Robert J. Henry is Professor of Innovation in Agriculture at the University of Queensland and Director of the Queensland Alliance for Agriculture and Food Innovation.

• Contributors ixPreface xiii1 Evolution of DNA Marker Technology in Plants 3Robert J. HenryIntroduction 4Early Marker Technologies 4Evolving Range of Applications of DNA Markers in Plants 12Applications 13Future Developments 15References 152 Whole-Genome Sequencing for Marker Discovery 21Mark EdwardsSequencing Strategies 22Sequencing Technologies 23Epigenetic Markers 31Genome-Wide Selection 32Data Analysis Resources 32References 33Color plate section located between pages 34 and 35.3 Amplicon Sequencing for Marker Discovery 35Timothy R. Sexton and Frances M. ShapterIntroduction 36Background 36Maximizing Efficiency Through Sample Pooling 38Limitations of Amplicon-Based MPS 44Bioinformatics 51Concluding Remarks 52Acknowledgments 52References 534 Transcriptome Sequencing for Marker Discovery 57Susan GilliesIntroduction 58Basic Approach 58Conclusions 64References 645 Molecular Markers in Plant Improvement 67Peter J. Prentis, Edward K. Gilding, Ana Pavasovic, Celine H. Frere, and Ian D. GodwinIntroduction 68Plant Domestication and Traditional Breeding 68Application of Molecular Markers to Breeding 70Next-Generation Approaches to QTL Discovery 75Conclusion 77References 786 Applications of Molecular Markers in Plant Conservation 81Maurizio Rossetto and Paul D. RymerIntroduction 82Traditional Approaches 86The Way Forward 91Conclusion 95References 967 Molecular Markers for Plant Biosecurity 99Andrew D.W. GeeringIntroduction 100The Present—PCR for Specific Diagnosis and for DNA Barcoding 101The Future—Next-Generation Sequencing Methods to Revolutionize Plant Quarantine Diagnostics 105Conclusions 110Acknowledgments 111References 1118 Molecular Markers for Harnessing Heterosis 119Gopala S. Krishnan, A.K. Singh, Daniel L.E.Waters, and Robert J. HenryIntroduction 120Molecular Markers for Understanding the GeneticBasis of Heterosis 122Molecular Diversity and Heterosis—Molecular Markers for Predicting Heterosis 123Conclusion 131References 1329 Genetic Variant Discovery and Its Use in Genome Characterization of Agronomically Important Crop Species 137Stephane Deschamps and Matthew A. CampbellIntroduction 138Sanger Resequencing 140Single Feature Polymorphisms 140Next-Generation Sequencing 143High-Density Genotyping using the Illumina Golden Gate Platform 153Genotyping by Sequencing 155Genome Characterization and Haplotypes 157Conclusions and Perspectives 159References 16010 Future Prospects of Molecular Markers in Plants 169Reyazul R. Mir and Rajeev K. VarshneyIntroduction 170Molecular Markers: The Past 172Molecular Markers: The Present 173Molecular Markers: The Future 175Novel Approaches or Platforms for Plant Breeding 180Conclusions 183Acknowledgments 184References 184Index 191

Robert J. Henry is Professor of Innovation in Agriculture at the University of Queensland and Director of the Queensland Alliance for Agriculture and Food Innovation.

