| Contributors | p. XVI |
| Abbreviations | p. XXI |
| Rice | p. 1 |
| Introduction | p. 1 |
| Taxonomy and Origin of Cultivated Rice | p. 1 |
| Dispersal of Cultivated Rice | p. 2 |
| Varietal Diversity of Rice | p. 3 |
| Rice Varietal Improvement | p. 4 |
| Rice-Breeding Challenges in the 21st Century | p. 5 |
| Construction of Molecular Linkage Maps in Rice | p. 6 |
| Molecular Mapping of Simple and Complex Traits in Rice | p. 16 |
| Disease Resistance | p. 17 |
| Insect Resistance | p. 20 |
| Traits Relevant for Hybrid Rice Breeding | p. 22 |
| Grain Quality | p. 26 |
| Abiotic Stress Tolerance | p. 27 |
| Important Agronomic Traits | p. 37 |
| QTL X Environment Interaction | p. 44 |
| Utilization of Wild Species for Mapping and Introgression of Agronomic Traits | p. 45 |
| Molecular Characterization of Rice Germplasm | p. 45 |
| Progress in Marker-Assisted Breeding | p. 46 |
| MAS for Disease Resistance | p. 47 |
| MAS for Insect Resistance | p. 47 |
| MAS for Grain Quality | p. 50 |
| MAS in Hybrid Rice Breeding | p. 50 |
| Gene Pyramiding | p. 51 |
| MAS for Other Traits and QTL | p. 51 |
| MAS for Introgression of Alien Genes | p. 52 |
| Map-Based Cloning of Rice Genes and QTL | p. 52 |
| Advanced Works | p. 55 |
| Rice Physical Maps | p. 55 |
| Tools for Rice Functional Genomics | p. 56 |
| DNA Microarray | p. 56 |
| Insertional Mutagenesis | p. 57 |
| Future Scope of Work | p. 58 |
| References | p. 60 |
| Wheat | p. 79 |
| Introduction | p. 79 |
| Molecular Markers - Types and Availability | p. 80 |
| Construction of Molecular Maps | p. 80 |
| Genetic Maps | p. 81 |
| Transcript Genetic Maps or Functional Maps | p. 84 |
| Physical Maps | p. 84 |
| Application of Molecular Markers in Wheat Genetics and Breeding | p. 87 |
| Gene Tagging and QTL Analysis for MAS | p. 87 |
| Map-Based Cloning (MBC) of Genes in Wheat | p. 97 |
| Allelic Diversity | p. 99 |
| Comparative Mapping and Synteny | p. 108 |
| Impact of Genomics Research on Wheat Genetics and Breeding | p. 109 |
| Transcriptomics and Functional Genomics | p. 110 |
| Comparative Genomics and Bioinformatics | p. 111 |
| Novel Approaches | p. 112 |
| Concluding Remarks | p. 114 |
| References | p. 114 |
| Maize | p. 135 |
| Introduction | p. 135 |
| Brief History of the Crop | p. 135 |
| Botanical Description | p. 135 |
| Economic Importance | p. 135 |
| Breeding Objectives | p. 136 |
| Classical Mapping Efforts | p. 137 |
| Classical Breeding Achievements | p. 137 |
| Limitations of Classical Endeavors and Utility of Molecular Mapping | p. 137 |
| Construction of Genetic Maps | p. 137 |
| Brief History of Mapping Efforts | p. 137 |
| First-Generation Maps | p. 138 |
| Second-Generation Maps | p. 139 |
| Gene Mapping | p. 140 |
| Quantitative Trait Loci (QTL) Analysis | p. 142 |
| Marker-Assisted Breeding | p. 144 |
| Map-Based Cloning | p. 144 |
| Future Scope of Works | p. 145 |
| Maize Genome Sequencing | p. 145 |
| Next-Generation Marker Development: SNP | p. 145 |
| Map-Based Cloning Using Information of Sorghum and Rice Genome Sequences | p. 146 |
| References | p. 146 |
| Barley | p. 155 |
| Introduction | p. 155 |
| Genus Hordeum | p. 155 |
| Taxonomic Position of Barley | p. 155 |
| Gene Pools of Barley | p. 155 |
| The Wild Progenitor of Barley | p. 156 |
| Domestication of Barley | p. 157 |
| Important Traits for Domestication | p. 159 |
| Migration and History of Barley Cultivation | p. 161 |
| Construction of Genetic Maps | p. 162 |
| Gene Mapping | p. 167 |
| Resistance Genes | p. 170 |
| Genes Related to Abiotic Stresses | p. 177 |
| Traits Important for Domestication | p. 177 |
| Analysis of Quantitative Trait Loci | p. 178 |
| Marker-Assisted Breeding | p. 195 |
| Map-Based Cloning of Resistance Genes in Barley | p. 196 |
| mlo and Ror Genes | p. 196 |
| Mla and Rar Genes | p. 197 |
| Rpg Genes | p. 198 |
| Future Scope of Works | p. 198 |
| References | p. 199 |
| Oat | p. 211 |
| Introduction | p. 211 |
| Brief History and Biology of Oat | p. 211 |
| Oat Grain Composition, Other Grain Quality Factors, and Agronomic Traits and Their Relation to Breeding Objectives | p. 212 |
| Limitations of Conventional Genetics and Breeding Approaches and the Utility of Molecular Mapping | p. 214 |
