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Rice Genetics IV Edited by G.S. Khush, D.S. Brar, and B. Hardy 2001 Science Publishers, Inc. CIP data will be provided on request. SCIENCE PUBLISHERS, INC. Post Office Box 699 Enfield, New Hampshire 03784 United States of America Internet site: http://www.scipub.net [email protected] (marketing department) [email protected] (editorial department) [email protected] (for all other enquiries) ISBN 1-57808-167-X © 2001 International Rice Research Institute Suggested citation: Khush GS, Brar DS, Hardy B, editors. 2001. Rice genetics IV. Proceedings of the Fourth International Rice Genetics Symposium, 22-27 October 2000, Los Baños, Philippines. Enfield, NH (USA). Science Publishers, Inc., and Los Baños (Philippines): International Rice Research Institute. 488 p. Cover design: Juan Lazaro IV Page makeup and composition: Mayanne A Wensceslao Cover: A dense molecular genetic map; BAC, YAC, PAC, and EST libraries; and genomic sequences have become key resources for functional genomics of rice (figure above courtesy of M. Yano). Microarray is another new technology for understanding gene expression for complex traits. The gene expression pattern is shown on a glass slide after hybridization with fluorescently labeled probes derived from rice plants under salts stress (photo below courtesy of H. Bohnert). Published by Science Publishers, Inc., Enfield, NH, USA. Printed in India Contents FOREWORD vii ACKNOWLEDGMENTS viii OPENING ADDRESS ix W.G. Padolina Overview Rice genetics from Mendel to functional genomics 3 G.S. Khush and D.S. Brar Application of Mendelian genetics in rice breeding 27 J.N. Rutger and D.J. Mackill The Rockefeller Foundation’s International 39 Program on Rice Biotechnology J.C. O’Toole, G.H. Toenniessen, T. Murashige, R.R. Harris, and R.W. Herdt Molecular markers, genetic diversity, and evolution Evolution and domestication of rice 63 H. Morishima Rice: a central genome for the genetics of all cereals 79 M. Gale, G. Moore, and K. Devos Phylogeny of the genus Oryza as revealed by molecular approaches 89 Song Ge, Tao Sang, Bao-Rong Lu, and De-Yuan Hong Miniature inverted repeat transposable elements help 107 create genomic diversity in maize and rice S.R. Wessler, A. Nagel, and A. Casa Microsatellite markers in rice: abundance, 117 diversity, and applications S.R. McCouch, S. Temnykh, A. Lukashova, J. Coburn, G. DeClerck, S. Cartinhour, S. Harrington, M. Thomson, E. Septiningsih, M. Semon, P. Moncada, and Jiming Li Molecular mapping and marker-assisted selection 137 for major-gene traits in rice D.J. Mackill and Junjian Ni iii QTL mapping in rice: a few critical considerations 153 Zhi-Kang Li Genetic and molecular basis of heterosis in rice 173 Qifa Zhang, Jinping Hua, Sibin Yu, Lizhong Xiong, and Caiguo Xu Structural and functional genomics The International Rice Genome Sequencing Project: 189 progress and prospects T. Sasaki, T. Matsumoto, T. Baba, K. Yamamoto, J. Wu, Y. Katayose, and K. Sakata Strategies and techniques for finishing genomic sequence 197 M. de la Bastide, D. Johnson, V. Balija, and W.R. McCombie Sequence-tagged connector/DNA fingerprint framework 215 for rice genome sequencing R.A. Wing, Yeisoo Yu, G. Presting, D. Frisch, T. Wood, Sung-Sick Woo, M. Arief Budiman, Long Mao, Hye Ran Kim, T. Rambo, E. Fang, B. Blackmon, J.L. Goicoechea, S. Higingbottom, M. Sasinowski, J. Tomkins, R.A. Dean, C. Soderlund, W.R. McCombie, R. Martienssen, M. de la Bastide, R. Wilson, and D. Johnson Naturally occurring allelic variations as a new resource 227 for functional genomics in rice M. Yano Deletion mutants for functional genomics: progress 239 in phenotyping, sequence assignment, and database development H. Leung, C. Wu, M. Baraoidan, A. Bordeos, M. Ramos, S. Madamba, P. Cabauatan, C. Vera Cruz, A. Portugal, G. Reyes, R. Bruskiewich, G. McLaren, R. Lafitte, G. Gregorio, 239J. Bennett, D. Brar, G. Khush, P. Schnable, G. Wang, and J. Leach Generation of T-DNA insertional tagging lines in rice 253 Gynheung An, Jong-Seong