Table Of ContentAPPLICATIONS
OF GENETIC
AND GENOMIC
RESEARCH
IN CEREALS
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Woodhead Publishing
Series in Food Science,
Technology and Nutrition
APPLICATIONS
OF GENETIC
AND GENOMIC
RESEARCH
IN CEREALS
Edited by
Thomas Miedaner
State Plant Breeding Institute, University of Hohenheim,
Stuttgart, Germany
Viktor Korzun
Global Lead Scientific Affairs, KWS SAAT SE,
Einbeck, Germany
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CONTENTS
Contributors xi
In Commemoration xv
Editorial: Genetics Became to be Genomics xvii
Section 1 Techniques 1
1. High-Throughput Genotyping for Cereal
Research and Breeding 3
Martin W. Ganal, Jörg Plieske, Anja Hohmeyer, Andreas Polley,
Marion S. Röder
1.1 Introduction 3
1.2 SNP Markers 4
1.3 Genotyping-by-Sequencing (GBS) 6
1.4 Array-Based Genotyping 7
1.5 High-Throughput Individual SNP Marker Genotyping 13
1.6 Summary and Outlook 14
References 15
2. Progress in Sequencing of Triticeae Genomes
and Future Uses 19
M. Timothy Rabanus-Wallace, Nils Stein
2.1 Introduction 19
2.2 Triticeae Genome Assemblies 24
2.3 Current and Future Directions 40
References 43
3. Next-Generation Sequencing Enabled Genetics
in Hexaploid Wheat 49
Laura-Jayne Gardiner, Ryan Joynson, Anthony Hall
3.1 Forward Genetics 50
3.2 Population Genetics 56
3.3 Reverse Genetics 58
3.4 Hidden Variation 59
References 60
v
vi Contents
4. Rapid Gene Cloning in Wheat 65
M. Asyraf Md. Hatta, Burkhard Steuernagel, Brande B.H. Wulff
4.1 Map-Based Cloning of Genes in Triticeae 65
4.2 Gene Cloning Using Whole-Genome Sequencing in Plants 66
4.3 Mutational Genomics: Cloning Genes by Sequence Comparison
of Multiple Mutant Alleles 70
4.4 Genome Complexity in Triticeae 73
4.5 Whole Genome Assembly of Wheat 73
4.6 Gene Cloning Using Genome Complexity Reduction 77
4.7 The Poor Agronomy of Wild Relatives of Wheat and Barley 82
References 85
5. High-Efficiency Transformation Techniques 97
Yuji Ishida, Yukoh Hiei, Toshihiko Komari
5.1 Introduction 97
5.2 Transformation Methods in Cereals 98
5.3 Wheat 99
5.4 Barley 104
5.5 Other Small Grain Cereals 107
5.6 Future Tasks in Transformation of Small Grain Cereals 109
5.7 Conclusion 113
Acknowledgments 113
References 115
6. Site-Directed Genome Modification in Triticeae Cereals
Mediated by Cas Endonucleases 121
Jochen Kumlehn
6.1 Introduction 121
6.2 Functionality of RNA-Guided Cas Endonucleases and Principles
of Their Utilization 122
6.3 Use of Cas Endonucleases to Validate Gene Function and to
Improve Plant Performance 124
6.4 Further Progress in Technology Development 125
6.5 Off-Target Mutations 127
6.6 Perspective 127
References 131
Contents vii
Section 2 Traits 135
7. Marker-Based Harnessing of Genetic Diversity to
Improve Resistance of Barley to Fungal and Viral Diseases 137
Dragan Perovic, Doris Kopahnke, Antje Habekuss, Frank Ordon,
Albrecht Serfling
7.1 Introduction 137
7.2 Marker Development for Major Resistance Genes in Barley 143
7.3 Recent Developments in Marker Technologies and Their Application 144
7.4 Gene Isolation and Detection of Natural Variation 147
7.5 Conclusions 150
References 151
8. Gene-Based Approaches to Durable Disease Resistance
in Triticeae Cereals 165
Patrick Schweizer
8.1 Background 165
8.2 Gene-Based Approaches 166
8.3 Conclusions 176
References 177
9. Global Journeys of Adaptive Wheat Genes 183
Miguel Sanchez-Garcia, Alison R. Bentley
9.1 Introduction 183
9.2 Plant Height 185
9.3 Flowering Time 189
9.4 Future Outlook 194
Acknowledgments 195
References 195
