Rice Functional Genomics Rice Functional Genomics Challenges, Progress and Prospects

Edited by

NARAYANA M. UPADHYAYA Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry Canberra, ACT 2601, Australia Narayana M. Upadhyaya Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry Canberra, ACT 2601, Australia

Library of Congress Control Number: 2006939781

ISBN-10: 0-387-48903-7 e-ISBN-10: 0-387-48914-2 ISBN-13: 978-0-387-48903-2 e-ISBN-13: 978-0-387-48914-8

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987654321 springer.com Foreword

In 1991 Gurdev Khush and I edited the first book containing summaries of research results in Rice Biotechnology. In comparing that book with this one, what a difference 15 years can make! How excited we were back then with publication of the first molecular genetic map of rice using DNA markers (120 RFLPs) and with genetic transformation of the recalcitrant cereals, which had finally been achieved using DNA uptake by and plant regeneration from rice protoplasts— though efficiencies were very low and some of the regenerated plants looked rather peculiar. Even then, rice was beginning to be considered a model monocot for molecular genetic research, in part because leading laboratories confirmed an earlier report from India suggesting rice had a relatively small genome. Just as important, in my opinion, rice was achiev- ing model status because the scientists generating the knowledge base and creating enabling technologies readily shared them with numerous other scientists who then made further advances in rice molecular biology. Not only did the scientists freely provide results and materials to others, but they also offered training in their use and combined and integrated results from different laboratories to advance the science. It is clear from the chapters of this book that such a spirit of collaboration is still promoting advances in rice genomics and keeping rice at the forefront of the field. As rice yeast artificial chromosome (YAC) bacterial artificial chromosome (BAC) P1-derived artificial chromosome (PAC), cosmid, and fosmid libraries became available, they too are shared and have laid the foundations for success in map-based cloning, rice genome sequencing, and comparative mapping across species. Similarly, more than one million rice expressed sequence tags (ESTs) have been developed by several laboratories, more than for any other plant species, and shared with all researchers. Perhaps the most significant collaboration has been the International Rice Genome Sequencing Project undertaken by laboratories in ten countries with contributions from two corporations. Despite many bumps along the way, the leaders of the project were able to keep all parties committed to generating a complete and highly accurate rice genome sequence with all data immediately placed in the public domain. Completed in 2004, this sequence solidified the model status of rice, and, as demonstrated in several chapters of this book, has become an extremely valuable resource for fundamental research in VI F oreword genomics and for crop genetic improvement. Similar collaborations continue with the International Rice Functional Genomics Consortium, the Oryza Map Alignment Project, and the International Rice Information System. This book presents an excellent review of recent advances in determining the function of 30,000 to 40,000 genes of rice and in using this knowledge to identify agronomically important genes in rice, wild relatives of rice, and other cereals. It is fortuitous that rice has come to serve as the model for monocot research because rice also happens to feed half of humanity, including many of the world’s poor. We know from past experience that genetic modifica- tions in rice development and productivity can lead to transformations in agriculture that help to feed and improve the lives of hundreds of millions of people. An international rice research system is in place that has, and will continue to use scientific progress and knowledge, such as that presented here, to make such genetic improvements in rice for the benefit of human- kind. The authors and editors who have contributed to this book are to be commended for synthesizing our knowledge of rice functional genomics in a format that will both advance the science and facilitate such applications.

Gary H. Toenniessen Managing Director Interim President, Alliance for Green Revolution in Africa The Rockefeller Foundation New York, NY 10018-2702, USA

Preface

My continuous association with rice research dates back to 1990, when I started as a postdoctoral research fellow at CSIRO Plant Industry thanks to the generous support of the Rockefeller Foundation under its International Rice Biotechnology Program. By that time, rice had already been recog- nized as a model species for cereal biotechnology, not only because of its status as a staple food for resource-poor Asia with half the world’s population and the urgent need to increase the rice production to meet the growing demand, but also because of well understood rice genetics and the availability of a large number of molecular markers. Progress with trans- gene delivery and expression has been more rapid with rice than with any other cereal because of the efficient rice tissue culture and transformation systems developed over the years. In the mid-1990s, rice was further established as a model species for cereal genome research, because of its small genome size, ease with which it could be transformed, and its gene order and gene sequence similarities with other cereals. A consortium of publicly funded laboratories formed The International Rice Genome Sequencing Project (IRGSP) in 1997 to produce a high-quality, map-based sequence of the rice genome using the cultivar Nipponbare of Oryza sativa ssp. japonica. I was fortunate enough to continue to work on rice even after the conclusion of our Rockefeller-funded project in 1997, thanks to the support and encouragement of CSIRO Plant Industry’s then Chief Dr. Jim Peacock and Genomics Program leader Dr. Liz Dennis. We knew that with the im- minent availability of the complete rice genome sequence, the challenge to the scientific community would be in identifying functions for each of the expected 25,000 to 50,000 plant genes. Along with a few other groups worldwide, we embarked on developing functional genomics tools and resources in the form of transposon insertional mutants and mutagens. Genome-wide research tools, resources, and approaches such as data min- ing for structural similarities, gene expression profiling at the RNA level with expressed sequence tags (ESTs), microarray and DNA chip-based analyses, gene expression profiling at the protein level (proteomics), gene knockouts or loss of function studies with naturally occurring alleles, induced deletion mutants and insertional mutants, and gene expression

