Molecular Markers in Plants E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 356

Veröffentlichungsjahr: 2012

Beschreibung

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.

Leseprobe

Contents

Cover

Title Page

Copyright

Contributors

Preface

Chapter 1: Evolution of DNA Marker Technology in Plants

Introduction

Early Marker Technologies

Evolving Range of Applications of DNA Markers in Plants

Applications

Future Developments

References

Chapter 2: Whole-Genome Sequencing for Marker Discovery

Sequencing Strategies

Sequencing Technologies

Epigenetic Markers

Genome-Wide Selection

Data Analysis Resources

References

Chapter 3: Amplicon Sequencing for Marker Discovery

Introduction

Background

Maximizing Efficiency Through Sample Pooling

Limitations of Amplicon-Based MPS

Bioinformatics

Concluding Remarks

Acknowledgments

References

Chapter 4: Transcriptome Sequencing for Marker Discovery

Introduction

Basic Approach

Conclusions

References

Chapter 5: Molecular Markers in Plant Improvement

Introduction

Plant Domestication and Traditional Breeding

Application of Molecular Markers to Breeding

Next-Generation Approaches to QTL Discovery

Conclusion

References

Chapter 6: Applications of Molecular Markers in Plant Conservation

Introduction

Traditional Approaches

The Way Forward

Conclusion

References

Chapter 7: Molecular Markers for Plant Biosecurity

Introduction

The Present—PCR for Specific Diagnosis and for DNA Barcoding

The Future—Next-Generation Sequencing Methods to Revolutionize Plant Quarantine Diagnostics

Conclusions

Acknowledgments

References

Chapter 8: Molecular Markers for Harnessing Heterosis

Introduction

Molecular Markers for Understanding the Genetic Basis of Heterosis

Molecular Diversity and Heterosis—Molecular Markers for Predicting Heterosis

Conclusion

References

Chapter 9: Genetic Variant Discovery and Its Use in Genome Characterization of Agronomically Important Crop Species

Introduction

Sanger Resequencing

Single Feature Polymorphisms

Next-Generation Sequencing

High-Density Genotyping using the Illumina Golden Gate Platform

Genotyping by Sequencing

Genome Characterization and Haplotypes

Conclusions and Perspectives

References

Chapter 10: Future Prospects of Molecular Markers in Plants

Introduction

Molecular Markers: The Past

Molecular Markers: The Present

Molecular Markers: The Future

Novel Approaches or Platforms for Plant Breeding

Conclusions

Acknowledgments

References

Index

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Library of Congress Cataloging-in-Publication Data

Molecular markers in plants / editor, Robert J. Henry. p. cm. Includes bibliographical references and index. ISBN 978-0-470-95951-0 (hardback : alk. paper) 1. Plant breeding. 2. Genetic markers. 3. Plant genetics. 4. Crop improvement. I. Henry, Robert J. SB123.M58 2013 634.9′56--dc232012019771

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Contributors

Matthew A. Campbell DuPont Pioneer Johnston, Iowa, United States

Stéphane Deschamps DuPont Agricultural Biotechnology Experimental Station – P.O. Box 80353 200 Powder Mill Road Wilmington, DE 19880-0353

Mark Edwards Southern Cross Plant Sciences Southern Cross University Lismore, Australia

Celine H. Frere School of Agricultural and Food Sciences University of Queensland Brisbane, Australia

Andrew D.W. Geering Cooperative Research Centre for National Plant Biosecurity and the Queensland Alliance for Agriculture and Food Innovation The University of Queensland Ecosciences Precinct Brisbane, Queensland, Australia

Edward K. Gilding School of Agricultural and Food Sciences University of Queensland Brisbane, Australia

Susan Gillies Southern Cross Plant Sciences Southern Cross University Lismore, Australia

Ian D. Godwin School of Agricultural and Food Sciences University of Queensland Brisbane, Australia

Robert J. Henry Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane, Queensland, Australia

Pavana J. Hiremath International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India

Gopala S. Krishnan Division of Genetics Indian Agricultural Research Institute New Delhi, India

Ana Pavasovic School of Biomedical Science Queensland University of Technology Brisbane, Australia

Peter J. Prentis School of Earth, Environmental and Biological Sciences Queensland University of Technology Brisbane, Australia