Further Reading 200
10. Durum Wheat as a Bridge Between Wild Emmer Wheat
Genetic Resources and Bread Wheat 201
Valentina Klymiuk, Andrii Fatiukha, Lin Huang, Zhen-zhen Wei,
Tamar Kis-Papo, Yehoshua Saranga, Tamar Krugman, Tzion Fahima
10.1 Introduction 201
10.2 Obstacles for Gene Transfer Between Tetraploid and Hexaploid Wheat 204
viii Contents
10.3 Changes in Recombination Rates After Crosses With Wheat Wild Relatives 205
10.4 Wild Emmer Wheat Gene Pool 206
10.5 Transferring of High Grain Protein Content QTLs From Wild
Emmer 208
10.6 Improvement of Resistance to Stripe Rust Using Wild
Emmer Genes 214
10.7 Utilization of Wild Emmer Powdery Mildew Resistance Gene Pool 216
10.8 Introgression of FHB Quantitative Resistance QTLs Originating
From Wild Emmer Wheat 218
10.9 Improvement of Drought Resistance Using QTLs From Wild Emmer 219
10.10 Alternative Ways for Transferring of Useful Genes From Durum Into
Bread Wheat 220
10.11 Advantages of Using Durum for Bridging Crosses 221
10.12 Modern Genomic Tools That Can Accelerate the Concept
of Bridge-Crosses 222
Acknowledgments 224
References 225
Section 3 Breeding 231
11. Modern Field Phenotyping Opens New Avenues for Selection 233
Tobias Würschum
11.1 Phenotyping Platforms for Plant Breeding 234
11.2 Sensors for Precision Phenotyping 238
11.3 The Concept of Sensor Fusion 240
11.4 Data Storage and Analysis 242
11.5 Traits Assessed by Sensors 243
11.6 A Possible Future of Precision Phenotyping in the Field 246
References 247
12. Application of Genetic and Genomic Tools in Wheat
for Developing Countries 251
Susanne Dreisigacker, Deepmala Sehgal, Ravi P. Singh,
Carolina Sansaloni, Hans-Joachim Braun
12.1 Introduction 251
12.2 Key Breeding Priorities for Wheat Improvement in Developing Countries 252
12.3 Application of Genetic and Genomic Tools in the CIMMYT
Wheat Breeding Pipeline 255
12.4 Gene Discovery and Genomic Prediction 256
12.5 Deployment of Genomics-Assisted Breeding Strategies 259
12.6 Exploring Genetic Resources 262
12.7 Tracking Crop Varieties 265
Contents ix
12.8 Wheat Case Study 266
12.9 Evidence From Other Crops 267
References 268
13. Genomic Selection in Wheat 273
Daniel W. Sweeney, Jin Sun, Ella Taagen, Mark E. Sorrells
13.1 Introduction 273
13.2 High-Throughput Phenotyping 277
13.3 Genotype by Environment Interaction 279
13.4 Genomic Selection for Wheat Disease Resistance 287
13.5 Genomic Selection in Wheat for Nutritional Traits 291
13.6 Genomic Selection for Wheat Quality Traits 292
13.7 Future Prospects 295
13.8 Conclusion 296
References 297
Further Reading 301
14. “SpeedGS” to Accelerate Genetic Gain in Spring Wheat 303
Kai P. Voss-Fels, Eva Herzog, Susanne Dreisigacker, Sivakumar Sukumaran,
Amy Watson, Matthias Frisch, Ben Hayes, Lee T. Hickey
14.1 Introduction 303
14.2 Accelerating Genetic Gain Using Modern Breeding Tools 305
14.3 Integrating Rapid Generation Advancement and Genomic Selection 309
14.4 Speeding Up Genetic Gain Through SpeedGS—A Simulation 310
14.5 Exploiting Genetic Resources Using Speed Breeding 314
14.6 Future Opportunities and Challenges 317
14.7 Simulation Materials and Methods 319
References 323
15. Genomics-Based Hybrid Rye Breeding 329
Thomas Miedaner, Viktor Korzun, Eva Bauer
15.1 Introduction 329
15.2 Hybrid-Enabling Technologies 331
15.3 Genomic Resources in Rye 333
15.4 Marker-Based Introgression Libraries for Using PGRs 336
15.5 QTL Mapping of Quantitative Traits 337
15.6 Genome-Wide Prediction and Genomic Selection (GS) 340
15.7 Conclusion 343
References 344
Index 349