VIII Preface knock-down (gene silencing) studies with RNAi have all become integral parts of plant functional genomics including that of rice. I have been in touch with these facets of Rice Functional Genomics through my involvement as a member of the International Rice Functional Genomics Consortium, a voluntary organization with a mandate to coordi- nate research in the post-sequencing functional genomics era by exploring ways to consolidate international rice functional genomics resources and to build common strategies to achieve our common goals. We, as a scientific community, still have a long way to go in fully understanding the key genes controlling important agronomic characters before they can be exploited by classical or transformation breeding for crop improvement. The chapters in this book focus on most of the aforementioned aspects of rice functional genomics and are authored by leading researchers in their respective fields. I am indebted to chapter coordinators, coauthors, and reviewers for their extremely valuable contributions. Sincere thanks to my colleagues at CSIRO Plant Industry—Drs. Qian-Hao Zhu, John Wat- son, and Andrew Eamens, for assisting me with technical editing of vari- ous chapters. My thanks to Drs. Danny Llewellyn, Peter Waterhouse, Ming-Bo Wang, Alan Richardson, Chris Helliwell, Xue-Rong Zhou, Mr Neil Smith, Miss Kerrie Ramm, and others for proofreading the chapters. I thank Springer for inviting me to edit this book, which has been a challenging and rewarding experience for me.

Narayana M. Upadhyaya CSIRO Plant Industry GPO Box 1600, Canberra, ACT 2601 Australia October 19, 2006

Contents

Foreword...... V

Preface...... VII

Contributors...... XIX

1 Introduction ...... 1 Narayana M. Upadhyaya and Elizabeth S. Dennis

2 Rice Genome Sequence: The Foundation for Understanding the Genetic Systems...... 5 Takashi Matsumoto, Rod A. Wing, Bin Han and Takuji Sasaki Reviewed by Satoshi Tabata

2.1 The Importance of the Accurate Genome Sequence of Rice ...... 5 2.2 Construction of the Sequence-Ready Physical Maps...... 7 2.3 Two-Step Strategy for Completion of Rice Genome Sequencing ...... 10 2.4 An Alternative Approach—the Whole Genome Shotgun Sequencing of Rice ...... 13 2.4.1 Whole Genome Shotgun Sequencing of japonica Rice (Syngenta) ...... 13 2.4.2 Whole Genome Shotgun Sequencing of indica Rice (BGI) ...... 13 2.4.3 Comparison of Genome Sequences Derived from Whole Genome Shotgun Sequencing and Clone-by-Clone Shotgun Sequencing (IRGSP) ...... 13 2.5 Initial Analysis of the Rice Genome...... 14 2.6 Current Status and Future Developments ...... 16 Acknowledgments ...... 17 References...... 17

3 Rice Genome Annotation: Beginnings of Functional Genomics...... 21 Takeshi Itoh Reviewed by C. Robin Buell and Battazar A. Antonio

3.1 Introduction...... 21 3.2 Computational Methods of Annotation...... 22 X Contents

3.3 Automated Annotation System...... 24 3.4 Comprehensive Genome Annotation and Curation ...... 25 3.5 From Annotations to Functional Genomics...... 26 Acknowledgments ...... 27 References ...... 27

4 Genome-Wide RNA Expression Profiling in Rice ...... 31 Shoshi Kikuchi, Guo-Liang Wang, and Lei Li Reviewed by Lee Tarpley and Iain Wilson

4.1 Introduction ...... 31 4.2 Rice Transcriptome—from EST Collection to Microarray ...... 32 4.2.1 Rice EST Collection and the First cDNA Microarray System Based on the EST Clones ...... 32 4.2.2 Full-Length cDNA Project ...... 35 4.2.3 Oligoarray Systems ...... 37 4.3 Deep Transcriptome Analysis of the Rice Genome...... 38 4.3.1 Principles of Different SAGE Techniques ...... 40 4.3.2 Development of the Robust-LongSAGE (RL-SAGE) Method ...... 42 4.3.3 Application of RL-SAGE for Defense Transcriptome Analysis in Rice ...... 43 4.3.4 MPSS for Expression Profiling ...... 44 4.3.5 Deep Transcriptome Analysis Using MPSS...... 44 4.4 Transcriptional Analysis Using Genome Tiling Microarrays...... 45 4.4.1 Principle of Genome Tiling Microarrays...... 46 4.4.2 Application of Genome Tiling Microarray Analysis in Rice...... 47 4.5 Perspective...... 52 Acknowledgments ...... 53 References ...... 54