Jeon, Sichul Lee, Ki-Hong Jung, Sung-Hoon Jun, Dong-Hoon Jeong, Jinwon Lee, Seonghoe Jang, Shin-Young Lee, Kiyoung Yang, Byoungho Lee, Sinok Moon, Kyungsook An, Min-Jung Han, Jung-Hwa Yu, Namok Lee, Su-Young An, Sun-Hee Park, Eun-Sik Song, In-Soon Park, and Hyun-Sook Lee Transposons and functional genomics in rice 263 R. Greco, P.B.F. Ouwerkerk, C. Sallaud, A. Kohli, C. Favalli, T. Beguiristain, L. Colombo, E. Pè, P. Puigdomènech, E. Guiderdoni, P. Christou, J.H.C. Hoge, and A. Pereira iv Retrotransposons of rice as a tool for the functional 279 analysis of genes H. Hirochika, A. Mayo, M. Yamazaki, S. Takeda, K. Abe, R. Hirochika, G.K. Agrawal, T. Watanabe, K. Sugimoto, T. Sasaki, K. Murata, K. Tanaka, K. Onosato, A. Miyazaki, Y. Yamashita, and N. Kojima Bioinformatics and the rice genome 293 B.A. Antonio, K. Sakata, and T. Sasaki Gene isolation and function Enhancing deployment of genes for blast resistance: 309 opportunities from cloning a resistance gene/avirulence gene pair B. Valent, G.T. Bryan, Y. Jia, L. Farrall, S.A. McAdams, K.N. Faulk, and M. Levy Molecular signaling in disease resistance of rice 323 K. Shimamoto, A. Takahashi, and T. Kawasaki Structure, function, and evolution of disease 335 resistance genes in rice Guo-Liang Wang, Hei Leung, and P. Ronald Isolation of candidate genes for tolerance of abiotic stresses 345 H.J. Bohnert, S. Kawasaki, C.B. Michalowski, Hong Wang, N. Ozturk, M. Deyholos, and D. Galbraith Molecular dissection of cell death in rice 365 H. Uchimiya, M. Kawai, M. Yamaguchi, and M. Umeda Molecular tools for achieving synthetic apomixis in hybrid rice 377 J. Bennett, X.-Z. Bi, A. Kathiresan, and G.S. Khush Transformation Engineering for virus resistance in rice 405 N.M. Upadhyaya, Z. Li, M-B. Wang, S. Chen, Z-X. Gong, and P.M. Waterhouse Transgenic approaches for generating rice tolerant 423 of dehydration stress Z.Q. Cheng, J. Targolli, J. Su, C.K. He, F. Li, and R. Wu High-level expression of C4 photosynthetic genes 439 in transgenic rice M. Matsuoka, H. Fukayama, M.S.B. Ku, and M. Miyao Transgene integration, organization, and expression 449 in cereals P. Christou, R.M. Twyman, Xiangdong Fu, E. Wegel, A. Kohli, and E. Stoger v Gene silencing and its reactivation in transgenic rice 465 T.C. Hall, S.P. Kumpatla, P. Kharb, L. Iyer, M. Cervera, Y. Jiang, T. Wang, G. Yang, P. Teerawanichpan, J. Narangajavana, and J. Dong Workshop reports Rice molecular breeding workshop 484 Functional genomics workshop 485 Bioinformatics workshop 487 RICE GENETICS COOPERATIVE 488 vi Foreword This is the Fourth International Rice Genetics Symposium in the series of symposia held at IRRI every five years. The first, held in 1985, led to the birth of the Rice Genetics Cooperative (RGC). The RGC took the lead in organizing these symposia and greatly enhanced international collaboration. In the same year, the Rockefeller Foundation established its International Program on Rice Biotechnology, which has played a major role in advancing frontiers of knowledge on cellular and molecular genetics of rice, international collaboration, and human resource development. In the second symposium, a unified system of numbering rice chromosomes and linkage groups was adopted. The orientation of classical and molecular maps was one of the many highlights of the third symposium. The fourth symposium brought together 520 rice scientists from 32 countries and provided an excellent forum for scientists from developed and developing countries to share information on the latest advances in rice science and to develop collaborative research arrangements. The symposium featured 31 plenary lectures in seven sessions, 130 contributory papers in six concurrent sessions, and 240 poster presentations on different aspects of rice genetics. World famous geneticists delivered plenary lectures covering a wide range of topics from classical genetics to the most advanced research on sequencing of the rice genome and functional genomics. Various sessions provided an important forum for reviewing the