Applications of genetic and genomic research in cereals

Front Cover......Page 1
Applications of Genetic and Genomic Research in Cereals......Page 4
Copyright......Page 5
Contents......Page 6
Contributors......Page 12
In Commemoration......Page 16
Editorial: Genetics Became to be Genomics......Page 18
 References......Page 22
 Further Reading......Page 23
Section 1: Techniques......Page 24
  1.1  Introduction......Page 26
  1.2  SNP Markers......Page 27
  1.3  Genotyping-by-Sequencing (GBS)......Page 29
  1.4  Array-Based Genotyping......Page 30
   1.4.2  Wheat......Page 32
   1.4.3  Rye/Triticale......Page 35
  1.5  High-Throughput Individual SNP Marker Genotyping......Page 36
  1.6  Summary and Outlook......Page 37
  References......Page 38
  2.1  Introduction......Page 42
   2.1.1  The Assembly of Complex Plant Genomes......Page 43
   2.1.2  Triticeae Genome Sequencing and Genomic Resources......Page 45
   2.2.1  Barley and Close Relatives......Page 47
   2.2.2  Bread Wheat and Close Relatives......Page 58
  2.3  Current and Future Directions......Page 63
   2.3.1  A streamlined Workflow......Page 64
   2.3.2  Assembly Applications: Unlocking Diversity......Page 65
  References......Page 66
 Chapter 3 Next-Generation Sequencing Enabled Genetics in Hexaploid Wheat......Page 72
  3.1  Forward Genetics......Page 73
   3.1.1  Mapping-by-Sequencing......Page 74
   3.2.1  Genome-Wide Association Studies......Page 79
   3.2.2  Exome Capture......Page 80
  3.3  Reverse Genetics......Page 81
   3.4.1  Epigenetic Variation......Page 82
  References......Page 83
  4.1  Map-Based Cloning of Genes in Triticeae......Page 88
  4.2  Gene Cloning Using Whole-Genome Sequencing in Plants......Page 89
  4.3  Mutational Genomics: Cloning Genes by Sequence Comparison of Multiple Mutant Alleles......Page 93
  4.5  Whole Genome Assembly of Wheat......Page 96
   4.6.1  Exome Capture......Page 100
   4.6.2  RNA-Seq......Page 103
   4.6.3  Chromosome Flow Sorting......Page 104
  4.7  The Poor Agronomy of Wild Relatives of Wheat and Barley......Page 105
   4.7.1  Future Perspectives......Page 106
  References......Page 108
  5.1  Introduction......Page 120
  5.2  Transformation Methods in Cereals......Page 121
  5.3  Wheat......Page 122
   5.3.2  Tissue Culture......Page 124
   5.3.3  Selection Markers......Page 125
   5.3.5  Genotype of Wheat......Page 126
  5.4  Barley......Page 127
   5.4.1  Barley Tissues and Culture Techniques......Page 128
   5.4.2  Selection Markers......Page 129
   5.5.1  Oat......Page 130
   5.5.3  Triticale......Page 131
   5.6.1  Means to Overcome Genotype Differences......Page 132
   5.6.2  Gene Editing......Page 134
   5.6.3  Development of Useful Traits and Commercialization of Biotechnology Crops......Page 135
  Acknowledgments......Page 136
  References......Page 138
  6.1  Introduction......Page 144
  6.2  Functionality of RNA-Guided Cas Endonucleases and Principles of Their Utilization......Page 145
  6.3  Use of Cas Endonucleases to Validate Gene Function and to Improve Plant Performance......Page 147
  6.4  Further Progress in Technology Development......Page 148
  6.6  Perspective......Page 150
  References......Page 154
Section 2: Traits......Page 158
  7.1  Introduction......Page 160
  7.2  Marker Development for Major Resistance Genes in Barley......Page 166
  Markers and Marker techniques......Page 167
  7.4  Gene Isolation and Detection of Natural Variation......Page 170
   7.4.1  From QTL Mapping Toward Identification of Candidate Genes......Page 171
   7.4.2  Isolation of Major Resistance Genes in Barley......Page 172
  7.5  Conclusions......Page 173
  References......Page 174
  8.1  Background......Page 188
    8.2.1.1  Gene or Allele Introgression by Backcrossing......Page 189
    8.2.1.3 Gene Editing......Page 191
    8.2.2.1 Race-Nonspecific Resistance Genes......Page 192
    8.2.2.2 Stacked Defense-Related or Resistance Genes......Page 194
    8.2.2.3 Susceptibility Factors......Page 195
   8.2.3  Engineered Nonhost Resistance......Page 197
    8.2.3.2 Nonhost-Like Resilience to Defense Suppression......Page 198
  8.3  Conclusions......Page 199
  References......Page 200
  9.1  Introduction......Page 206
   9.2.1  First Dwarfing Genes ( Rht-8c, Rht-B1b, and Rht-D1b)......Page 208
   9.2.2  Pleiotropic Effects......Page 210
   9.2.3  Alternative Dwarfing Genes......Page 211
   9.3.1  Vernalization......Page 212
   9.3.2  Photoperiod......Page 214
