
8.1.2;18.2 Searching QTLs and Genes for Tolerance to Abiotic Stress;485
8.1.2.1;18.2.1 Candidate Gene Approach;515
8.1.2.2;18.2.2 Exploiting the ‘‘-omics’’ Platforms;516
8.1.3;18.3 QTLs and Genes for Tolerance to Abiotic Stress;518
8.1.3.1;18.3.1 Tolerance to Drought;519
8.1.3.1.1;18.3.1.1 Barley;520
8.1.3.1.2;18.3.1.2 Wheat;522
8.1.3.2;18.3.2 Tolerance to Salinity;524
8.1.3.3;18.3.3 Tolerance to Low Nutrients;525
8.1.3.3.1;18.3.3.1 Nitrogen;526
8.1.3.3.2;18.3.3.2 Phosphorus;528
8.1.3.4;18.3.4 Tolerance to Aluminium Toxicity;529
8.1.3.5;18.3.5 Tolerance to Boron Toxicity;531
8.1.3.6;18.3.6 Tolerance to Zinc and Manganese Deficiency;532
8.1.3.7;18.3.7 Tolerance to Waterlogging;533
8.1.3.8;18.3.8 Tolerance to Low Temperature;534
8.1.3.9;18.3.9 Tolerance to High Temperature;536
8.1.4;18.4 Genomics of Genotype x Environment Interaction Under Conditions of Abiotic Stress;537
8.1.5;18.5 Prospects of Genomics-Assisted Improvement of Tolerance to Abiotic Stress;538
8.1.6;References;540
8.2;Genomics of Biotic Interactions in the Triticeae;562
8.2.1;19.1 Disease Epidemics and Current Threats;562
8.2.1.1;19.1.1 Plant Defenses Employed in Response to Biotic Stress;563
8.2.1.2;19.1.2 Integrative Genomics Holds the Keys to Durable Resistance;564
8.2.2;19.2 The Toolbox for Investigating Biotic Interactions;565
8.2.2.1;19.2.1 Molecule Profiling Approaches;565
8.2.2.2;19.2.2 Integration of Phenotypic, Genetic and Physical-Map Data;566
8.2.2.3;19.2.3 High-Throughput Functional Analysis;568
8.2.3;19.3 Triticeae-Fungal ‘‘Host’’ Interactions;572
8.2.4;19.4 Triticeae-Fungal ‘‘Nonhost’’ Interactions;574
8.2.5;19.5 Triticeae Interactions with Insects, Viruses, Worms and Bacteria;576
8.2.6;19.6 Pathogen Genomics;577
8.2.6.1;19.6.1 Fusarium graminearum (Fusarium Head Blight);577
8.2.6.2;19.6.2 Puccinia graminis (Stem Rust);578
8.2.6.3;19.6.3 Mycosphaerella graminicola (Septoria Tritici Blotch);579
8.2.6.4;19.6.4 Stagonospora nodorum (Stagonospora Nodorum Blotch);580
8.2.6.5;19.6.5 Blumeria graminis (Powdery Mildew);580
8.2.6.6;19.6.6 Barley Yellow Dwarf Virus (BYDV);581
8.2.7;19.7 Synthesis;582
8.2.8;References;583
8.3;Developmental and Reproductive Traits in the Triticeae;593
8.3.1;20.1 Introduction;593
8.3.2;20.2 Gene Catalogues;596
8.3.3;20.3 Identifying Flowering Time Genes in the Triticeae;597
8.3.3.1;20.3.1 The Candidate Gene Method;597
8.3.3.2;20.3.2 The Positional Cloning Method;598
8.3.3.3;20.3.3 The Positional Cloning/Candidate Gene Hybrid Method;599
8.3.4;20.4 Identifying Inflorescence Development Genes in the Triticeae;601
8.3.4.1;20.4.1 The Candidate Gene Method;601
8.3.4.2;20.4.2 The Positional Cloning Method;601
8.3.5;20.5 Understanding Gene Function;602
8.3.5.1;20.5.1 The Analysis of Genetic Pathways;602
8.3.5.2;20.5.2 Validation of Candidate Flowering Genes;604
8.3.6;20.6 Advances in Triticeae Genomics and Gene Identification;605
8.3.7;20.7 Using Flowering and Inflorescence Genes in Triticeae Breeding;607
8.3.8;References;607
8.4;Genomics of Quality Traits;612
8.4.1;21.1 Introduction;612
8.4.2;21.2 Genomics of Barley Quality;613
8.4.2.1;21.2.1 Human Food;613
8.4.2.2;21.2.2 Malting and Brewing;615
8.4.2.2.1;21.2.2.1 beta-amylase;616
8.4.2.3;21.2.3 QTL associated with malting quality;617
8.4.2.4;21.2.4 Germination as a Key Variable in Barley Quality;620
8.4.3;21.3 Genomics of Wheat Quality;622
8.4.3.1;21.3.1 The Wheat Flour Proteins;623
8.4.3.1.1;21.3.1.1 High Molecular Weight Glutenin Subunits (HMWGS);626
8.4.3.1.2;21.3.1.2 Low Molecular Weight Glutenin Subunits (LMWGS);627
8.4.3.2;21.3.2 Seed Storage Protein Gene Structure and Variation;628
8.4.3.2.1;21.3.2.1 Assaying Variation in Seed Storage Proteins;630
