Cover Page

Contents

Cover

Title Page

Copyright

Foreword

Preface

Chapter 1: Translational Genomics in Crop Breeding for Biotic Stress Resistance: An Introduction

Introduction

Improving Disease Resistance in Cereals

Improving Disease Resistance in Legumes

Improving Disease Resistance in Vegetables

Improving Disease Resistance in Cassava and Brassica

Summary and Outlook

References

Chapter 2: Bacterial Blight Resistance in Rice

The Disease and Pathogen

Factors Affecting Pathogenicity of Xoo

Xoo Resistance in Rice

Conclusion and Future Prospects

References

Chapter 3: The Genetic Basis of Disease Resistance in Maize

Introduction

Understanding the Intruders: Diseases of Maize

Understanding the System: Genetic Architecture of Disease Resistance in Maize and Biological Insights

Translating Knowledge to Action: Breeding for Disease Resistance

Conclusions

References

Chapter 4: Genomics-Assisted Breeding for Fusarium Head Blight Resistance in Wheat

Introduction

Genomics-Assisted Breeding for FHB Resistance

MAS for the Major FHB Resistance Gene Fhb1

MAS for QTL Other than Fhb1 and MAS for Multiple QTL Simultaneously

MAS for FHB Resistance QTL Available in European Winter Wheat

MAS for Improving FHB Resistance in Tetraploid Wheat

Conclusions and Summary

References

Chapter 5: Virus Resistance in Barley

Introduction

Important Viral Pathogens of Barley

Breeding for Virus Resistance – Some Case History

Genomics-Based Breeding for Virus Resistance in Barley

References

Chapter 6: Molecular Breeding for Striga Resistance in Sorghum

Introduction

Development of Bioassays and Dissecting Striga Resistance Mechanisms

Understanding Host-Parasite Biology: Exploring Pathway Stages as Entry Points for Breeding Resistance to Striga

Striga Diversity, Racial Differentiation, and its Implications on Striga Resistance Breeding

QTL Analysis and Marker-Assisted Selection for Improving Striga Resistance

Recent Development in Marker-Assisted Backcrossing for Development of Striga Resistance Products

Advances in Genomics and Applications for Striga Resistance Research

Managing Striga in Sorghum: Current Technologies and Strategies

Conclusion

Acknowledgment

References

Chapter 7: Nematode Resistance in Soybean

Introduction

Overview of Nematode Problems in Soybean Production

Nematode Biology and Host Response to Nematodes

Candidate Genes for Host Plant Resistance and Host-Nematode Interaction

Breeding Strategy and Variety Development for Nematode Resistance and Tolerance

New Genomics Approaches and Biotechnology

Other Omics-Based Crop Improvement

Transgenic Approaches to Crop Improvement

Acknowledgments

References

Chapter 8: Marker-Assisted Selection for Biotic Stress Resistance in Peanut

Significance of Peanut

Genetic Structure of Peanut (Groundnut)

Genetic Linkage Maps of Arachis

Marker-Assisted Breeding of Peanut

Conclusion

Acknowledgments

References

Chapter 9: Organization of Genes Conferring Resistance to Anthracnose in Common Bean

Introduction

The Pathogen, Colletotrichum lindemuthianum

Genetic Resistance to Anthracnose

Linkage Analysis in Resistance to Bean Anthracnose

Characterized Resistance Genes to C. lindemuthianum

Implications

Future Prospects

References

Chapter 10: Enabling Tools for Modern Breeding of Cowpea for Biotic Stress Resistance

Introduction

Pioneering the Use of SSR Markers for Introgression of Striga Resistance

SNPs in Cowpea Breeding for Biotic Stress Resistance

High Quality Consensus Genetic Map

Fingerprinting of Cultivars and Other Prospective Parents

Biotic Stresses and Genetic Marker Resources

Genetically-Modified Cowpea for Control of Maruca Pod Borer and Cowpea Weevil

Tools and Genetic Resources for Cowpea Breeders

Challenges for Adoption of Modern Breeding Tools in Cowpea Improvement

Summary and Conclusions

Acknowledgements

References

Chapter 11: Disease Resistance in Chickpea

Introduction

Ascochyta Blight (AB)

Fusarium Wilt (Foc)

Botrytis Gray Mold (BGM)