• Contributors ixPreface xiii1 Evolution of DNA Marker Technology in Plants 3Robert J. HenryIntroduction 4Early Marker Technologies 4Evolving Range of Applications of DNA Markers in Plants 12Applications 13Future Developments 15References 152 Whole-Genome Sequencing for Marker Discovery 21Mark EdwardsSequencing Strategies 22Sequencing Technologies 23Epigenetic Markers 31Genome-Wide Selection 32Data Analysis Resources 32References 33Color plate section located between pages 34 and 35.3 Amplicon Sequencing for Marker Discovery 35Timothy R. Sexton and Frances M. ShapterIntroduction 36Background 36Maximizing Efficiency Through Sample Pooling 38Limitations of Amplicon-Based MPS 44Bioinformatics 51Concluding Remarks 52Acknowledgments 52References 534 Transcriptome Sequencing for Marker Discovery 57Susan GilliesIntroduction 58Basic Approach 58Conclusions 64References 645 Molecular Markers in Plant Improvement 67Peter J. Prentis, Edward K. Gilding, Ana Pavasovic, Celine H. Frere, and Ian D. GodwinIntroduction 68Plant Domestication and Traditional Breeding 68Application of Molecular Markers to Breeding 70Next-Generation Approaches to QTL Discovery 75Conclusion 77References 786 Applications of Molecular Markers in Plant Conservation 81Maurizio Rossetto and Paul D. RymerIntroduction 82Traditional Approaches 86The Way Forward 91Conclusion 95References 967 Molecular Markers for Plant Biosecurity 99Andrew D.W. GeeringIntroduction 100The Present—PCR for Specific Diagnosis and for DNA Barcoding 101The Future—Next-Generation Sequencing Methods to Revolutionize Plant Quarantine Diagnostics 105Conclusions 110Acknowledgments 111References 1118 Molecular Markers for Harnessing Heterosis 119Gopala S. Krishnan, A.K. Singh, Daniel L.E.Waters, and Robert J. HenryIntroduction 120Molecular Markers for Understanding the GeneticBasis of Heterosis 122Molecular Diversity and Heterosis—Molecular Markers for Predicting Heterosis 123Conclusion 131References 1329 Genetic Variant Discovery and Its Use in Genome Characterization of Agronomically Important Crop Species 137Stephane Deschamps and Matthew A. CampbellIntroduction 138Sanger Resequencing 140Single Feature Polymorphisms 140Next-Generation Sequencing 143High-Density Genotyping using the Illumina Golden Gate Platform 153Genotyping by Sequencing 155Genome Characterization and Haplotypes 157Conclusions and Perspectives 159References 16010 Future Prospects of Molecular Markers in Plants 169Reyazul R. Mir and Rajeev K. VarshneyIntroduction 170Molecular Markers: The Past 172Molecular Markers: The Present 173Molecular Markers: The Future 175Novel Approaches or Platforms for Plant Breeding 180Conclusions 183Acknowledgments 184References 184Index 191

Robert J. Henry is Professor of Innovation in Agriculture at the University of Queensland and Director of the Queensland Alliance for Agriculture and Food Innovation.

• Contributors ixPreface xiii1 Evolution of DNA Marker Technology in Plants 3Robert J. HenryIntroduction 4Early Marker Technologies 4Evolving Range of Applications of DNA Markers in Plants 12Applications 13Future Developments 15References 152 Whole-Genome Sequencing for Marker Discovery 21Mark EdwardsSequencing Strategies 22Sequencing Technologies 23Epigenetic Markers 31Genome-Wide Selection 32Data Analysis Resources 32References 33Color plate section located between pages 34 and 35.3 Amplicon Sequencing for Marker Discovery 35Timothy R. Sexton and Frances M. ShapterIntroduction 36Background 36Maximizing Efficiency Through Sample Pooling 38Limitations of Amplicon-Based MPS 44Bioinformatics 51Concluding Remarks 52Acknowledgments 52References 534 Transcriptome Sequencing for Marker Discovery 57Susan GilliesIntroduction 58Basic Approach 58Conclusions 64References 645 Molecular Markers in Plant Improvement 67Peter J. Prentis, Edward K. Gilding, Ana Pavasovic, Celine H. Frere, and Ian D. GodwinIntroduction 68Plant Domestication and Traditional Breeding 68Application of Molecular Markers to Breeding 70Next-Generation Approaches to QTL Discovery 75Conclusion 77References 786 Applications of Molecular Markers in Plant Conservation 81Maurizio Rossetto and Paul D. RymerIntroduction 82Traditional Approaches 86The Way Forward 91Conclusion 95References 967 Molecular Markers for Plant Biosecurity 99Andrew D.W. GeeringIntroduction 100The Present—PCR for Specific Diagnosis and for DNA Barcoding 101The Future—Next-Generation Sequencing Methods to Revolutionize Plant Quarantine Diagnostics 105Conclusions 110Acknowledgments 111References 1118 Molecular Markers for Harnessing Heterosis 119Gopala S. Krishnan, A.K. Singh, Daniel L.E.Waters, and Robert J. HenryIntroduction 120Molecular Markers for Understanding the GeneticBasis of Heterosis 122Molecular Diversity and Heterosis—Molecular Markers for Predicting Heterosis 123Conclusion 131References 1329 Genetic Variant Discovery and Its Use in Genome Characterization of Agronomically Important Crop Species 137Stephane Deschamps and Matthew A. CampbellIntroduction 138Sanger Resequencing 140Single Feature Polymorphisms 140Next-Generation Sequencing 143High-Density Genotyping using the Illumina Golden Gate Platform 153Genotyping by Sequencing 155Genome Characterization and Haplotypes 157Conclusions and Perspectives 159References 16010 Future Prospects of Molecular Markers in Plants 169Reyazul R. Mir and Rajeev K. VarshneyIntroduction 170Molecular Markers: The Past 172Molecular Markers: The Present 173Molecular Markers: The Future 175Novel Approaches or Platforms for Plant Breeding 180Conclusions 183Acknowledgments 184References 184Index 191