5 Rice Proteomics: A Step Toward Functional Analysis of the Rice Genome ...... 61 Setsuko Komatsu Reviewed by Lee Tarpley

5.1 Significance ...... 61 5.2 Database Based on 2D-PAGE ...... 63 5.2.1 Strategy to Determine Amino Acid Sequences for Construction of the Rice Proteome Database...... 63 5.2.2 Format and Content of the Rice Proteome Database...... 65 5.2.3 How to Use the Rice Proteome Database...... 66 5.2.4 Cataloging of Proteins in the Rice Proteome Database ...... 67 5.2.5 Future Prospects of the Rice Proteome Database ...... 67 Content s XI

5.3 Functional Analysis Using Differential Proteomics ...... 68 5.3.1 Stresses ...... 68 5.3.2 Hormones ...... 74 5.4 Future Prospects...... 77 5.4.1 Two-Dimensional Liquid Chromatography and Fluorescence Two-Dimensional Difference Gel Electrophoresis...... 77 5.4.2 Identification of Protein Modification for Functional Analysis ...... 79 5.4.3 Protein-Protein Interaction Analyses for Functional Prediction...... 81 5.4.4 Concluding Remarks ...... 83 Acknowledgment...... 83 References...... 83

6 Metabolomics: Enabling Systems-Level Phenotyping in Rice Functional Genomics ...... 91 Lee Tarpley and Ute Roessner Reviewed by Tony Ashton

6.1 Significance ...... 91 6.2 Plant Sampling and Chemical Analysis...... 92 6.3 Case Studies in Rice Metabolomics...... 94 6.4 Case Studies Integrating Functional Genomic Levels ...... 96 6.5 Time and Space Limitations in Integrated Functional-Genomic Analyses ...... 98 6.6 Metabolite Response to Perturbation ...... 99 6.7 Databases and Resources ...... 99 6.8 Data Analysis...... 102 6.9 Summary...... 104 References...... 105

7 Use of Naturally Occurring Alleles for Crop Improvement ...... 109 Anjali S. Iyer-Pascuzzi, Megan T. Sweeney, Neelamraju Sarla, and Susan R. McCouch Reviewed by Evans Lagudah

7.1 Introduction...... 110 7.1.1 Why Study Natural Variation?...... 110 7.2 A Plant Breeder’s View on Utilizing Natural Variation ...... 111 7.2.1 Importance of Germplasm Conservation for Crop Improvement ...... 111 7.3 Understanding Evolutionary History Through Natural Variation...... 113 7.3.1 Origins of Natural Variation: A Short History of Orzya sativa...... 113 7.3.2 Genetic Markers: Assessing Diversity and Population Structure in O. sativa ...... 114 XII Contents

7.4 Natural Variation and Functional Genomics: Utilizing Germplasm to Identify Useful Alleles ...... 116 7.4.1 Genetic Markers and Their Use in Mapping ...... 116 7.4.2 Mapping Populations...... 116 7.4.3 Association Mapping...... 128 7.4.4 Gene Identification and Development of Perfect Markers for Applications in Breeding...... 130 7.5 Natural Variation and Epistasis ...... 132 7.6 Natural Variation or Mutant Analysis?...... 133 7.7 Natural Variation versus Transgenic Approaches for Crop Improvement...... 135 7.8 Conclusions ...... 137 References ...... 137

8 Chemical- and Irradiation-Induced Mutants and TILLING...... 149 Ramesh S. Bhat, Narayana M. Upadhyaya, Abed Chaudhury, Chitra Raghavan, Fulin Qiu, Hehe Wang, Jianli Wu, Kenneth McNally, Hei Leung, Brad Till, Steven Henikoff and Luca Comai Reviewed by Phil Larkin

8.1 Introduction ...... 150 8.2 Mutagens and Mutagenesis...... 151 8.2.1 Chemical Mutagens...... 152 8.2.2 Irradiation Mutagens ...... 155 8.2.3 Raising Mutant Populations ...... 157 8.3 Rice Mutant Stocks and Databases...... 158 8.3.1 USA Mutant Stocks...... 159 8.3.2 IRRI Mutant Stocks and Database...... 159 8.3.3 China Mutant Stocks ...... 160 8.3.4 Taiwan Mutant Stock ...... 160 8.3.5 Japan Mutant Stock and Database...... 161 8.4 Forward Genetics with Mutants...... 161 8.4.1 Phenotyping...... 161 8.4.2 Map-Based Cloning...... 162 8.4.3 Detecting Genomic Changes Using Genome-Wide Chips ...... 163 8.5 Reverse Genetics with Mutants ...... 164 8.5.1 PCR Screening ...... 165 8.5.2 TILLING ...... 165 8.6 TILLING in Rice...... 166 8.6.1 Seattle TILLING Project ...... 166 8.6.2 Other Technical Improvements in Rice TILLING ...... 168 8.6.3 TILLING Case Studies for Specific Traits...... 168 8.7 Future Prospects ...... 172 Acknowledgments ...... 173 References ...... 174

