Life science projects in Japan
Former name: Genome, post genome projects in Japan
| Rice Genome Research Project | |
| Project Name | Rice Genome Research Project |
| Start Year | 1991 |
| End Year | 2004 |
| Implementing Period | 1991-2004 (Phase 1: 1991-1997, Phase 2: 1998-2004), Green Technology Project (2005-2006), Comprehensive implementation of agricultural genome research (2007), New genome project for agricultural expansion (2008-2011) |
| Budget Amount | 44.16 billion yen (1992-2008) |
| Major Researchers | Chief Researcher: Takuji Sasaki (National Institute of Agrobiological Sciences) Other Leading Researchers: Takashi Matsumoto, Akio Miyao, Masahiro Yano and Yoshiaki Nagamura (all National Institute of Agrobiological Sciences) Major Research Institute: National Institute of Agrobiological Sciences |
| Summary | Elucidation of mechanism of expression of toxicity at the genomic level by gene-expression analysis |
| Major Features of Project | * Phase 1 of Rice Genome Research Project (1991-1997) Rice Genome Research Program (RGP), a joint collaboration between the National Institute of Agrobiological Sciences (NIAS) and the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), succeeded in establishing a high-density linkage map, aligning YAC clones, and partially sequencing the rice genome. The RGP successfully established a high-density linkage map of rice with more than 3000 DNA markers accurately positioned in the genome and subsequently used these markers to align DNA fragments cloned in yeast artificial chromosome (YAC) thereby reproducing more than 60% of the rice genome. Moreover, the partial nucleotide sequences of about 20,000 different genes, which were actually expressed in rice, were also clarified. * Phase 2 of Rice Genome Research Project (1998-2004) The genome sequence of the japonica cultivar Nipponbare was completed by the International Rice Genome Sequencing Project (IRGSP) in December 2004, and the results were published in the August 11, 2005 issue of Nature. The RGP took charge of sequencing a total of 6 out of 12 chromosomes corresponding to about 55% of all DNA letters in the genome. ( http://rgp.dna.affrc.go.jp/E/Foreword.html ) * After "Rice Genome Research Project" The following 3 research issues have started in Green Technology Project (2005-2006) (). - "Comparative genomics for understanding the diversity of cereal crops" - "Genetic and molecular dissection of quantitative traits in rice" - "Development and demonstration of crop genomic breeding technology" After that, "Comprehensive implementation of agricultural genome research" (2007) () and "New genome project for agricultural expansion" (2008-2011) () succeeded to "Rice Genome Research Project". Although a tentative milestone of complete rice genome sequence has been achieved in fiscal year 2004, the ongoing budget provides for commercial application studies. As for acquired data, many databases have been created for specific purposes in various projects, but these databases have not been organized and made available at a single site. Such data, along with other types of data, are in the process of being integrated into the Agriculture, Forestry and Fisheries-related Genomic Information Integrated Database. |
| Description of Project | Excerpts from "RGP Foreword"( http://rgp.dna.affrc.go.jp/E/Foreword.html ): In Japan, the Ministry of Agriculture, Forestry and Fisheries (MAFF) embarked on a large-scale project on rice genome analysis in 1991. As this project was expected to have participation by leading rice researchers in Japan, and would require a lot of resources and manpower, a joint collaboration between the National Institute of Agrobiological Sciences (NIAS) and the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF) was formed to undertake this enormous task. This research team has been referred to as the