2. The Rice Genome Resource Center as an outlet for distribution of biological materials from the rice genome project

National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

The Rice Genome Research Program (RGP) was initiated in 1991 and evolved seven years later into a second phase with the aim of elucidating the complete sequence of the rice genome. Then, from 1998, several projects focusing on the analysis of genome function were launched to complement the genome sequencing effort. These include studies on map-based cloning, expression profiling, mutant panel development, full-length cDNA library, DNA-marker aided selection, proteome analysis and rice genome simulators. Currently, these projects have yielded significant outputs, which could serve as valuable tools in understanding the structure and function of the rice genome. Foremost among these accomplishments is the completion of the high-quality draft sequence of the entire rice genome by the international sequencing collaboration and the sequencing of chromosome 1 (Sasaki et al., 2002), chromosome 4 (Feng et al., 2002) and chromosome 10 (The Chromosome 10 Sequencing Consortium, 2003) to finished quality level. The rice full-length cDNA project has generated a collection of 28,469 non-redundant sequences representing a comprehensive collection of rice transcriptome (The Rice Full-length cDNA Consortium, 2003). Using the retrotransposon Tos17, a mutant panel of 50,000 lines carrying about 500,000 insertions has been developed as a resource for forward and reverse genetics (Hirochika, 2002; Miyao et al., 2003). Studies on map-based cloning and marker-aided selection have led to the characterization of many quantitative trait loci (QTL) in rice and the development of novel mapping populations that can be directly used for rice breeding programs (Yano and Ebitani, 2002).

These resources must be made available to the scientific community to enable rapid progress in research that will lead to a thorough understanding of the rice plant. With this primary goal, the National Institute of Agrobiological Sciences (NIAS) established the Rice Genome Resource Center (RGRC) on April 1, 2003 to consolidate the distribution of biological materials generated from various projects on rice genomics. The next stage in rice genome research is to focus on determining the function of the 40-60,000 genes predicted in the genome and on applying various genomics tools in rice breeding. An unlimited access to rice DNA and seed stocks will provide a broad community of scientists with the necessary materials for conducting functional and applied genomics research. The genetic stocks currently available for distribution include the rice full-length cDNA clones, insertion mutant lines and plant materials for genetic analysis. Information on these materials and other details for making requests are available through the RGRC website at http://www.rgrc.dna.affrc.go.jp/ (Fig. 1).

A complete list of rice full-length cDNA sequences can be accessed through the database KOME (Knowledge-based Oryza Molecular biological Encyclopedia) at http://cdna01.dna.affrc.go.jp/cDNA/. It also provides functional annotation of each sequenced clone and facilitates various searches through BLAST, accession number, domain name and general key words. The Tos17 insertion mutant lines can be accessed through the Rice Insertion Mutant Database at http://tos.nias.affrc.go.jp/. An in silico screening by BLAST search against flanking sequences from the insertion mutant lines can be made and the results provide links to phenotype data and photographic images. The plant materials for genetic analysis include backcross inbred lines (BIL), double-haploid lines (DHL) and chromosome segment substitution lines (CSSL), derived from various crosses of japonica and indica rice, and characterized using RFLP markers. The genotype data for each population are provided in the RGRC site, and other details about the markers can be accessed through the RGP website (http://rgp.dna.affrc.go.jp/Publicdata.html). We are now accepting requests for these biological materials. Inquiries and suggestions can also be made by e-mail at rgrc@dna.affrc.go.jp.

Even with the completion of the rice genome sequence, there is still a lot of work to be done before a complete knowledge of the biology of the rice plant can be totally elucidated. We hope that the biological materials provided by the RGRC will be useful for formulating new concepts, developing innovative avenues of research, and making new scientific discoveries to achieve this ultimate goal.


Hirochika, H., 2001. Contribution of the Tos17 retrotransposon to rice functional genomics. Curr. Opin. Plant Biol. 4:118-122.

Feng, Q. et al., 2002. Sequence and analysis of rice chromosome 4. Nature 420: 316-320.

Miyao, A. et al., 2003. Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15: 1771-1780.

Sasaki, T. et al., 2002. The genome sequence and structure of rice chromosome 1. Nature 420: 312-316.

The Rice Chromosome 10 Sequencing Consortium, 2003. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300: 1566-1569.

The Rice Full-length cDNA Consortium, 2003. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376-379.

Yano, M. and T. Ebitani. 2002. Development of a series of chromosome segment substitution lines and their utilization in the genetic analysis of quantitative traits in rice. NIAS Annual Report p. 27-28.