Molecular Markers in Plants

  • ID: 2171355
  • Book
  • 216 Pages
  • John Wiley and Sons Ltd
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The use of molecular technologies has increased rapidly in recent years in the study, improvement, and conservation of plants and crops. Molecular analysis has unlocked many secrets of plant development and the applications of these new findings holds great promise for meeting the food, fuel, and conservation needs of future generations. Molecular Markers in Plants reviews past technologies and techniques as well as explores the future potential these advances will have on the plant and crop science communities.

Molecular Markers in Plants opens with foundational chapters that review the development and evolution of molecular breakthroughs in early marker technologies through to whole–genome and transcriptome sequencing. The focus then shifts to application of these technologies with chapters looking at the application of molecular markers in plant improvement, conservation, and biosecurity efforts. The final chapter looks forward to future prospects for the use of molecular markers in plants.

Providing a timely synthesis of key advances in this dynamic field, Molecular Markers in Plants brings together the work of a globally renowned team of researchers. This indispensable volume will be an essential resource for anyone working in the molecular crop and plant sciences.

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Contributors ix

Preface xiii

1 Evolution of DNA Marker Technology in Plants 3Robert 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 57Susan Gillies

Introduction 58

Basic Approach 58

Conclusions 64

References 64

5 Molecular Markers in Plant Improvement 67Peter 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

TheWay Forward 91

Conclusion 95

References 96

7 Molecular Markers for Plant Biosecurity 99Andrew 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 119Gopala 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 137Stephane 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 169Reyazul 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

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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.

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