Applications of Genetic and Genomic Research in Cereals (Woodhead Publishing Series in Food Science, Technology and Nutrition)

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