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 Printed on acid-free paper. © 2007 Springer Science+Business Media, LLC All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. 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 laborato- ries, 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 popu- lation 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 ce- real 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 con- clusion 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 chap- ters. 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