Robert J. Henry 
Molecular Markers in Plants [PDF ebook] 

Contributors ix
Preface xiii
1 Evolution of DNA Marker Technology in Plants 3
Robert J. Henry
Introduction 4
Early Marker Technologies 4
Evolving Range of Applications of DNA Markers in Plants 12
Applications 13
Future Developments 15
References 15
2 Whole-Genome Sequencing for Marker Discovery 21
Mark Edwards
Sequencing Strategies 22
Sequencing Technologies 23
Epigenetic Markers 31
Genome-Wide Selection 32
Data Analysis Resources 32
References 33
Color plate section located between pages 34 and 35.
3 Amplicon Sequencing for Marker Discovery 35
Timothy R. Sexton and Frances M. Shapter
Introduction 36
Background 36
Maximizing Efficiency Through Sample Pooling 38
Limitations of Amplicon-Based MPS 44
Bioinformatics 51
Concluding Remarks 52
Acknowledgments 52
References 53
4 Transcriptome Sequencing for Marker Discovery 57
Susan Gillies
Introduction 58
Basic Approach 58
Conclusions 64
References 64
5 Molecular Markers in Plant Improvement 67
Peter J. Prentis, Edward K. Gilding, Ana Pavasovic, Celine H. Frere, and Ian D. Godwin
Introduction 68
Plant Domestication and Traditional Breeding 68
Application of Molecular Markers to Breeding 70
Next-Generation Approaches to QTL Discovery 75
Conclusion 77
References 78
6 Applications of Molecular Markers in Plant Conservation 81
Maurizio Rossetto and Paul D. Rymer
Introduction 82
Traditional Approaches 86
The Way Forward 91
Conclusion 95
References 96
7 Molecular Markers for Plant Biosecurity 99
Andrew D.W. Geering
Introduction 100
The Present–PCR for Specific Diagnosis and for DNA Barcoding 101
The Future–Next-Generation Sequencing Methods to Revolutionize Plant Quarantine Diagnostics 105
Conclusions 110
Acknowledgments 111
References 111
8 Molecular Markers for Harnessing Heterosis 119
Gopala S. Krishnan, A.K. Singh, Daniel L.E.Waters, and Robert J. Henry
Introduction 120
Molecular Markers for Understanding the Genetic
Basis of Heterosis 122
Molecular Diversity and Heterosis–Molecular Markers for Predicting Heterosis 123
Conclusion 131
References 132
9 Genetic Variant Discovery and Its Use in Genome Characterization of Agronomically Important Crop Species 137
Stephane Deschamps and Matthew A. Campbell
Introduction 138
Sanger Resequencing 140
Single Feature Polymorphisms 140
Next-Generation Sequencing 143
High-Density Genotyping using the Illumina Golden Gate Platform 153
Genotyping by Sequencing 155
Genome Characterization and Haplotypes 157
Conclusions and Perspectives 159
References 160
10 Future Prospects of Molecular Markers in Plants 169
Reyazul R. Mir and Rajeev K. Varshney
Introduction 170
Molecular Markers: The Past 172
Molecular Markers: The Present 173
Molecular Markers: The Future 175
Novel Approaches or Platforms for Plant Breeding 180
Conclusions 183
Acknowledgments 184
References 184
Index 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.