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Molecular Markers in Plants



Molecular Markers in Plants

Robert J. Henry (Editor)

ISBN: 978-1-118-47299-6 September 2012 Wiley-Blackwell 216 Pages

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Molecular Markers in Plants surveys an array of technologies used in the molecular analysis of plants. The role molecular markers play in plant improvement has grown significantly as DNA sequencing and high-throughput technologies have matured. This timely review of technologies and techniques will provide readers with a useful resource on the latest molecular technologies.

Molecular Markers in Plants not only reviews past achievements, but also catalogs recent advances and looks forward towards the future application of molecular technologies in plant improvement. Opening chapters look at the development of molecular technologies. Subsequent chapters look at a wide range of applications for the use of these advances in fields as diverse as plant breeding, production, biosecurity, and conservation. The final chapters look forward toward future developments in the field.

Looking broadly at the field of molecular technologies, Molecular Markers in Plants will be an essential addition to the library of every researcher, institution, and company working in the field of plant improvement.

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