Rust

Genetic Resources and Breeding Progress

Progress in Introgression of Resistance Genes

Conclusions and Future Prospects

Acknowledgments

References

Chapter 12: Resistance to Late Blight in Potato

Introduction

History of Late Blight Resistance Breeding

Sources of Resistance to P. infestans

R genes

R1

R2

Rpi-blb2

Rpi1

RB/Rpi-blb1

Rpi-phu1

Rpi-mcq1

Rber

R3

References

Web pages

Chapter 13: Late Blight of Tomato

Introduction

Significance of Tomato

Significance of Late Blight

Late Blight Disease Control

Identification of Resistance Resources and Breeding for LB resistance in Tomato

Future Prospects

Conclusions

Acknowledgments

References

Chapter 14: Marker-Assisted Selection for Disease Resistance in Lettuce

Introduction

Molecular Markers and Marker-Assisted Selection

Marker-Assisted Selection for Disease Resistance

Mapped Resistance Genes

Study of the Lettuce Genome

Appendix: Assays for Marker-Assisted Selection

Acknowledgements

References

Chapter 15: Marker-Assisted Breeding for Cassava Mosaic Disease Resistance

Introduction

Cassava Breeding and Genetics

Benefits of Molecular Markers for Genetic Improvement

Cassava Mosaic Disease

CMD Epidemic

CMG Situation in Africa

Breeding for CMD Resistance

Sources of CMD Resistance

Genetic Mapping of CMD Resistance Genes

Marker-Assisted Breeding for CMD2 Resistance in Cassava

CMD2 Resistance Profile

BAC Sequencing Reveals New Markers for CMD2 Gene

Significance and Impact of MAB for CMD Resistance

Future MAB Targets for CMD Resistance

References

Chapter 16: Genetics and Gene Mapping of Disease Resistance in Brassica

Introduction

Sclerotinia

Clubroot

Blackleg

Genetic Mapping of Resistance to Other Brassica Diseases

Summary

References

Appendix I – Contributors

Appendix II – Reviewers

Index

Title Page

Foreword

Drs. Rajeev K. Varshney and Roberto Tuberosa have done a great service by bringing out this important book, Translational Genomics for Crop Breeding, Vol. 1: Biotic Stresses. This volume deals with the application of genomics in crop breeding for biotic stress tolerance. It will be useful to refer briefly to the transformational role the new genetics based on genomic applications is playing today in improving agriculture, industry, medicine, and environment, following the elucidation of the double-helix structure of the DNA molecule 60 years ago by James Watson, Francis Crick, Maurice Wilkins, and Rosalind Franklin. Their discovery opened up uncommon opportunities for the advancement of science as related to all aspects of life. During recent decades, many Nobel Prizes in Physiology and Medicine have gone to molecular geneticists. At the same time, public concern about the proper measurement of risks and benefits has grown, particularly in the fields of agricultural and food biotechnology. Biotechnology provides an opportunity to convert bioresources into economic wealth. This has to be done in such a manner as to ensure no adverse impact either on the environment or on human and animal health. The bottom line of Indian national agricultural biotechnology policy should be the economic well-being of farm families, food security of the nation, health security of the consumer, protection of the environment, and the security of our national and international trade in farm commodities.

This volume is an epitome of advances in the area of translational genomics application for improving crops with resilience to important components of biotic stress. Integration of high-throughput genotyping with precise phenotyping is the key for dissecting mechanism of complex traits at the molecular level. There are a number of races and biotypes known for a particular disease and insect, and so it is necessary to have a complete knowledge of the causal organism so that race-specific or biotype-specific resistance can be attained. This encourages optimal and target approach to breeding for the trait of interest. Hence, a more holistic approach and, more importantly, a holistic perspective such as that of systems biology is the need of the hour. The chapters in this volume not only provide in-depth review of the problem at hand but also enlighten readers about the advances and possibility of integrating genomics approach in tackling a research problem. In addition, the successful example and success stories discussed are thought provoking to young plant scientists and make them prepare for the challenges ahead.

New approaches for identifying marker-trait association such as genome-wide and candidate gene association studies are gaining fast acceptance due to advantages such as amenability to phenotype at multi-location for multiple traits and genotyping only once, not at each generation. In addition, marker-trait association is validated simultaneously in order to allow the deployment of markers directly in the breeding program. Another upcoming and promising approach termed as genomic selection is fast gaining importance among the crop specialists. It relies on the genomic-assisted breeding values, rather than phenotypic selection alone, in order to select the lines for crossing and advancing them to next generation. These approaches along with others are covered comprehensively in this book.

