Genetics and Genomics of the Triticeae

Foreword

Preface

Acknowledgments

Contents

Contributors

Part I: Genetics of the Triticeae

Scientific Names in the Triticeae

1.1 The Triticeae

1.2 Why so Many Names?

1.2.1 Impact of New Technologies on the Taxonomy of the Triticeae

1.2.2 Integrating New Information into the Taxonomy of the Triticeae

1.3 Interaction of Taxonomy and Nomenclature-Some Examples

1.3.1 Multiple Names at the Generic Level: Pseudoroegneria

1.3.2 Multiple Names at the Generic Level: Elymus

1.3.3 Additional Problems with Generic Changes

1.3.4 Multiple Names at the Species Level and Below: The Triticum monococcum Complex

1.4 Taxonomic Treatment in this Chapter

1.4.1 Taxonomic Treatment in this Chapter: The Genera

1.4.2 Taxonomic Treatment in this Chapter: The Species

1.5 Nomenclatural Web Sites

1.6 Appendix

References

Triticeae Genetic Resources in ex situ Genebank Collections

2.1 Introduction

2.2 Material and Methods

2.2.1 Information Sources: Online Databases and Reports

2.2.2 Information Extraction and Processing

2.2.3 Handling of Nomenclature

2.3 List of Cultivated and Useful Triticeae Species

2.3.1 Aegilops - Goat Grass

2.3.2 x Aegilotriticum

2.3.3 Agropyron - Wheatgrass

2.3.4 Amblyopyrum

2.3.5 Brachypodium - False Brome

2.3.6 Dasypyrum - Mosquitograss

2.3.7 Elymus - Wheatgrass, Wild Rye

2.3.8 Eremopyrum - False Wheatgrass

2.3.9 Heteranthelium

2.3.10 Hordeum - Barley

2.3.11 Kengyilia

2.3.12 Leymus - Wildrye

2.3.13 Pascopyrum - Wheatgrass

2.3.14 Psathyrostachys - Wildrye

2.3.15 Pseudoroegneria - Wheatgrass

2.3.16 Secale - Rye

2.3.17 Thinopyrum - Wheatgrass

2.3.18 x Triticosecale - Triticale

2.3.19 Triticum - Wheat

2.3.20 x Tritordeum

2.4 Overview of ex situ Collections of Triticeae

2.4.1 Overview by Countries and Institutions

2.4.2 Overviews by Genera and Species

2.4.3 Collections of Genetic Stocks and Mutants

2.4.4 Triticum

2.4.5 Hordeum

2.4.6 x Triticosecale

2.4.7 Aegilops

2.4.8 Secale

2.4.9 Elymus

2.4.10 Agropyron

2.4.11 Other Triticeae Species

2.4.12 Brachypodium

2.5 Outlook and Conclusions

2.6 Appendix: Online Databases

References

Domestication of the Triticeae in the Fertile Crescent

3.1 Origins of Cultivated Plants and Agriculture - A Brief Historical Overview

3.2 Evolution and Domestication of Triticeae

3.2.1 Wheat Evolution and Domestication

3.2.1.1 Diploid Wheats

3.2.1.2 Tetraploid Wheats

3.2.1.3 Hexaploid Wheats - Bread Wheat

3.2.2 Barley Evolution and Domestication

3.2.3 Rye Evolution and Domestication

3.3 Traits Modified by Domestication

3.3.1 Free-Threshing

3.3.2 Brittle-Rachis

3.3.3 Seed Size and Grain Yield

3.3.4 Kernel Rows in the Ear

3.3.5 Plant Height

3.3.6 Grain Hardness

3.3.7 Tillering

3.3.8 Reduced Seed Dormancy

3.3.9 Control of Flowering Time

3.3.10 Photoperiod

3.3.11 Vernalization

3.3.12 Heading Time

3.3.13 Conclusions and Final Considerations

References

Cytogenetic Analysis of Wheat and Rye Genomes

4.1 Introduction

4.2 The Five Phases of Formal Wheat Cytogenetics Research

4.3 Wheat Anchor Karyotype

4.4 Wheat Chromosome Differentiation

4.5 Rye Anchor Karyotype

4.6 Future Prospects

References

Applying Cytogenetics and Genomics to Wide Hybridisations in the Genus Hordeum

5.1 Introduction

5.2 Cytological Characterisation and Chromosome Nomenclature of Barley Chromosomes

5.3 Cytogenetics and Species Relationships

5.4 Physical Mapping of the Barley Genome

5.5 Generation of Haploid Barley Through Wide Hybridisation and Uniparental Chromosome Elimination