latest advances in rice research and for in-depth discussion and exchange of information on classical genetics, biosystematics and evolution, molecular markers, transformation, genome organization, gene isolation, regulation of gene expression, sequencing of the rice genome, and bioinformatics. Also during the symposium, three workshops were held on molecular breeding, functional genomics, and bioinformatics. These workshops led to initiatives among the national agricultural research and extension systems to join the international pro- gram in these three areas. I am pleased to see that the plenary lectures have been published in this book. The concurrent and poster presentations will be published in a supplementary volume. I would like to thank the organizing committee and other colleagues at IRRI who have devoted a great deal of time to organizing this symposium. IRRI would espe- cially like to acknowledge the Rockefeller Foundation for its financial support for this symposium. RONALD P. CANTRELL Director General International Rice Research Institute vii Acknowledgments We would like to thank the following members of the organizing committee for the Fourth International Rice Genetics Symposium: John Bennett, Swapan Datta, Mike Jackson, Zhikang Li, and Hei Leung. We would also like to give special thanks to Ronald P. Cantrell, Ren Wang, and William Padolina for their scientific and financial support. Financial support provided by the Rockefeller Foundation is gratefully ac- knowledged. Thanks are due to Ike Navarro for logistics support. We also thank Yollie Aranguren, Elma Nicolas, Emily Alcantara, and George Reyes for secretarial help and processing of the manuscripts. We appreciate the valuable services provided by different teams in the following areas: Communication and Publications Services, Food and Housing Services, Visitors, Exhibition, and Conference Services, Physical Plant Services, and a secretarial pool. viii Opening address W.G. Padolina Rice is the principal food of nearly half of the world’s people and more than 90% of the crop is grown in developing countries, where food supply is an acute problem.
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  • Diversity in the Oryza Genus Duncan a Vaughan�, H Morishimay and K Kadowaki

    Diversity in the Oryza Genus Duncan a Vaughan, H Morishimay and K Kadowaki

    139 Diversity in the Oryza genus Duncan A VaughanÃ, H Morishimay and K Kadowakià The pan-tropical wild relatives of rice grow in a wide variety of however, that the characters that define the Oryza genus habitats: forests, savanna, mountainsides, rivers and lakes. The were clarified [2,3]. The principle morphological charac- completion of the sequencing of the rice nuclear and cytoplasmic teristics of the genus include rudimentary sterile lemmas, genomes affords an opportunity to widen our understanding of the bisexual spikelets, and narrow, linear, herbaceous leaves genomes of the genus Oryza. Research on the Oryza genus has with scabrous margins. begun to help to answer questions related to domestication, speciation, polyploidy and ecological adaptation that cannot be The basic nomenclature of Oryza species has changed little answered by studying rice alone. The wild relatives of rice have since the 1960s (for review see [4]). Tateoka [5] analyzed furnishedgenes for the hybrid rice revolution, and other genes from species across the whole genus on the basis of studies Oryza species with major impact on rice yields and sustainable rice carried out in the world’s main herbaria and in the field production are likely to be found. Care is needed, however, when in Asia and Africa. His work clarified the basic groups of using wild relatives of rice in experiments and in interpreting the species within the genus, and he called these groups results of these experiments. Careful checking of species identity, species complexes (Table 1). Since the 1960s, four new maintenance of herbarium specimens and recording of genebank Oryza species have been described, O.