| Development of Molecular Linkage Maps in Oat | p. 215 |
| Mapping in Diploid Oats | p. 215 |
| Hexaploid Mapping: Kanota x Ogle | p. 217 |
| Other Hexaploid Oat Maps | p. 218 |
| Comparative and Integrative Mapping | p. 219 |
| Integration of Genetic and Chromosomal Maps | p. 219 |
| Gene Mapping | p. 220 |
| Gene mapping in Segregating Populations | p. 220 |
| Gene Tagging | p. 226 |
| DNA Sequence-Based Mapping | p. 226 |
| QTLs in Oat | p. 228 |
| Detection of QTLs | p. 228 |
| Integrative and Comparative QTL Investigations | p. 228 |
| Marker-Assisted Breeding | p. 229 |
| PCR-Based Markers | p. 232 |
| Pc68 and Pc94 Case Studies | p. 232 |
| Advances Toward MAS for Other Traits | p. 234 |
| Future Scope and Related Oat Genomic Research | p. 235 |
| References | p. 237 |
| Secale | p. 243 |
| Introduction | p. 243 |
| Morphology | p. 243 |
| Cytology | p. 243 |
| Origin of Cultivated Rye | p. 243 |
| Distribution of the Genus Secale | p. 244 |
| Classification of the Genus Secale | p. 245 |
| Phylogenetic Relationships Among Secale Species Utilizing AFLP Analysis | p. 247 |
| Molecular Taxonomy of Secale | p. 248 |
| Distinction Among Annual Species | p. 248 |
| Distinction Among Perennial Species | p. 248 |
| Genetic Diversity Among Cultivated Rye Genotypes | p. 249 |
| Utilization of Molecular Markers in Rye Systematics | p. 249 |
| A Review of Linkage Mapping in Rye | p. 250 |
| Mapping Population and Linkage Maps | p. 250 |
| Markers | p. 252 |
| Mapping Programs | p. 253 |
| Segregation Distortion | p. 253 |
| References | p. 253 |
| Sorghum | p. 257 |
| Introduction | p. 257 |
| Center of Origin | p. 257 |
| Domestication | p. 257 |
| Taxonomic Position | p. 258 |
| Brief Morphology | p. 259 |
| Cytogenetic Structure | p. 260 |
| Economic Importance | p. 260 |
| Breeding Objectives | p. 264 |
| Classical Breeding Achievements | p. 265 |
| Limitations of Classical Endeavors and Utility of Molecular Mapping | p. 265 |
| Construction of Genetic Maps | p. 267 |
| First-Generation Genetic Maps | p. 267 |
| Integrated Genetic Maps | p. 267 |
| Comparative Mapping | p. 269 |
| Gene Mapping | p. 286 |
| Detection of Quantitative Trait Loci (QTL) | p. 287 |
| Marker-Assisted Breeding | p. 290 |
| Marker Conversions | p. 290 |
| Marker-Assisted Selection | p. 291 |
| Physical Mapping in Sorghum | p. 291 |
| Structural Genomics | p. 293 |
| Functional Genomics | p. 294 |
| Development of ESTs | p. 295 |
| Gene Function Analysis | p. 295 |
| Future Prospects | p. 297 |
| References | p. 297 |
| Pearl Millet | p. 303 |
| Introduction | p. 303 |
| Brief History | p. 303 |
| Botanical Description | p. 303 |
| Economic Importance | p. 304 |
| Breeding Objectives and Achievements | p. 304 |
| Classical Mapping Efforts | p. 305 |
| Classical vs. Molecular Maps in Pearl Millet | p. 306 |
| Construction of Genetic Maps | p. 306 |
| Brief History of Mapping Efforts | p. 306 |
| First-Generation Genetic Maps | p. 307 |
| Comparative Genetic Mapping in Pearl Millet | p. 315 |
| Quantitative-Trait Loci (QTL) Analyses | p. 315 |
| Domestication Syndrome | p. 315 |
| Drought Tolerance | p. 316 |
| Downy Mildew Resistance | p. 317 |
| Mendelization of QTLs | p. 317 |
| Marker-Assisted Breeding | p. 317 |
| Map-Based Cloning | p. 318 |
| Future Scope of Work | p. 319 |
| References | p. 319 |
| Foxtail Millet | p. 325 |
| Introduction | p. 325 |
| Setaria Complex | p. 325 |
| Molecular Maps of Foxtail Millet | p. 327 |
| Mapping Genetic Factors Underlying Plant Architecture | p. 327 |
| Conclusion and Perspectives | p. 330 |
| References | p. 332 |
| Finger Millet | p. 333 |
| Introduction | p. 333 |
| Brief History of the Crop | p. 333 |
| Botanical Descriptions | p. 333 |
| Economic Importance | p. 335 |
| Breeding Objectives | p. 335 |
| Classical Breeding Achievements | p. 336 |
| Genetic Mapping in Finger Millet | p. 337 |
| Brief History of Mapping Efforts | p. 337 |
| First-Generation Genetic Maps | p. 337 |
| Comparative Genetic Maps | p. 338 |
| Future Scope of Work | p. 339 |
| References | p. 342 |
| Subject Index | p. 345 |
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