8.4.3.3;21.3.3 Flour Color;631
8.4.3.3.1;21.3.3.1 The Yellowness of Flour and Its End Products;632
8.4.3.3.2;21.3.3.2 The Finely Divided Bran Specks in Flour;632
8.4.3.4;21.3.4 Flour Paste Viscosity;634
8.4.4;21.4 Grain Hardness and Carbohydrates in Wheat and Barley;634
8.4.4.1;21.4.1 Starch Content;634
8.4.4.2;21.4.2 Starch Composition;635
8.4.4.3;21.4.3 Non-Starch Polysaccharides;636
8.4.4.4;21.4.4 Grain Hardness;636
8.4.5;21.5 Traits that Are Not Analysed at the Genomic Level to Date;637
8.4.5.1;21.5.1 Milling Yield;637
8.4.5.2;21.5.2 Water Absorption;638
8.4.5.3;21.5.3 Grain Protein Content;638
8.4.6;21.6 Impact of New Technologies;639
8.4.7;21.7 Conclusions;640
8.4.8;References;641
9;Part IV: Early Messages;654
9.1;Linkage Disequilibrium and Association Mapping in the Triticeae;655
9.1.1;22.1 Introduction;655
9.1.2;22.2 Linkage Disequilibrium;656
9.1.2.1;22.2.1 Measurement and Interpretation of Linkage Disequilibrium;656
9.1.2.2;22.2.2 LD Estimates for the Triticeae;658
9.1.3;22.3 Association Analysis;662
9.1.3.1;22.3.1 Population Structure;662
9.1.3.2;22.3.2 Association Mapping Strategies;663
9.1.3.3;22.3.3 Association Mapping in the Triticeae;665
9.1.3.4;22.3.4 Germplasm Panels;667
9.1.3.5;22.3.5 Simulations;669
9.1.4;22.4 Future Needs and Directions;671
9.1.4.1;22.4.1 Fine-Mapping;671
9.1.4.2;22.4.2 Breeding Applications;672
9.1.4.3;22.4.3 Association Breeding;673
9.1.4.4;22.4.4 Marker Assisted Recurrent Selection;676
9.1.4.5;22.4.5 Genomic Selection;677
9.1.5;References;677
9.2;Triticeae Genome Structure and Evolution;684
9.2.1;23.1 Structure of Triticeae Genomes;684
9.2.1.1;23.1.1 Genome Size;684
9.2.1.2;23.1.2 Overall Structure;685
9.2.1.3;23.1.3 Tandem Repeated Sequences;686
9.2.1.3.1;23.1.3.1 Centromeric Regions;687
9.2.1.3.2;23.1.3.2 Telomeric Region;689
9.2.1.3.3;23.1.3.3 Interstitial Sites;691
9.2.1.3.4;23.1.3.4 rRNA Genes;692
9.2.1.4;23.1.4 Interspersed Repeated Sequences;694
9.2.2;23.2 Genome Evolution;695
9.2.2.1;23.2.1 TEs and Triticeae Genome Evolution;695
9.2.2.2;23.2.2 Gene Order Paradox;696
9.2.2.3;23.2.3 Conservative and Dynamic Strata of Triticeae Genomes;697
9.2.2.4;23.2.4 Recombination and Gene Content Evolution Along the Centromere-Telomere Axis of Triticeae Chromosomes;698
9.2.2.4.1;23.2.4.1 Variation in Gene Density Along Chromosomes;699
9.2.2.4.2;23.2.4.2 The Cause of Correlation Between Gene Density and Recombination Rate;700
9.2.2.5;23.2.5 The Evolutionary Significance of Repeated DNA;701
9.2.3;23.3 Conclusions;702
9.2.4;References;702
9.3;Wheat and Barley Genome Sequencing;711
9.3.1;24.1 Introduction;711
9.3.2;24.2 History of Sequencing in Higher Plants;714
9.3.2.1;24.2.1 The First Plant Genome Model - Arabidopsis thaliana;718
9.3.2.2;24.2.2 The First Economically Important Plant Genome - Rice;718
9.3.2.3;24.2.3 The First Tree Genome - Poplar Genome Sequence;720
9.3.2.4;24.2.4 Two Grapevine Sequences;721
9.3.2.5;24.2.5 The First Moderately-Sized Plant Genome Sequence - Maize;721
9.3.2.6;24.2.6 Other Plant Genome Projects;722
9.3.3;24.3 Current Status of Triticeae Genome Sequencing;723
9.3.3.1;24.3.1 EST Sequencing;723
9.3.3.2;24.3.2 GSS;724
9.3.3.3;24.3.3 Contiguous Genomic DNA Sequences;725
9.3.4;24.4 Next Generation Sequencing (NGS) Technologies;726
9.3.4.1;24.4.1 Roche-454 GSFLX;727
9.3.4.2;24.4.2 Illumina Genome Analyzer;728
9.3.4.3;24.4.3 Applied Biosystems SOLiD (Sequencing by Oligo Ligation and Detection);728
9.3.4.4;24.4.4 HeliScope, Helicos;729
9.3.4.5;24.4.5 Impact on Triticeae Genome Sequencing;729
9.3.5;24.5 The Future of Triticeae Genome Sequencing;731
9.3.6;24.6 Outlook;733
9.3.7;References;734
10;Index;741