Oscar Riera-Lizarazu International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India

Maurizio Rossetto National Herbarium of NSW Royal Botanic Gardens and Domain Trust Sydney, Australia

Reyazul R. Mir International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India

Paul D. Rymer Hawkesbury Institute for the Environment University of Western Sydney Richmond, Australia

Timothy R. Sexton Department of Forest Sciences The University of British Columbia Vancouver, British Columbia, Canada

Frances M. Shapter Southern Cross Plant Sciences Southern Cross University Lismore, Australia

A.K. Singh Division of Genetics Indian Agricultural Research Institute New Delhi, India

Rajeev K. Varshney International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India; CGIAR-Generation Challenge Programme Mexico; School of Plant Biology Faculty of Natural and Agricultural Sciences The University of Western Australia Crawley, Australia

Daniel L.E. Waters Southern Cross Plant Science Southern Cross University Lismore, Australia

Preface

Plants are fundamental to life, being the basis of our food production and an essential part of the global ecosystem on which life on earth depends. Plants have been used as a source of a wide range of materials, but the threat of exhaustion of fossil oil supplies has resulted in a renewed evaluation of plants as a source of energy and biomaterials. Molecular analysis of plants has found many applications in plant improvement, in the management of plant production, and the conservation of plant resources. Molecular markers are routinely used to identify plants for forensic or intellectual property applications. Molecular tools have become key contributors to the management of wild plant populations helping to conserve biodiversity. The relentless need for the continuous development of genetically improved crops to satisfy the demands of a global human population growing in number and affluence is now strongly supported by molecular marker technology.

Recent dramatic advances in DNA sequencing are now providing cost-effective options for the discovery of very large numbers of markers for any plant species. These developments significantly change the approach to marker discovery and analysis in plants and greatly expand the potential range of applications. This book outlines the technologies for molecular analysis of plants in support of plant breeding, production, and conservation. The techniques that have been used in the past are reviewed in relation to recent developments and future potential. This book updates earlier volumes on this topic featuring significant advances in both the technology and application of markers.

Robert Henry University of Queensland

1

Evolution of DNA Marker Technology in Plants

Robert J. Henry

Contents

Introduction

Early Marker Technologies

Evolving Range of Applications of DNA Markers in Plants

Applications

Future Developments

References

Introduction

Genetic markers are key tools for plant identification and plant improvement (Henry, 2001). Genetic marker technology has evolved rapidly with early methods based on phenotyping or isozymes being replaced by DNA-based methods of increasing sophistication. Early markers were few in number and difficult to assay. The ultimate development of the technology will provide simple methods to assess all genetic variation in the genome. This chapter provides a brief account of the development of genetic marker technology and its application to plants over the last 30 years. This perspective is provided as background and context for the accounts of the latest technologies (Henry et al., 2012) to follow in subsequent chapters.

Molecular marker technology has evolved though several phases. Early methods employing non-DNA-based methods were replaced by DNA-based methods as the technologies for DNA analysis improved. Early hybridization-based methods were displaced rapidly following the development of polymerase chain reaction (PCR). PCR-based methods greatly increased the feasibility of high-throughput marker screening. Early PCR-based methods relied upon arbitrary primers because of a lack of sequence information for many species. These in turn were overtaken by the widespread adoption of more robust microsatellite or simple sequence repeat (SSR) markers. Single nucleotide polymorphisms (SNPs) have more recently replaced SSR markers as larger volumes of sequence data became available (Henry, 2008). Second-generation sequencing technologies have greatly accelerated the move to sequence-based markers. Ongoing improvements in DNA sequencing promise a continued convergence of sequencing and genotyping technologies. Third-generation sequencing promises delivery of technology for routine sequencing of even complex plant genomes enabling ready marker discovery and analysis.

Molecular markers have a wide range of applications in biological systems including plants. Molecular makers are very useful in identification of plants and in determining the relationships between plants. Plant identification may be important in plant breeding, plant production and processing, policing of intellectual property rights, and forensic applications. Determination of genetic relationships is required in evolutionary and conservation genetic analyses and in selection of germplasm in plant breeding. Plant breeding is often directly supported by marker-assisted selection.