Contents XIII

9 T-DNA Insertion Mutants as a Resource for Rice Functional Genomics...... 181 Emmanuel Guiderdoni, Gynheung An, Su-May Yu, Yue-ie Hsing and Changyin Wu Reviewed by Alain Lecharny and Michel Delseny

9.1 Introduction...... 182 9.2 Agrobacterium-Mediated Transformation of Rice...... 183 9.3 T-DNA as an Insertional Mutagen...... 185 9.4 Rice T-DNA Insertional Mutant Populations ...... 188 9.4.1 Korea ...... 188 9.4.2 China ...... 190 9.4.3 France ...... 192 9.4.4 Taiwan...... 194 9.4.5 Current Collection of T-DNA Insertion Lines and FSTs...... 194 9.5 Current Knowledge on T-DNA Integration in Rice...... 195 9.6 T-DNA Insertion Specificity in Rice ...... 198 9.6.1 Preference Among and Along Rice Chromosomes ...... 198 9.6.2 Preference for Integration into Intergenic versus Genic Regions and Regulatory versus Coding Regions...... 201 9.6.3 Preference for Insertion in Expressed Genes...... 203 9.6.4 Preference for GC Content and DNA Structure ...... 203 9.6.5 Preference for Functional Category of Genes...... 204 9.6.6 Estimation of the Number of Lines Required to Saturate the Rice Genome ...... 204 9.7 Gene and Enhancer Trapping with T-DNA in Rice...... 204 9.8 Forward Genetics Screens and Gene Isolation Using T-DNA Insertion Lines...... 208 9.8.1 Gene Trapping...... 209 9.8.2 Activation Tagging...... 211 9.9 Reverse Genetics with T-DNA Mutants in Rice...... 212 9.10 Conclusion and Prospects ...... 213 Acknowledgments ...... 215 References...... 215

10 Transposon Insertional Mutants: A Resource for Rice Functional Genomics ...... 223 Qian-Hao Zhu, Moo Young Eun, Chang-deok Han, Chellian Santhosh Kumar, Andy Pereira, Srinivasan Ramachandran, Venkatesan Sundaresan, Andrew L. Eamens, Narayana M. Upadhyaya and Ray Wu Reviewed by Tony Pryor and John M. Watson

10.1 Introduction...... 224 10.2 Transposon Tagging Systems ...... 225 10.2.1 Activity of Transposons in Rice...... 225 10.2.2 One-Element System versus Two-Element System...... 229 10.2.3 Design of Constructs...... 232 XIV Contents

10.2.4 Gene and Enhancer Traps ...... 236 10.2.5 Transiently Expressed Transposase System...... 238 10.2.6 A High-Throughput System to Index Transposants...... 238 10.2.7 Using Endogenous Transposons ...... 240 10.2.8 Inducible Transposition...... 243 10.3 Mutagenesis Strategies ...... 245 10.3.1 Random or Non-targeted Mutagenesis...... 245 10.3.2 Localized or Targeted Mutagenesis ...... 246 10.4 Transposon Insertional Mutant Populations ...... 247 10.4.1 CSIRO Plant Industry Population ...... 248 10.4.2 EU (Wageningen) Population ...... 249 10.4.3 National University of Singapore Population ...... 250 10.4.4 Korea Population ...... 251 10.4.5 UC Davis Population ...... 254 10.5 Gene Discovery by Transposon Tagging...... 256 10.5.1 Forward and Reverse Genetics Strategies...... 256 10.5.2 Other Approaches for Mutation Identification...... 259 10.5.3 Tagging Efficiency...... 260 10.5.4 Confirmation of Tagged Gene ...... 261 10.6 Future Prospects ...... 261 References ...... 262

11 Gene Targeting by Homologous Recombination for Rice Functional Genomics ...... 273 Shigeru Iida, Yasuyo Johzuka-Hisatomi, and Rie Terada Reviewed by Barbara Hohn and Charles White

11.1 Introduction ...... 273 11.2 Gene Targeting by Homologous Recombination...... 278 11.2.1 Gene-Specific Selection and Gene-Specific Screening...... 279 11.2.2 Strong Positive-Negative Selection for Enriching Targeted Homologous Recombinants ...... 280 11.3 Potential Approaches for Homologous Recombination-Dependent Gene Targeting...... 282 11.4 Concluding Remarks ...... 285 Acknowledgments ...... 286 References ...... 286

12 RNA Silencing and Its Application in Functional Genomics...... 291 Shaun J. Curtin, Ming-Bo Wang, John M. Watson, Paul Roffey, Chris L. Blanchard, and Peter M. Waterhouse Reviewed by Werner Aufsatz