I hope this book will be widely read by scientists and scholars, since we must harness the best in the new genetics to overcome the serious threats to human well-being caused by malnutrition, hunger, and disease. The contents of the book show the ways to enhancing productivity in perpetuity without ecological harm. I congratulate and thank Drs. Varshney and Tuberosa for their labor of love in helping harness the best in modern science for enhancing the quality of human life.

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MS Swaminathan
Founder Chairman
M S Swaminathan
Research Foundation

Chennai
Date: June 15, 2013

Preface

Recent years have witnessed significant progress in the area of crop genomics mainly due to advances in next-generation sequencing and high-throughput genotyping. Such advances are driving genomics-assisted breeding (GAB), a discipline that has grown tremendously during the past decade, particularly for its applications to improve crop productivity and quality. This quantum leap has been possible through the continuous effort and dedication of those engaged in the translation of the findings of genomics research into improved genotypes and populations. As we anticipate a further reduction in genotyping/sequencing cost, translational genomics is expected to become a more integral part of crop breeding.

Biotic stress is one of the major factors behind crop losses. While a number of reports have been available on genomics approaches such as deciphering marker-trait association either through linkage or association mapping, some success stories have also been reported in recent years on translational aspects of this genomics research in crop breeding. However, the ever-changing and dynamic world of causal organisms of diseases and pests pose serious challenges to crop specialists to identify new resistant alleles and to target disease and pest resistance as well as to accelerate development of superior lines with enhanced resistance to biotic stresses. Therefore, there was an urgent need for a book in which translational genomics activities for resistance to key pests and diseases, success stories completed and in progress, and useful take-home messages from GAB efforts in different crops would be compiled. Along these lines, the 16 chapters of Translational Genomics for Crop Breeding, Volume 1: Biotic Stresses include not only details on the aforementioned issues but also address perspectives and challenges in translational genomics for developing superior varieties and lines with enhanced resistance to biotic stresses.

We thank the authors (Appendix I) of different chapters for their commendable effort in summarizing the published and unpublished research and putting all the pieces together in a well-knitted, up-to-date manner, for the benefit of the research challenge in hand. In addition, the cooperation they have extended in terms of timely completion and revision of chapters is greatly appreciated. While editing this book, the strong support received from many other colleagues (Appendix II) willing to review the chapters is equally appreciated. Their constructive comments and suggestions have been instrumental in further improving the contents.

The editors are also grateful to colleagues and staff from their respective laboratories who helped complete the editing of the two volumes in parallel with their demanding responsibilities. In particular, Manish Roorkiwal, B. Manjula, Pawan Khera, and Mahendar Thudi helped RKV with the editorial work. The editors also wish to thank their respective families, as the editorial work for this book took away precious moments they should have spent together with their families. RKV is thankful to his wife Monika for her constant encouragement and support, and to Prakhar (son) and Preksha (daughter) for their love and cooperation. Similarly, RT is equally thankful to his wife Kay for her support and editorial help. RKV would also like to extend his sincerest thanks to Dr. William D. Dar, Director General, ICRISAT, for his guidance and support in completing this book. The cooperation and help received from Justin Jeffryes, Anna Ehlers, Kelvin Matthews, Erin Topp of Wiley Publishers, and Shikha Sharma of Aptara Corp. during various stages of development and completion of this book are gratefully acknoweldged. RKV would also like to mention that the book was edited during the tenure of RKV as Director, Center of Excellence in Genomics (CEG), ICRISAT, Hyderabad (India), Theme Leader – Comparative and Applied Genomics (CAG), Generation Challenge Programme (GCP) and Adjunct positions at the University of Western Australia, Crops Research Institute of Guangdong Academy of Agricultural Sciences (GAAS), China and BGI-Hongkong Research Institute, China.

We hope that this book will be helpful and useful as a ready guide to students, young researchers, crop specialists, GAB and translational genomics practitioners, and policy makers for developing crops more resilient to biotic stress.

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(Rajeev K. Varshney)

Hyderabad, India
June 10, 2013

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(Roberto Tuberosa)

Bologna, Italy
June 11, 2013