Contents -- FOREWORD -- ACKNOWLEDGMENTS -- RICE-A MODEL GENOME FOR CEREAL RESEARCH -- Rice as a reference genome and more R.L. Phillips, W.E. Odland, and A.L. Kahler -- Rice as a reference -- Finding orthologous genes and quantitative trait loci (QTLs) -- Value of rice for cloning genes underlying QTLs -- American wildrice as a case study -- References -- Notes -- The complete rice genome sequence: a gold mine for future rice research T. Sasaki, T. Matsumoto, J. Wu, and N. Namiki -- Overview of the rice genome structure -- Utility of rice genome sequence information -- Conclusions -- References -- Notes -- Annotation of the rice genome Shu Ouyang, Wei Zhu, J. Hamilton, Haining Lin, M. Campbell, Yuandan Lee, R.L. Malek, Aihui Wang, Qiaoping Yuan, B. Haas, J. Wortman, and C.R. Buell -- Construction of a rice transcript assembly -- Repetitive sequences in the rice genome -- TIGR Rice Genome Browser -- Noncoding RNAs -- snoRNAs and snRNAs -- miRNAs -- Transfer RNAs -- Mapping of genetic markers and microsatellite repeats -- SNPs and indel identification between indica and japonica -- Conclusions -- References -- Notes -- STRUCTURAL GENOMICS AND RESOURCES -- The Oryza map alignment project (OMAP): a new resource for comparative genomics studies within Oryza R.A. Wing, H.R. Kim, J.L. Goicoechea, Y. Yu, D. Kudrna, A. Zuccolo, S.S. Ammiraju Jetty, M. Luo, W. Nelson, C. Soderlund, P. San Miguel, N. Gill, J. -- Results -- Development of the OMAP BAC library resource -- Development of wild species FPC/STC physical maps -- BAC end sequencing -- BAC fingerprinting -- Analysis of structural variation between O. sativa and three A genome wild species accessions used in OMAP -- Summary, conclusions, and future research -- References -- Notes.

Analysis of oligo hybridization properties by high-resolution tiling microarrays in rice Xiangfeng Wang, Lei Li, Viktor Stolc, Waraporn Tongprasit, Chen Chen, Jun Wang, Songgang Li, and Xing Wang Deng -- Characteristics of the rice genome and its annotation -- Tiling-path microarray analysis in rice -- Using tiling microarrays to experimentally analyze probe hybridization properties -- Experimental design of the high-resolution rice tiling microarray -- Tiling-array raw data processing workflow -- Mapping tiling-array signals to annotated gene models -- Oligo hybridization properties analysis -- Relationship between GC composition and hybridization strength -- Relationship between oligo melting temperature and hybridization strength -- Impact of oligo repetitiveness on hybridization experiments -- Conclusions and prospects -- References -- Notes -- Tissue culture-induced mutations and overexpression of full-length cDNAs as a tool for functional analysis of rice genes H. Hirochika, A. Miyao, M. Yamazaki, A. Takahashi, G.K. Agrawal, C. Cheng, Y. Yamashita, M. Harada, H. Nakamura, M. Hakata, and -- Forward and reverse genetics using Tos17 -- Forward genetics -- Reverse genetics -- Limitations and future prospects -- References -- Notes -- Analysis of genome sequences from the maternal and paternal parents of an elite rice hybrid Jun Yu, Gane K.-S. Wong, Siqi Liu, Jian Wang, and Huanming Yang -- Rice genome sequences produced through a whole-genome shotgun approach are of high quality -- Preliminary analysis of the PA64S genome assembly -- In search of genes and their variations involved in hybrid vigor -- References -- Notes -- DEVELOPMENTAL BIOLOGY AND GENE REGULATION -- T-DNA tagging for developmental biology G. An, D.-H. Jeong, S. An, and S. Park -- Results -- Generation of activation tagging lines and isolation of tag end sequences.

Distribution of T-DNA insertions -- Distribution of T-DNA insertions into intergenic regions -- Analysis of activation tagging patterns -- Discussion -- Generation of activation tagging lines to provide a wide variety of mutants -- Establishing a database of T-DNA insertion sites for reverse genetics approaches -- More than a quarter of the expressed genes are tagged -- Gene expression in mature leaves is more preferentially enhanced by activation tagging -- References -- Notes -- Novel insights into the genomics of rice root adaptive development C. Périn, J. Rebouillat, A.M.C. Brasileiro, A. Diévart, P. Gantet, J.C. Breitler, A.A.T. Johnson, B. Courtois, N. Ahmadi, M. de Raissac, D. Luquet, M. Conte, D. This, P.K. Pati, Q.H. -- Rice root system organization, morphology, and anatomy -- Rice root morphology -- Comparative radial anatomy of embryonic and postembryonic roots -- Root meristem structure -- Genetic and molecular control of constitutive root development -- Natural genetic variation and QTL mapping of constitutive root developmental traits -- Molecular control -- Plasticity of root architecture -- Natural genetic variation and QTL mapping of adaptive root developmental traits -- Molecular response of root developmental genes to stresses -- Novel tools for investigating root developmental processes -- Gene discovery and HTP gene validation through knockout (KO) analyses -- Two-photon laser scanning microscope -- Catalogue of lines with distinct GAL4:GFP-marked cell types -- Cell-specific ectopic expression and inactivation of genes -- Global expression profiles at a cell-specific resolution -- Conclusions and prospects -- References -- Notes.

