Rice Genetics Newsletter, Vol. 20

Rgn20

1.	Oryzabase (Integrated Rice Database) in 2004
	Y. YAMAZAKI, Y. NAGATO¹, N. KURATA National Institute of Genetics, Mishima, 411-8540 Japan 1) Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan

Oryzabase was developed in 2000 under the management of rice genetic resources committee (under MEXT; the Ministry of Education, Culture, Sports, Science and Technology in Japan) as one of the extensions of Rice Genetic Resource Database established in 1996. Its main feature was having integrated genetic maps and mutant images (Yamazaki et al. 2000) together with genetic resources information. The most recent (ver.3.0) of many versions (Yamazaki et al. 2003a, 2003b) of Oryzabase includes (1) genetic resources including wild rice collections and collections treated in the national bioresource project, (2) genomic information with genetic and physical maps, (3) genes with their ontology, (4) developmental stages and specific gene expression in them, (5) mutant collections relating to resources, (6) rice basic information, and (7) worldwide rice related information.

Oryzabase is available online at http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp.

In 2003, the contents of Oryzabase have been advanced and added with new items shown below.

1. Resource order system

The National BioResource Project (NBRP) started in 2002 and all resources developed by the project were made available for users. Oryzabase implemented a resource order system by which the user can send request e-mail automatically to the resource center by clicking the request button at the desired accession on the screen. Users should send a MTA (material transfer agreement) form by postal mail later and the resource center will send the requested material to users after receiving the MTA. It is projected that, by the end of the first half of the project, 2007, more than twenty thousand accessions including wild rice, landraces, MNUinduced mutants and chromosome fragments substitution lines between O. sativa and other AA species, will be available and the information will be incorporated into the database.

2. Genomic information

Oryzabase ver. 3.0 incorporates genomic sequences and gene information of chromosome 1 and 10 available in the public data provided by DDBJ/EMBL/GenBank and IRGSP (the International Rice Genome Sequencing Project).

3. Developmental stages of organs accompanied with gene expression profiles

The information of characterized developmental stages is partially available in the latest version of Oryzabase. For each organ (embryo, leaf, panicle, spikelet, stamen, ovule), their anatomical data (histological observation with tissue sections, SEM; scanning electron microscope images), gene expression data from in situ hybridization experiments, mutants and Ds-GUS enhancer trap lines are assigned respectively to its corresponding stages (Kurata et al. 2003). A Web-based data submission system was also developed and newly submitted data will automatically be incorporated into the Oryzabase.

4. Plant Ontology

There are several different systems to describe plant traits, phenotypic characters and developmental stages depending upon their purposes. Although Counce et al. (Counce et al. 2000) proposed a uniform system for expressing rice development in order to communicate among different projects, it is insufficient to classify some of the data in Oryzabase. Oryzabase proposes a new plant ontology that consists of 3 basic parts; Time (growth and/or developmental stages), Location (organs) and Character (morphological and/or biochemical characteristics). Each part is divided into elements based on discrete criteria and each element assigns a characteristic code. All events and phenotypic characters can be expressed by combining the code variously. Characteristic features of this system are its flexibility and simplicity for operation by computer users. It is, however, not easy for researchers to understand and use. So Oryzabase also provides a plant ontology viewer that enables users to understand its concept by operating it.

5. Comparative studies among different organisms

Resources for comparative analysis among different organisms were added to Oryzabase.

(1) GOALL is a viewer of gene ontology and it is accessible from Oryzabase (Ref.2). By using the new function of GOALL, all genes between two organisms can be compared. For example, genes that commonly exist in two organisms or genes that exist only in one organism but not in the other can be retrieved at once.

(2) Comparative maps are now available from Oryzabase. Barley and wheat EST clones that have sequences homologous to rice clones are displayed together into the rice linkage maps, so that researchers can easily find the corresponding clones of other plant species.

Reconstruction and data accumulation will be successively made in coming years.

Reference

Counce, P.A., Keisling, T.C. and Mitchell, A.J. 2000. A uniform, objective, and adaptive system for expressing rice development. Crop Sci. 40: 436-443.

Kurata, N., Nagato, Y., Ito, J-I. Kohara, M., Ikeda, K., Yamaki, T., Kitano, H., Ito, Y., Miyoshi, K., Nonomura, K. and Yamazaki, Y. 2003. A database for rice organ development with cell and gene markers, integrated in the Oryzabase. Plant & Animal Genome XI Abstract p297.

Yamazaki, Y., Yoshimura, A., Nagato, Y. and Kurata, N. 2000. Oryzabase-Integrated map and mutant database-. Plant & Animal Genome VIII Abstract p54.

Yamazaki, Y., Yoshimura, A., Nagato, Y. and Kurata, N. 2002. Recent advances in Oryzabase (integrated rice database). Rice Genetic Newsletters 19: 7-9.

Yamazaki, Y., Yamakawa, T., Ueno, S., Yoshimura, A., Nagato, Y. and Kurata, N. 2003. Oryzabase -integrated rice science database-. Plant & Animal Genome XI Abstract p289.