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.
References
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.
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