Molecular signaling in disease resistance of rice K. Shimamoto, A. Nakashima, M. Fujiwara, N.T. Phuong, L. Chen, H.L. Wong, D. Miki, K. Imai, S. Maisonneuve, H. Takahashi, Y. Kawaguchi, S. Hirai, and T. Kawasaki -- Seven OsRac genes in rice -- Downstream factors of OsRac1 signaling in defense response -- NADPH oxidase (RBOH) -- Metallothionein -- Phytoalexin -- Defense genes -- MAP kinase -- Cinnamoyl-CoA reductase for lignin biosynthesis -- Upstream factors of OsRac1 signaling in defense response -- Heterotrimeric G protein α subunit -- Other upstream factors that are possibly involved in OsRac1-mediated disease resistance in rice -- Emerging technologies for the study of molecular signaling in disease resistance of rice -- Proteomics -- Gene-specific RNA silencing for the functional identification of rice genes -- References -- Notes -- APPLIED GENETICS -- QTLs in rice breeding: examplesfor abiotic stresses D.J. Mackill, B.C.Y. Collard, C.N. Neeraja, R.M. Rodriguez, S. Heuer, and A.M. Ismail -- Development and spread of mega varieties -- Big QTLs versus small QTLs -- A case study of QTL breeding: submergence tolerance -- Using gene markers for QTL introgression -- Implications for breeding for rainfed conditions -- References -- Notes -- Isolation of a QTL gene controlling grain number and QTL pyramidingto combine loci for grain number and plant height in rice M. Ashikari, S. Lin, T. Yamamoto, T. Takashi, A. Nishimura, E.R. Angeles, Q. Qian, H. Kitano, and M. Matsuoka -- QTL analysis -- QTL cloning -- QTL pyramiding -- Toward an application of QTLs for a new green revolution -- References -- Notes -- Genetic and molecular dissection of flowering time in rice M. Yano and T. Izawa -- Genetic analysis of genes controlling heading date -- Varietal variations in heading date and daylength response -- Identification of QTLs for heading date.

Molecular analysis of genes involved in heading date -- Map-based cloning of QTLs -- Cloning of other QTLs -- Naturally occurring allelic variations in genes for PS -- Model of genetic control of heading in rice -- Future prospects -- References -- Notes -- Understanding broad-spectrum durable resistance in rice J.E. Leach, R. Davidson, B. Liu, P. Manosalva, R. Mauleon, G. Carrillo, M. Bruce, J. Stephens, M.G. Diaz, R. Nelson, C. Vera Cruz, and H. Leung -- Genetic materials for dissecting "durable" resistance -- What are the candidate genes? -- Are candidate DR genes associated with disease QTLs? -- The oxalate oxidase gene is a strong candidate for contributing to rice defense responses -- Is expression of OXO candidate genes correlated with increased disease resistance? -- Application of candidate gene-aided selection in breeding -- The whole-genome approach to identify additional candidate genes -- QTL alignment and orthologous genes across cereals -- Conclusions -- References -- Notes -- Identification and transfer of trait-enhancing alleles from wild species S.R. McCouch, M. Sweeney, J. Li, H. Jiang, M. Thomson, E. Septiningsih, P. Moncada, J. Xiao, J. Coburn, E. Fraker, A. Garris, T. Tai, C. Martínez, J. Tohme, M. Sugiono, A. McCl -- Population structure of O. sativa -- Challenges of intraspecific breeding -- Challenges of interspecific breeding -- Population structure of O. rufipogon -- Exploring the genetic potential of wild and exotic germplasm for rice improvement -- Objectives -- Approach -- Materials and methods -- Results -- Identifying genes underlying QTLs for domestication and transgressive variation -- Grain size -- Red pericarp -- References -- Notes -- Genomics-based strategies for the development of "green super rice" Qifa Zhang -- The definition of "green super rice" -- Progress in research toward development of green super rice.

Identifying genes for developing insect-resistant rice.