12.1 Introduction ...... 291 12.2 Discovery of RNA Silencing ...... 292 Contents XV

12.3 RNA Silencing Pathways...... 295 12.3.1 MicroRNA and Trans-Acting siRNA Pathways ...... 296 12.3.2 Repeat-Associated Small Interfering RNA and RNA-Directed DNA Methylation ...... 296 12.4 Proteins Involved in RNA Silencing Pathways ...... 299 12.4.1 The Dicer-Like Proteins...... 299 12.4.2 Hua Enhancer 1...... 303 12.4.3 The Double-Stranded RNA-Binding Protein Family...... 305 12.4.4 The Argonaute Protein Family...... 305 12.4.5 RNA-Dependent RNA Polymerase (RdRP)...... 307 12.4.6 DNA Methyltransferases...... 307 12.5 RNA Silencing and Anti-Viral Defense...... 307 12.6 Gene Silencing Platforms in Plants...... 310 12.6.1 Delivery by Transgenes...... 313 12.6.2 Transient Delivery by Viral Vectors — Virus-Induced Gene Silencing ...... 321 12.6.3 Transient Delivery by Agrobacterium Infection and Biolistics...... 323 12.7 Future Prospects of Gene Silencing Technology in Plants ...... 323 References...... 324

13 Activation Tagging Systems in Rice...... 333 Alexander A.T. Johnson, Su-May Yu, and Mark Tester Reviewed by Michael Ayliffe and Venkatesan Sundaresan

13.1 Introduction...... 333 13.2 Classical Activation Tagging: Enhancer Element-Mediated Gene Activation ...... 335 13.2.1 Classical Activation Tagging in Plants ...... 335 13.2.2 Structure and Function of the CaMV 35S Activation Tagging System...... 336 13.2.3 Variations to the CaMV 35S Activation Tagging System ...... 338 13.2.4 CaMV 35S Activation Tagging Resources in Rice...... 339 13.3 Transactivation Tagging: Transcriptional Activator-Mediated Gene Activation in Specific Cell Types...... 341 13.3.1 Gene Expression at the Cell Type–Specific Level...... 341 13.3.2 Origin of the GAL4 Enhancer Trapping System...... 342 13.3.3 GAL4 Enhancer Trapping in Plants...... 343 13.3.4 Cell Type–Specific Activation of Target Genes Using GAL4 Transactivation...... 344 13.3.5 Cell Type–Specific Activation Tagging Using GAL4 Transactivation...... 346 13.4 Future Perspectives...... 348 Acknowledgments ...... 349 References...... 349 XVI Contents

14 Informatics Resources for Rice Functional Genomics ...... 355 Baltazar A. Antonio, C. Robin Buell, Yukiko Yamazaki, Immanuel Yap, Christophe Perin, and Richard Bruskiewich Reviewed by Wm L. Crosby and Richard Cooke

14.1 Introduction ...... 356 14.2 NIAS Informatics Resources ...... 359 14.2.1 INtegrated Rice Genome Explorer...... 359 14.2.2 RGP Annotation Databases...... 361 14.2.3 KOME...... 362 14.2.4 Rice PIPELINE...... 362 14.3 TIGR Informatics Resources ...... 363 14.4 Oryzabase ...... 366 14.4.1 Database Contents...... 366 14.4.2 Genetic Stocks ...... 368 14.4.3 Comparative Genomics Resources ...... 368 14.5 Gramene...... 369 14.5.1 Genome Browser ...... 370 14.5.2 Maps and Markers...... 370 14.5.3 QTL, Genes, and Proteins...... 371 14.5.4 Ontology ...... 372 14.5.5 Database Availability...... 372 14.6 CIRAD Informatics Resources ...... 373 14.6.1 OryGenesDB...... 373 14.6.2 Oryza Tag Line ...... 375 14.6.3 Greenphyl...... 376 14.7 IRRI Informatics Resources...... 377 14.7.1 The International Rice Information System...... 378 14.7.2 Current Developments ...... 379 14.8 Insertion Mutant Databases ...... 380 14.8.1 Tos17 Insertion Mutant Database...... 380 14.8.2 Rice Mutant Database...... 381 14.8.3 Rice Ds Tagging Lines...... 381 14.8.4 Taiwan Rice Insertional Mutants Database...... 382 14.8.5 Shanghai T-DNA Insertion Population...... 383 14.8.6 Rice T-DNA Insertion Sequence Database...... 383 14.8.7 Rice FST Database at UC Davis ...... 384 14.8.8 CSIRO Rice FST Database and RGMIMS ...... 384 14.8.9 RiceGE: Rice Functional Genomic Browser ...... 385 14.9 Integration of Rice Functional Genomics Information ...... 386 14.9.1 High-Speed Networks...... 386 14.9.2 Grid Computing ...... 387 14.9.3 Web Integration ...... 387 14.10 Rice Functional Genomics Network...... 388 Acknowledgments ...... 389 References ...... 389 Content s XVII