5.6 Practical Breeding Applications of Cytogenetics

References

Methods for Genetic Analysis in the Triticeae

6.1 Construction of High Quality Dense Genetic Maps

6.1.1 Multilocus Ordering

6.1.2 Map Verification Procedures

6.1.3 Complication due to ‘Pseudo-Linkage’ and Negative Interference

6.1.4 Increasing the Stability of Multilocus Maps

6.1.5 Building Consensus Maps

6.2 QTL Mapping

6.2.1 Multiple Trait Analysis

6.2.2 Paradoxical Consequences of Variance-Covariance Effect

6.2.3 Multiple Environments

6.3 High-Resolution Mapping Based on Selective DNA Pooling

6.3.1 Standard Selective DNA Pooling Approach to QTL Mapping

6.3.2 Linkage Analysis (RIL)

6.3.3 Association Analysis

6.3.4 Simulations

6.3.5 Example of RIL Data Analysis by FPD

6.3.6 Example of Association Analysis by FPD

6.4 Final Comments

References

Genetic Mapping in the Triticeae

7.1 Introduction

7.2 Genetic Linkage Maps

7.2.1 Wheat Genetic Linkage Maps

7.2.2 Durum Genetic Linkage Maps

7.2.3 Barley Genetic Linkage Maps

7.2.4 Rye Genetic Linkage Maps

7.2.5 Triticale Genetic Linkage Maps

7.3 Physical Linkage Maps

7.4 Map Curation

7.5 Consensus Maps

7.6 QTL Mapping

7.6.1 Practical Considerations for QTL Mapping

7.7 High-Resolution Mapping

7.8 Future Directions

References

Early Stages of Meiosis in Wheat- and the Role of Ph1

8.1 The Introduction

8.2 Chromosome Sorting for Meiosis

8.3 Recombination- Factors Affecting its Distribution

8.4 Polyploids

8.5 Chromosome Pairing Loci

8.6 The Ph1 Locus

8.7 Exploitation of Chromosome Pairing Loci

References

Part 2: Tools, Resources and Approaches

A Toolbox for Triticeae Genomics

9.1 Introduction

9.2 Molecular Markers

9.2.1 Restriction Fragment Length Polymorphism (RFLP) Clones

9.2.2 Simple Sequence Repeat (SSR) Markers

9.2.3 Amplified Fragment Length Polymorphism (AFLP) Markers

9.2.4 Repeat-Based Markers

9.2.5 Diversity Array Technology (DArT) Markers

9.2.6 Single Nucleotide Polymorphism (SNP) Arrays

9.3 Expressed Sequence Tag (EST) Sequences and Microarrays

9.4 Bacterial Artificial Chromosome (BAC) Libraries

9.5 Outlook

References

Chromosome Genomics in the Triticeae

10.1 Introduction

10.2 Flow Cytogenetics

10.3 Applying Flow Cytogenetics to Triticeae Genomics

10.3.1 Hexaploid Wheat

10.3.2 Tetraploid Durum Wheat

10.3.3 Barley

10.3.4 Rye

10.3.5 A Toolkit for Triticeae Chromosome Sorting

10.4 Chromosome Genomics

10.4.1 Bacterial Artificial Chromosome (BAC) Libraries

10.4.2 BAC Contig Physical Maps and Positional Gene Cloning

10.4.3 Molecular Organization of Subgenomic Regions

10.4.4 Development of Molecular Markers

10.4.5 Physical and Genetic Mapping Using Flow-Sorted Chromosomes

10.4.6 Cytogenetic Mapping and Chromosome Structure

10.5 Conclusions

References

Physical Mapping in the Triticeae

11.1 Introduction

11.2 Generating a Physical Map - Basic Principles and Methods

11.2.1 Ordered-Marker Based Physical Mapping

11.2.1.1 Use of Cytogenetic Stocks and Chromosome-Microdissection

11.2.1.2 Fluorescence In Situ Hybridization (FISH)

11.2.1.3 Radiation Hybrid Mapping (RH) - HAPPY Mapping

11.2.2 Ordered-Clone Based Physical Mapping

11.2.2.1 Chromosome Walking

11.2.3 Optical Mapping

11.3 Physical Maps of Triticeae Genomes

11.3.1 Physical Maps of Diploid Triticeae Genomes

11.3.1.1 Aegilops Tauschii

11.3.1.2 Barley (Hordeum vulgare)

11.3.2 Physical Maps of Polyploid Triticeae Genomes

11.3.2.1 Bread wheat (Triticum aestivum)

11.4 Conclusion

References

Map-Based Cloning of Genes in Triticeae (Wheat and Barley)