Rice Genome Research Program or RGP. During the first phase of the project from 1991 to 1997, RGP has successfully established a high-density linkage map of rice with more than 3000 DNA markers accurately positioned in the genome and subsequently used these markers to align DNA fragments cloned in yeast artificial chromosome (YAC) thereby reproducing more than 60% of the rice genome. Moreover, the partial nucleotide sequences of about 20,000 different genes, which were actually expressed in rice, were also clarified. Building on the success of the first phase of the RGP, the MAFF launched two new large-scale projects in 1998 to accelerate the effort to reach the goal of completely unraveling the genetic phenomenon of rice. These projects focused on complete rice genome sequencing and functional characterization of the genome based on the complete sequence. The project on functional genome characterization comprised many sub-areas tackled mainly by the NIAS and by researchers from various universities and other research institutes in Japan. The RGP also collaborated in several sub-areas of this project to achieve the target goals. On the other hand, only the RGP was engaged in the genome sequencing project, but a consortium of laboratories in 10 countries, which participated in the International Rice Genome Sequencing Project (IRGSP), collaborated in sequencing the 12 chromosomes. The RGP took charge of sequencing a total of 6 chromosomes corresponding to about 55% of all DNA letters in the genome. The genome sequence of the japonica cultivar Nipponbare was completed by the IRGSP in December 2004 and the results were published in the August 11, 2005 issue of Nature. The RGP ably fulfilled the responsibilities as the core of the IRGSP, and significantly contributed to establish Japan as a global leader in the rice genome research. |
| Public Release Status | As soon as each BAC sequencing was completed, the corresponding rice genome information has been released. The whole genome sequence is also available. |
| Classification of Database Public Release Status | Shared |
| Public Database | - Whole rice genome sequence IRGSP 4.0 ( http://rgp.dna.affrc.go.jp/J/IRGSP/Build4/build4.html ) - Rice genome annotation database (WhoGA) ( http://rgp.dna.affrc.go.jp/whoga/index.html.en ) - Rice genome map integrated database (INE) (Service is currently suspended. Contents were transferred to WhoGA.) - Current Genome Sequencing Status( http://rgp.dna.affrc.go.jp/cgi-bin/statusdb/status.pl ) - Mutant Panel Database (http://tos.nias.affrc.go.jp/~miyao/pub/tos17/ , Japanese) - Rice Annotation Project Database (RAP-DB) ( http://rapdb.dna.affrc.go.jp/ ) - Full-length rice cDNA database ( http://cdna01.dna.affrc.go.jp/cDNA/ ) - Rice Expression Database (RED) ( http://red.dna.affrc.go.jp/RED/ ) - Search Database for cis-element Motif (PLACE) ( http://www.dna.affrc.go.jp/PLACE/ ) - Rice Genome Automated Annotation System (Rice GAAS) ( http://ricegaas.dna.affrc.go.jp/ ) - Rice Proteome Database (RPD) ( http://gene64.dna.affrc.go.jp/RPD/main_en.html ) - Rice Mitochondrial Genome Information (RMG) ( http://rmg.rice.dna.affrc.go.jp/ ) - Blast Search (Kasalath BAC-end Sequence) website ( http://rgp.dna.affrc.go.jp/blast/runblast.html ) - Rice Protein Structural Database (RPSD) ( http://structure.rice.dna.affrc.go.jp/ , Japanese) - "Agri-Genome (Rice)" Rice Genome Analysis Research Related Database( http://www.nias.affrc.go.jp/project/inegenome/database_list.html ) |
| Data Download Site | - RAP-DB( http://rapdb.dna.affrc.go.jp/rapdownload/ ) - WhoGA(Rice) ( http://rgp.dna.affrc.go.jp/whoga/download.html.ja ) - KOME ( ftp://cdna01.dna.affrc.go.jp/pub/data/ ) |
| Website | - Agri-Genome (Rice) Project webpage ( http://www.nias.affrc.go.jp/project/inegenome/index.html , Japanese) - Rice Genome Research Program ( http://rgp.dna.affrc.go.jp/E/ ) |