15 The Oryza Map Alignment Project (OMAP): A New Resource for Comparative Genome Studies within Oryza...... 395 Rod A. Wing, Hye-Ran Kim, Jose Luis Goicoechea, Yeisoo Yu, Dave Kudrna, Andrea Zuccolo, Jetty Siva S. Ammiraju, Meizhong Luo, Will Nelson, Jianxin Ma, Phillip SanMiguel, Bonnie Hurwitz, Doreen Ware, Darshan Brar, David Mackill, Cari Soderlund, Lincoln Stein and Scott Jackson Reviewed by John M. Watson and Evans Lagudah

15.1 Introduction...... 395 15.2 Development of the OMAP BAC Library Resource ...... 397 15.3 Development of Wild Species FPC/STC Physical Maps...... 399 15.3.1 BAC End Sequencing ...... 399 15.3.2 BAC Fingerprinting ...... 399 15.3.3 Analysis of Structural Variation Between O. sativa and the 3 AA Genome OMAP Accessions...... 401 15.4 Summary, Conclusions, and Future Research...... 404 References...... 407

16 Application of Functional Genomics Tools for Crop Improvement ...... 411 Motoyuki Ashikari, Makoto Matsuoka and Masahiro Yano Reviewed by Elizabeth S. Dennis

16.1 Rice Genomics...... 411 16.2 Molecular Markers for Improved Breeding Efficiency...... 412 16.3 QTL Analysis...... 413 16.3.1 Genetic and Molecular Dissection of QTLs...... 415 16.3.2 QTL Application in Breeding...... 418 16.3.4 QTL Pyramiding for Breeding ...... 418 16.3.5 QTL Detection Using Chromosome Segment Substitution Lines...... 420 16.4 Use of Wild Species as a Source of Diversity for Breeding ...... 422 16.5 Molecular Breeding ...... 422 16.6 Outlook ...... 422 References...... 423

17 From Rice to Other Cereals: Comparative Genomics ...... 429 Richard Cooke, Benoit Piégu, Olivier Panaud, Romain Guyot, Jérome Salse, Catherine Feuillet and Michel Delseny Reviewed by Robert Henry and Elizabeth S. Dennis

17.1 Introduction...... 429 17.2 Origin and Evolution of Cereals ...... 431 XVIII Contents

17.3 Use of Comparative Genomics to Improve Genome Sequence Annotation ...... 433 17.4 Comparative Genomics and Conserved Noncoding Sequences: The Discovery of New Genes and New Signals ...... 436 17.5 Comparative Phylogeny of Multigene Families ...... 437 17.6 Revised “Circle Diagram” Model and Synteny Disruption ...... 443 17.7 The Rice Genome as a Model for Map-Based Cloning in Cereals ...... 450 17.8 Comparative QTL Mapping and Meta-Analysis of QTL ...... 454 17.9 Comparative Expression Profiling...... 457 17.10 Comparative Biology in the Era of Genomics...... 458 17.11 Genome Sequencing in Grasses: Beyond the Model ...... 461 Acknowledgments ...... 464 References ...... 464

Index...... 481

Contributors

Jetty Siva S. Ammiraju Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721 USA E-mail: [email protected]

Gynheung An Department of Life Science and National Research Laboratory of Plant Functional Genomics, Pohang University of Science and Technology, Hyoja-dong, Nam-gu, Pohang, Kyungbuk 790-784 Republic of Korea E-mail: [email protected]

Baltazar A. Antonio National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan E-mail: [email protected]

Motoyuki Ashikari Laboratory of Plant Bioresource, Development and Applied Division, Bioscience and Biotechnology Center, Nagoya University, Furocho, Chikusa-ku, Nagoya-shi, Aichi 464-8601 Japan E-mail: [email protected]

Tony Ashton* Genetic Engineering for Crop Improvement Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Werner Aufsatz* Gregor Mendel-Institut, GMI GmbH, Wien/Vienna A-1030 Austria E-mail: [email protected] XX Contributors

Michael Ayliffe* Genetic Engineering for Crop Improvement Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Ramesh S. Bhat University of Agricultural Sciences, Dharwad, Karnataka-580 005 India E-mail: [email protected]

Chris L. Blanchard School of Wine and Food Sciences, Charles Sturt University, Wagga Wagga, NSW 2678 Australia E-mail: [email protected]

Darshan Brar International Rice Research Institute, Los Baños, Metro Manila Philippines E-mail: [email protected]

Richard Bruskiewich International Rice Research Institute, Los Baños, Metro Manila Philippines E-mail: [email protected]

C. Robin Buell The Institute for Genomic Research (TIGR), Rockville, MD 20850 USA E-mail: [email protected]

Abed Chaudhury Genomics and Plant Development Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Contributors XXI

Luca Comai The University of California Davis Genome Center, Davis, CA 95616 USA E-mail: [email protected]