12.1 Introduction

12.2 Genes Isolated from Wheat and Barley by Positional Cloning

12.3 Genetic Mapping

12.4 Physical Mapping for Map-Based Cloning

12.5 Application and Problems of Chromosome Walking in Triticeae

12.6 Problems Caused by Repetitive Elements

12.7 Aspects of Sequencing and Identification of Candidate Genes

12.8 The Use and Limits of Model Genomes for Marker Development and Map-Based Cloning in Triticeae

12.9 Validation of Candidate Genes

12.10 The Role of Bioinformatics in Map-Based Cloning

12.11 Outlook

References

Functional Validation in the Triticeae

13.1 Introduction

13.2 Targeted Induced Local Lesions in Genomes (TILLING)

13.2.1 Mutagens and Mutation Frequency

13.2.2 Mutation Spectrum Analysis

13.2.3 Web-Based Computational Tools for TILLING

13.2.4 Populations for Reverse Genetics

13.2.5 Mutation Detection and Validation

13.2.6 Mutation Confirmation and Functional Validation

13.3 Transient Gene Validation Assays

13.3.1 Virus Induced Gene Silencing (VIGS)

13.3.2 Biolistic Approaches

13.3.3 Antisense Oligodeoxynucleotide

13.4 Stable Genetic Transformation

13.4.1 Transfer of Recombinant DNA into Plant Cells

13.4.2 Patterns of DNA-Integration

13.4.3 The Design of Transformation Vectors

13.4.4 Insertional Mutagenesis

13.4.5 Linking Manipulated Gene Expression with Gene Function

13.5 Final Remarks

References

Genomics of Transposable Elements in the Triticeae

14.1 Introduction

14.2 Structural Genomics

14.3 Functional Genomics

14.3.1 Direct Effects

14.3.2 Effects on Genes, Sequence Chimeras, and Gene Regulation

14.4 Comparative Genomics

14.5 Exploitation as Molecular Markers

14.6 Conclusions

References

Gene and Repetitive Sequence Annotation in the Triticeae

15.1 Triticeae Genomics

15.2 Triticeae Genome Sequence and Annotation Data

15.2.1 The Triticeae Transcriptome

15.2.2 The Triticeae Genomes

15.2.3 Genome Annotation: Structural and Functional Annotation

15.2.4 Comparative Genome Annotation

15.3 Repetitive Sequences in the Triticeae

15.3.1 Methods for the Identification of Transposable Elements

15.3.2 Problems with Transposable Elements in Triticeae Sequencing

15.3.3 Software for Repeat Recognition and Isolation

15.3.4 The Challenge of the Large Number: Quality in Quantity is Needed

References

Brachypodium distachyon, a New Model for the Triticeae

16.1 Model Systems in Biology

16.2 Introduction to Brachypodium distachyon

16.2.1 Genome Size and Polyploidy

16.2.2 Relationship to Other Grasses

16.3 Brachypodium as An Experimental System

16.3.1 Growth Requirements and Flowering Triggers

16.3.2 Germplasm Resources and Natural Diversity

16.3.3 Chemical and Radiation Mutagenesis

16.3.4 Transformation and T-DNA Tagging

16.3.5 Related Species

16.4 Genomic Resources

16.4.1 ESTs

16.4.2 BAC Library Resources

16.4.3 Physical and Genetic Maps

16.4.4 Whole Genome Sequencing

16.4.5 Bioinformatic Resources

16.5 Applications of Brachypodium as a Model for Grass Research

16.5.1 Brachypodium as Structural Model for Wheat and Barley Genomics

16.5.2 Brachypodium as a Functional Model

16.6 Future Prospects and Directions

References

Comparative Genomics in the Triticeae

17.1 Introduction

17.2 Comparative Genomics at the Genome Scale: Macrocolinearity