   9.3.3   Earliness per se (Eps) and Pleiotropic Effects......Page 216
  9.4  Future Outlook......Page 217
  References......Page 218
  Further Reading......Page 223
  10.1  Introduction......Page 224
  10.2  Obstacles for Gene Transfer Between Tetraploid and Hexaploid Wheat......Page 227
  10.3  Changes in Recombination Rates After Crosses With Wheat Wild Relatives......Page 228
  10.4  Wild Emmer Wheat Gene Pool......Page 229
  10.5  Transferring of High Grain Protein Content QTLs From Wild Emmer......Page 231
  10.6  Improvement of Resistance to Stripe Rust Using Wild Emmer Genes......Page 237
  10.7  Utilization of Wild Emmer Powdery Mildew Resistance Gene Pool......Page 239
  10.8  Introgression of FHB Quantitative Resistance QTLs Originating From Wild Emmer Wheat......Page 241
  10.9  Improvement of Drought Resistance Using QTLs From Wild Emmer......Page 242
  10.10  Alternative Ways for Transferring of Useful Genes From Durum Into Bread Wheat......Page 243
  10.11  Advantages of Using Durum for Bridging Crosses......Page 244
  10.12  Modern Genomic Tools That Can Accelerate the Concept of Bridge-Crosses......Page 245
  Acknowledgments......Page 247
  References......Page 248
Section 3: Breeding......Page 254
 Chapter 11 Modern Field Phenotyping Opens New Avenues for Selection......Page 256
  11.1  Phenotyping Platforms for Plant Breeding......Page 257
  11.2  Sensors for Precision Phenotyping......Page 261
  11.3  The Concept of Sensor Fusion......Page 263
  11.4  Data Storage and Analysis......Page 265
  11.5  Traits Assessed by Sensors......Page 266
  11.6  A Possible Future of Precision Phenotyping in the Field......Page 269
  References......Page 270
  12.1  Introduction......Page 274
  12.2  Key Breeding Priorities for Wheat Improvement in Developing Countries......Page 275
  12.3  Application of Genetic and Genomic Tools in the CIMMYT Wheat Breeding Pipeline......Page 278
   12.4.1  Progress in Genetic Mapping and Cloning of Disease Resistance Genes......Page 279
   12.4.2  Genome-Wide Association Analyses for Biotic and Abiotic Stress Resistance/Tolerance and Quality Traits......Page 280
   12.4.4  Progress in Genomic Prediction......Page 281
  12.5  Deployment of Genomics-Assisted Breeding Strategies......Page 282
  12.6  Exploring Genetic Resources......Page 285
  12.7  Tracking Crop Varieties......Page 288
  12.8  Wheat Case Study......Page 289
  12.9  Evidence From Other Crops......Page 290
  References......Page 291
  13.1  Introduction......Page 296
   13.2.1  High-Throughput Phenotyping Platforms......Page 300
   13.2.2  Application of High-Throughput Phenotyping in GS......Page 301
  13.3  Genotype by Environment Interaction......Page 302
   13.3.1  Use of Environmental Covariates in Prediction Models......Page 306
   13.3.2  Accounting for and Exploiting Epistasis......Page 309
  13.4  Genomic Selection for Wheat Disease Resistance......Page 310
   13.4.1  Wheat Rusts......Page 311
   13.4.2  Fusarium Head Blight......Page 312
   13.4.3  Other Wheat Diseases......Page 313
  13.5  Genomic Selection in Wheat for Nutritional Traits......Page 314
   13.6.1  Milling and Flour Quality......Page 315
   13.6.2  Preharvest Sprouting......Page 317
  13.7  Future Prospects......Page 318
  13.8  Conclusion......Page 319
  References......Page 320
  Further Reading......Page 324
  14.1  Introduction......Page 326
  14.2  Accelerating Genetic Gain Using Modern Breeding Tools......Page 328
  14.3  Integrating Rapid Generation Advancement and Genomic Selection......Page 332
  14.4  Speeding Up Genetic Gain Through SpeedGS—A Simulation......Page 333
  14.5  Exploiting Genetic Resources Using Speed Breeding......Page 337
  14.6  Future Opportunities and Challenges......Page 340
   14.7.4  Genetic Architecture of Traits......Page 342
   14.7.6  Assignment of Genetic Effects to Marker Loci......Page 343
   14.7.7  Phenotypes......Page 344
   14.7.9  Number and Duration of Breeding Cycles......Page 345
  References......Page 346
  15.1  Introduction......Page 352
  15.2  Hybrid-Enabling Technologies......Page 354
  15.3  Genomic Resources in Rye......Page 356
  15.4  Marker-Based Introgression Libraries for Using PGR s......Page 359
  15.5  QTL Mapping of Quantitative Traits......Page 360
  15.6  Genome-Wide Prediction and Genomic Selection (GS)......Page 363
  15.7  Conclusion......Page 366
  References......Page 367
Index......Page 372
Back Cover......Page 382