| Implementing Ministry/Agency | Ministry of Agriculture, Forestry and Fisheries (MAFF) |
| Commercialization Re | NA |
| Reports | - Agriculture, Forestry and Fisheries Research Council. "Progress of Rice Genome Sequencing." ( http://www.s.affrc.go.jp/docs/kankoubutu/ine_genome/ine_genome.htm , Japanese) - National Institute of Agrobiological Sciences publications include news, major research achievements, annual report and research materials ( http://www.nias.affrc.go.jp/project/inegenome/gt_seika.html , Japanese) |
| Evaluation Reports | All files and pages are written in Japanese. * 16th Meeting of Expert Panel on Evaluation, Council for Science and Technology Policy: Interim collection of evaluation results of "Functional analysis of rice genome" (idea) ( http://www8.cao.go.jp/cstp/tyousakai/hyouka/haihu16/siryo4.pdf ) * 17th Meeting of Expert Panel on Evaluation, Council for Science and Technology Policy: "Functional analysis of rice genome" evaluation report (idea) - http://www8.cao.go.jp/cstp/tyousakai/hyouka/haihu17/siryo1-4.pdf - http://www8.cao.go.jp/cstp/tyousakai/hyouka/haihu17/sanko1-4-1.pdf - http://www8.cao.go.jp/cstp/tyousakai/hyouka/haihu17/sanko1-4-2.pdf - http://www8.cao.go.jp/cstp/tyousakai/hyouka/haihu17/sanko1-4-3.pdf - http://www8.cao.go.jp/cstp/tyousakai/hyouka/haihu17/sanko1-4-4.pdf - http://www8.cao.go.jp/cstp/tyousakai/hyouka/haihu17/sanko1-4-5.pdf * 36th Meeting of Expert Panel on Evaluation, Council for Science and Technology Policy: About "Functional analysis of rice genome" - http://www8.cao.go.jp/cstp/output/iken021225_4.pdf - http://www8.cao.go.jp/cstp/siryo/haihu23/sanko3-4-1.pdf - http://www8.cao.go.jp/cstp/siryo/haihu23/sanko3-4-2.pdf - http://www8.cao.go.jp/cstp/siryo/haihu23/sanko3-4-3.pdf - http://www8.cao.go.jp/cstp/siryo/haihu23/sanko3-4-4.pdf - http://www8.cao.go.jp/cstp/siryo/haihu23/sanko3-4-5.pdf * Agenda of 78th Meeting of Expert Panel on Evaluation, Council for Science and Technology Policy ( http://www8.cao.go.jp/cstp/tyousakai/hyouka/haihu78/haihu-si78.html ) * Agenda of 79th Meeting of Expert Panel on Evaluation, Council for Science and Technology Policy ( http://www8.cao.go.jp/cstp/tyousakai/hyouka/haihu79/haihu-si79.html ) - Post evaluation result of "Functional analysis of rice genome" (idea)( http://www8.cao.go.jp/cstp/tyousakai/hyouka/haihu79/siryo2.pdf ) |
| Other Literatures | - List of rice genome related publications ( http://rgp.dna.affrc.go.jp/E/rgp/publicationlist/publist.html ) - List of achievements from Agri-Genome (Rice) Project ( http://www.nias.affrc.go.jp/project/inegenome/gt_seika.html , Japanese) - "Footprints of the International Rice Genome Sequencing Project (IRGSP)." Protein, Nucleic Acid and Enzyme Vol.48 No.5. "Introduction to Projects in Rice Genome Functional Analysis-Related Fields." Protein, Nucleic Acid and Enzyme Vol.48 No.5. - International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 436, 793-800 (2005). - "Genome Resource and Information Resource Generated from Rice Genome Research." Saibo Kogaku Vol.26 No.11. - "New Developments in Plant and Life Sciences by Complete Rice Genome Sequence." Jikken Igaku Vol.21 No.12. "Plant Genomic Research Protocol." Saibo Kogaku (supplementary volume) - Plant Cell Engineering Series 14. - "Rice Genome as Seen from Its Retroelements." Protein, Nucleic Acid and Enzyme Vol.50 No.3. - Rice Genome Research in Japan as a Frontrunner in Crop Genomics. Sci Technol Jpn Vol.18 No.71. - "Draft Rice Genome Sequence." Chemistry Today July 2002, No.376. "MAFF DNA Bank." Protein, Nucleic Acid and Enzyme Vol.44 No.1. - "Evolution of Rice Genome Project." Radioisotopes No.253. - "Evaluation of Nationally-Important Research and Development Projects Implemented by Council for Science and Technology Policy (2002): Rice Genome Functional Analysis Research" - "Reading Rice Genome Information, 2001." |