17.2.1 Marker Based Macrocolinearity Studies

17.2.2 Sequence Based Macrocolinearity Studies

17.3 Comparative Genomics at the ‘‘Locus-Based’’ Level: Microcolinearity

17.3.1 Interspecific Comparative Studies: Looking at 50-70 MY of Speciation

17.3.2 Intraspecific Comparisons: Microcolinearity Studies Within Few MY of Speciation

17.3.3 Intravarietal Comparisons: Microcolinearity Studies Within Few 10,000 Years of Speciation

17.4 Duplications in the Triticeae Genomes

17.5 Comparative Genomics as Tool for Gene Discovery and Marker Development

17.5.1 Colinearity-Based Gene Cloning in Triticeae

17.5.2 Comparative Genomics Supports Gene Annotation and Marker Development

17.6 Summary and Outlook

References

Part III: Genetics and Genomics of Triticeae Biology

Genomics of Tolerance to Abiotic Stress in the Triticeae

18.1 Introduction

18.2 Searching QTLs and Genes for Tolerance to Abiotic Stress

18.2.1 Candidate Gene Approach

18.2.2 Exploiting the ‘‘-omics’’ Platforms

18.3 QTLs and Genes for Tolerance to Abiotic Stress

18.3.1 Tolerance to Drought

18.3.1.1 Barley

18.3.1.2 Wheat

18.3.2 Tolerance to Salinity

18.3.3 Tolerance to Low Nutrients

18.3.3.1 Nitrogen

18.3.3.2 Phosphorus

18.3.4 Tolerance to Aluminium Toxicity

18.3.5 Tolerance to Boron Toxicity

18.3.6 Tolerance to Zinc and Manganese Deficiency

18.3.7 Tolerance to Waterlogging

18.3.8 Tolerance to Low Temperature

18.3.9 Tolerance to High Temperature

18.4 Genomics of Genotype x Environment Interaction Under Conditions of Abiotic Stress

18.5 Prospects of Genomics-Assisted Improvement of Tolerance to Abiotic Stress

References

Genomics of Biotic Interactions in the Triticeae

19.1 Disease Epidemics and Current Threats

19.1.1 Plant Defenses Employed in Response to Biotic Stress

19.1.2 Integrative Genomics Holds the Keys to Durable Resistance

19.2 The Toolbox for Investigating Biotic Interactions

19.2.1 Molecule Profiling Approaches

19.2.2 Integration of Phenotypic, Genetic and Physical-Map Data

19.2.3 High-Throughput Functional Analysis

19.3 Triticeae-Fungal ‘‘Host’’ Interactions

19.4 Triticeae-Fungal ‘‘Nonhost’’ Interactions

19.5 Triticeae Interactions with Insects, Viruses, Worms and Bacteria

19.6 Pathogen Genomics

19.6.1 Fusarium graminearum (Fusarium Head Blight)

19.6.2 Puccinia graminis (Stem Rust)

19.6.3 Mycosphaerella graminicola (Septoria Tritici Blotch)

19.6.4 Stagonospora nodorum (Stagonospora Nodorum Blotch)

19.6.5 Blumeria graminis (Powdery Mildew)

19.6.6 Barley Yellow Dwarf Virus (BYDV)

19.7 Synthesis

References

Developmental and Reproductive Traits in the Triticeae

20.1 Introduction

20.2 Gene Catalogues

20.3 Identifying Flowering Time Genes in the Triticeae

20.3.1 The Candidate Gene Method

20.3.2 The Positional Cloning Method

20.3.3 The Positional Cloning/Candidate Gene Hybrid Method

20.4 Identifying Inflorescence Development Genes in the Triticeae

20.4.1 The Candidate Gene Method

20.4.2 The Positional Cloning Method

20.5 Understanding Gene Function

20.5.1 The Analysis of Genetic Pathways

20.5.2 Validation of Candidate Flowering Genes

20.6 Advances in Triticeae Genomics and Gene Identification

20.7 Using Flowering and Inflorescence Genes in Triticeae Breeding

References

Genomics of Quality Traits

21.1 Introduction