Richard Cooke Laboratoire Génome et Développement des Plantes, UMR5096 Centre National de la Recherche Scientifique, University of Perpignan, Perpignan Cédex 66860 France E-mail: [email protected]

Wm L. Crosby* Department of Biological Sciences, University of Windsor, Windsor, ON N9B 3P4 Canada E-mail: [email protected]

Shaun J. Curtin Genomics and Plant Development Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Michel Delseny Laboratoire Genome et Développement des Plantes, UMR 5096 Centre National de la Recherche Scientifique, University of Perpignan, Perpignan, Cédex 66860 France E-mail: [email protected]

Elizabeth S. Dennis Genomics and Plant Development Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Andrew L. Eamens Genomics and Plant Development Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

XXII Contributors

Moo Young Eun Rice Functional Genomics and Molecular Breeding Lab, Cell and Genetics Division, National Institute of Agricultural Biotechnology (NIAB), Rural Development Administration, Suwon, 441-707 Republic of Korea E-mail: [email protected]

Catherine Feuillet UMR Amélioration et Santé des Plantes, INRA-UBP, 63100 Clermont Ferrand France E-mail: catherine. [email protected]

Jose Luis Goicoechea Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721 USA E-mail: [email protected]

Emmanuel Guiderdoni AMIS Department, UMR PIA 1096, CIRAD, Montpellier, Hérault F-34398 France E-mail: [email protected]

Romain Guyot Laboratoire Genome et Developpement des Plantes, UMR 5096 CNRS-IRD-UP, CNRS-IRD-Université de Perpignan, 34394 Montpellier cedex 5 France E-mail: romain. [email protected]

Bin Han National Center for Gene Research, Chinese Academy of Sciences, Shanghai, 200233 China E-mail: [email protected]

Chang-deok Han Division of Applied Life Science, BK21 Program, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701 Republic of Korea E-mail: [email protected] Contributors XXIII

Steven Henikoff Seattle TILLING Project Department of Biology and FHCRC, University of Washington, Seattle, WA 98195 USA E-mail: steveh@ fhcrc.org

Robert Henry* Southern Cross University, Lismore, NSW 2480 Australia E-mail: [email protected]

Barbara Hohn* Friedrich Miescher-Institut, Basel Switzerland E-mail: [email protected]

Yue-ie Hsing Institute of Botany, Academia Sinica, Nankang, Taipei 11529 Taiwan E-mail: [email protected]

Bonnie Hurwitz Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 USA E-mail: [email protected]

Shigeru Iida National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585 Japan E-mail: [email protected]

Takeshi Itoh National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan E-mail: [email protected]

XXIV Contributors

Anjali S. Iyer-Pascuzzi Department of Plant Breeding and Genetics, Cornell University Ithaca, NY 14853 USA E-mail: [email protected]

Scott Jackson Department of Agronomy, Purdue University, West Lafayette, IN 47907 USA E-mail: [email protected]

Alexander A.T. Johnson Australian Centre For Plant Functional Genomics PMB 1, Glen Osmond, South Australia 5064 Australia E-mail: [email protected]

Yasuyo Johzuka-Hisatomi National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585 Japan E-mail: [email protected]

Shoshi Kikuchi Laboratory of Gene Expression Department of Genetics, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602 Japan E-mail: [email protected]

HyeRan Kim Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721 USA E-mail: [email protected]

Setsuko Komatsu Laboratory of Gene Regulation, Department of Molecular Genetics, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan E-mail: [email protected]

Contributors XXV

Dave Kudrna Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721 USA E-mail: [email protected]

Chellian Santhosh Kumar Department of Plant Sciences, Life Sciences Addition 1002 University of California– Davis, Davis, CA 95616 USA E-mail: [email protected]

Evans Lagudah* Genetic Engineering for Crop Improvement Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Phil Larkin* Genetic Engineering for Crop Improvement Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Alain Lecharny * Bioinformatics Group, Institut National de la Recherche Agronomique (INRA)/CNRS—URGV, Evry cedex CP5708, 91057 France E-mail: [email protected]

Hei Leung International Rice Research Institute, Los Baños, Metro Manila Philippines E-mail: [email protected]

Lei Li Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA E-mail: [email protected] XXVI Contributors

Meizhong Luo Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721 USA E-mail: [email protected]

Jianxin Ma Department of Agronomy, Purdue University, West Lafayette, IN 47907 USA E-mail: [email protected]

David Mackill International Rice Research Institute, Los Baños, Metro Manila Philippines E-mail:[email protected]

Matsuoka Makato Laboratory of Plant Molecular Breeding, Development and Applied Division, Bioscience and Biotechnology Center, Nagoya University, Furocho, Chikusa-ku, Nagoya-shi, Aichi 464-8601 Japan E-mail: [email protected]

Takashi Matsumoto National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan E-mail: [email protected]

Susan R. McCouch Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA E-mail: [email protected]

