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Similarity of gene expression across a wide range of biological conditions can be efficiently used in characterization of gene function. We have constructed a rice gene coexpression database, RiceFREND (http://ricefrend.dna.affrc.go.jp/), to identify gene modules with similar expression profiles and provide a platform for more accurate prediction of gene functions. Coexpression analysis of 27 201 genes was performed against 815 microarray data derived from expression profiling of various organs and tissues at different developmental stages, mature organs throughout the growth from transplanting until harvesting in the field and plant hormone treatment conditions, using a single microarray platform. The database is provided with two search options, namely, 'single guide gene search' and 'multiple guide gene search' to efficiently retrieve information on coexpressed genes. A user-friendly web interface facilitates visualization and interpretation of gene coexpression networks in HyperTree, Cytoscape Web and Graphviz formats. In addition, analysis tools for identification of enriched Gene Ontology terms and cis-elements provide clue for better prediction of biological functions associated with the coexpressed genes. These features allow users to clarify gene functions and gene regulatory networks that could lead to a more thorough understanding of many complex agronomic traits.

Because plant reproductive development occurs only in adult plants, the juvenile-to-adult phase change is an indispensable part of the plant life cycle. We identified two allelic mutants, peter pan syndrome-1 (pps-1) and pps-2, that prolong the juvenile phase in rice (Oryza sativa) and showed that rice PPS is an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC1. The pps-1 mutant exhibits delayed expression of miR156 and miR172 and the suppression of GA biosynthetic genes, reducing the GA(3) content in this mutant. In spite of its prolonged juvenile phase, the pps-1 mutant flowers early, and this is associated with derepression of RAP1B expression in pps-1 plants independently of the Hd1-Hd3a/RFT1 photoperiodic pathway. PPS is strongly expressed in the fourth and fifth leaves, suggesting that it regulates the onset of the adult phase downstream of MORI1 and upstream of miR156 and miR172. Its ability to regulate the vegetative phase change and the time of flowering suggests that rice PPS acquired novel functions during the evolution of rice/monocots.

We describe how rice leaves are regionalized and regulated along the central-marginal axis. The shoot organization2 (sho2) mutant, a weak allele of SHOOTLESS4 that is a ZIPPY/ARGONAUTE7 homolog in rice, shows a variety of leaf abnormalities; filamentous leaves, bi- or trifurcated leaves, separation of the filamentous structure from the leaf blade or deletion of the margin. All of these phenotypes can be interpreted as combinatorial defects in the growth of the central, lateral and marginal domains along the central-marginal axis, on the condition that the growth of the central domain is predominant. The leaf founder cells for the lateral and marginal domains are recruited normally in sho2, indicating that sho2 is defective in the growth of leaf domains after the founder cells are recruited. The expression pattern of SHO2 in the outer layer of the shoot apical meristem and the adaxial surface of the leaf, as well as the altered expression of HD-ZIP III and ETTIN homologs in the central domain of sho2 leaves, suggest that normal development of the central domain is a prerequisite for the synchronous growth of the three domains. This synchrony is thought to be mediated by a small interfering RNA-dependent process.

In order to facilitate the functional analysis of rice genes, we produced about 50,000 insertion lines with the endogenous retrotransposon Tos17. Phenotypes of these lines in the M2 generation were observed in the field and characterized based on 53 phenotype descriptors. Nearly half of the lines showed more than one mutant phenotype. The most frequently observed phenotype was low fertility, followed by dwarfism. Phenotype data with photographs of each line are stored in the Tos17 mutant panel web-based database with a dataset of sequences flanking Tos17 insertion points in the rice genome (http://tos.nias.affrc.go.jp/). This combination of phenotypic and flanking sequence data will stimulate the functional analysis of rice genes.

In higher plants, leaves initiate in constant spatial and temporal patterns. Although the pattern of leaf initiation is a key element of plant shoot architecture, little is known about how the time interval between initiation events, termed plastochron, is regulated. Here, we present a detailed analysis of plastochron2 (pla2), a rice (Oryza sativa) mutant that exhibits shortened plastochron and precocious maturation of leaves during the vegetative phase and ectopic shoot formation during the reproductive phase. The corresponding PLA2 gene is revealed to be an orthologue of terminal ear1, a maize (Zea mays) gene that encodes a MEI2-like RNA binding protein. PLA2 is expressed predominantly in young leaf primordia. We show that PLA2 normally acts to retard the rate of leaf maturation but does so independently of PLA1, which encodes a member of the P450 family. Based on these analyses, we propose a model in which plastochron is determined by signals from immature leaves that act non-cell-autonomously in the shoot apical meristem to inhibit the initiation of new leaves.

New asymmetric conjugate reduction of beta,beta-disubstituted alpha,beta-unsaturated ketones and esters was accomplished with alkoxylhydrosilanes in the presence of chiral rhodium(2,6-bisoxazolinylphenyl) complexes in high yields and high enantioselectivity. (E)-4-Phenyl-3-penten-2-one and (E)-4-phenyl-4-isopropyl-3-penten-2-one were readily reduced at 60 degrees C in 95 % ee and 98 % ee, respectively, by 1 mol % of catalyst loading. (EtO)2MeSiH proved to be the best hydrogen donor of choice. tert-Butyl (E)-beta-methylcinnamate and beta-isopropylcinnamate could also be reduced to the corresponding dihydrocinnamate derivatives up to 98 % ee.