21.2 Genomics of Barley Quality

21.2.1 Human Food

21.2.2 Malting and Brewing

21.2.2.1 beta-amylase

21.2.3 QTL associated with malting quality

21.2.4 Germination as a Key Variable in Barley Quality

21.3 Genomics of Wheat Quality

21.3.1 The Wheat Flour Proteins

21.3.1.1 High Molecular Weight Glutenin Subunits (HMWGS)

21.3.1.2 Low Molecular Weight Glutenin Subunits (LMWGS)

21.3.2 Seed Storage Protein Gene Structure and Variation

21.3.2.1 Assaying Variation in Seed Storage Proteins

21.3.3 Flour Color

21.3.3.1 The Yellowness of Flour and Its End Products

21.3.3.2 The Finely Divided Bran Specks in Flour

21.3.4 Flour Paste Viscosity

21.4 Grain Hardness and Carbohydrates in Wheat and Barley

21.4.1 Starch Content

21.4.2 Starch Composition

21.4.3 Non-Starch Polysaccharides

21.4.4 Grain Hardness

21.5 Traits that Are Not Analysed at the Genomic Level to Date

21.5.1 Milling Yield

21.5.2 Water Absorption

21.5.3 Grain Protein Content

21.6 Impact of New Technologies

21.7 Conclusions

References

Part IV: Early Messages

Linkage Disequilibrium and Association Mapping in the Triticeae

22.1 Introduction

22.2 Linkage Disequilibrium

22.2.1 Measurement and Interpretation of Linkage Disequilibrium

22.2.2 LD Estimates for the Triticeae

22.3 Association Analysis

22.3.1 Population Structure

22.3.2 Association Mapping Strategies

22.3.3 Association Mapping in the Triticeae

22.3.4 Germplasm Panels

22.3.5 Simulations

22.4 Future Needs and Directions

22.4.1 Fine-Mapping

22.4.2 Breeding Applications

22.4.3 Association Breeding

22.4.4 Marker Assisted Recurrent Selection

22.4.5 Genomic Selection

References

Triticeae Genome Structure and Evolution

23.1 Structure of Triticeae Genomes

23.1.1 Genome Size

23.1.2 Overall Structure

23.1.3 Tandem Repeated Sequences

23.1.3.1 Centromeric Regions

23.1.3.2 Telomeric Region

23.1.3.3 Interstitial Sites

23.1.3.4 rRNA Genes

23.1.4 Interspersed Repeated Sequences

23.2 Genome Evolution

23.2.1 TEs and Triticeae Genome Evolution

23.2.2 Gene Order Paradox

23.2.3 Conservative and Dynamic Strata of Triticeae Genomes

23.2.4 Recombination and Gene Content Evolution Along the Centromere-Telomere Axis of Triticeae Chromosomes

23.2.4.1 Variation in Gene Density Along Chromosomes

23.2.4.2 The Cause of Correlation Between Gene Density and Recombination Rate

23.2.5 The Evolutionary Significance of Repeated DNA

23.3 Conclusions

References

Wheat and Barley Genome Sequencing

24.1 Introduction

24.2 History of Sequencing in Higher Plants

24.2.1 The First Plant Genome Model - Arabidopsis thaliana

24.2.2 The First Economically Important Plant Genome - Rice

24.2.3 The First Tree Genome - Poplar Genome Sequence

24.2.4 Two Grapevine Sequences

24.2.5 The First Moderately-Sized Plant Genome Sequence - Maize

24.2.6 Other Plant Genome Projects

24.3 Current Status of Triticeae Genome Sequencing

24.3.1 EST Sequencing

24.3.2 GSS

24.3.3 Contiguous Genomic DNA Sequences

24.4 Next Generation Sequencing (NGS) Technologies

24.4.1 Roche-454 GSFLX

24.4.2 Illumina Genome Analyzer

24.4.3 Applied Biosystems SOLiD (Sequencing by Oligo Ligation and Detection)

24.4.4 HeliScope, Helicos

24.4.5 Impact on Triticeae Genome Sequencing

24.5 The Future of Triticeae Genome Sequencing

24.6 Outlook

References

Index