Kenneth McNally International Rice Research Institute, Los Baños, Metro Manila Philippines E-mail: [email protected]

Contributors XXVII

Will Nelson Arizona Genomics Computational Laboratory, University of Arizona, Tucson, AZ 85721 USA E-mail: [email protected]

Oliver Panaud Laboratoire Genome et Developpement des Plantes, UMR 5096 CNRS-IRD-UP, University of Perpignan, Perpignan FR-66860 France E-mail: [email protected]

Andy Pereira Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061 USA E-mail: [email protected]

Christophe Perin AMIS Department, UMR PIA 1096, CIRAD, Montpellier, Hérault F-34398 France E-mail: [email protected]

Benoit Piég u Laboratoire Genome et Developpement des Plantes, UMR 5096 CNRS-IRD-UP, University of Perpignan, Perpignan 66860 France E-mail: [email protected]

Tony Pryor* Genetic Engineering for Crop Improvement Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Fulin Qiu International Rice Research Institute, Los Baños, Metro Manila Philippines E-mail: [email protected]

XXVIII Contributors

Chitra Raghavan International Rice Research Institute, Los Baños, Metro Manila Philippines E-mail: [email protected]

Srinivasan Ramachandran Rice Functional Genomics Group, Tamasek Lifesciences Laboratory 1, Research Link, National University of Singapore, Singapore 117 604 E-mail: [email protected]

Ute Roessner Australian Centre for Plant Functional Genomics, School of Botany, The University of Melbourne, Parkville, Victoria 3010 Australia E-mail: [email protected]

Paul Roffey School of Wine and Food Sciences, Charles Sturt University Wagga Wagga, NSW 2678 Australia E-mail: [email protected]

Jé rome Salse Institut National de la Recherche Agronomique (INRA) UMR ASP Clermont-Ferrand 66860 France E-mail: [email protected]

Phillip SanMiguel Department of Agronomy and Genomics Core Facility, Purdue University, West Lafayette, IN 47907 USA E-mail: [email protected]

Neelamraju Sarala Directorate of Rice Research, Rajendranagar, Hyderabad, AP 500 030 India E-mail: [email protected]

Contributors XXIX

Takuji Sasaki National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan E-mail: [email protected]

Cari Soderlund Arizona Genomics Computational Laboratory, University of Arizona, Tucson, AZ 85721 USA E-mail: [email protected]

Lincoln Stein Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 USA E-mail: [email protected]

Venkatesan Sundaresan Department of Plant Sciences, Life Sciences Addition 1002 University of California– Davis, Davis, CA 95616 USA E-mail: [email protected]

Megan T. Sweeney Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA E-mail: [email protected]

Satoshi Tabata* The Department of Plant Gene Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan E-mail: [email protected]

Lee Tarpley Texas A&M Agricultural Research and Extension Center, Beaumont, TX 77713 USA E-mail: [email protected]

XXX Contributors

Rie Terada National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585 Japan E-mail: [email protected]

Mark Tester Australian Centre for Plant Functional Genomics, PMB1, Glen Osmond, South Australia 5064 Australia E-mail: [email protected]

Brad Till Seattle TILLING Project, Department of Biology and FHCRC, University of Washington, Seattle, WA 98195 USA E-mail: [email protected]

Narayana M. Upadhyaya Genomics and Plant Development Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Guo-Liang Wang Department of Plant Pathology, Ohio State University, Columbus, OH 43210 USA E-mail: [email protected]

Hehe Wang International Rice Research Institute, Los Baños, Metro Manila Philippines E-mail: [email protected]

Ming-Bo Wang Genomics and Plant Development Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Contributors XXXI

Doreen Ware USDA-ARS, North Atlantic Area (NAA) Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY 14853 USA E-mail: [email protected]

Peter M. Waterhouse Genomics and Plant Development Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

John M. Watson Genomics and Plant Development Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Charles White* CNRS UMR6547, Université Blaise Pascal, Aubière 63177 France E-mail: [email protected]

Iain Wilson* Genomics and Plant Development Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Rod A. Wing Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721 USA E-mail: [email protected]

Changyin Wu National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070 China E-mail: [email protected]

XXXII Contributors

Jianli Wu International Rice Research Institute, Los Baños, Metro Manila Philippines E-mail: [email protected]

Ray Wu Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA E-mail: [email protected]

Yukiko Yamazaki National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540 Japan E-mail: [email protected]

Masahiro Yano Applied Genomics Laboratory, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan E-mail: [email protected]

Immanuel Yap Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA E-mail: [email protected]

Su-May Yu Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529 Taiwan E-mail: [email protected]

Yeisoo Yu Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721 USA E-mail: [email protected]

Contributors XXXIII

Qian-Hao Zhu Genomics and Plant Development Program, CSIRO Plant Industry, Canberra, ACT 2601 Australia E-mail: [email protected]

Andrea Zuccolo Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721 USA E-mail: [email protected]

* Contributed as reviewers of one or more Chapters