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■ Beginnings of the Microarray Project
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The year 2000 was highly notable for the subject of genome structural analyses. On June 26th, it was announced that the structural analysis of the human genome had been essentially completed. Also on 14th of December it was announced that the structural analysis of the genome of a higher plant, Arabidopsis thaliana, had been completed. Now it appears that the focus of genome research will change from structural analysis to an analysis of function. The rice genome project began in Japan in1991, and this first research stage lasted for 7 years until 1997. The foundations of the rice genome research project were obtained using three techniques. 1. The RFLP technique was used to develop the high-density genome sequencing map; 2. Large amounts of cDNA clonal analysis was done, and 3. YAC was used for assigning onto physical maps.
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■ Beginning the Microarray Project
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The second stage of the rice genome project began in 1998. This is based on the results accumulated during the first research stage. During the second stage, the final goal is not only to determine the complete nucleotide sequence of the genome, but also to elucidate the function of the rice genes. A number of projects were begun to accomplish the latter including "the mutant panel project" utilizing retrotransposon tagged lines, "the map-based cloning project" utilizing chromosomal locations, and "the molecular breeding project" utilizing DNA marker selection. In addition, a new project, "Analysis of gene functions in the rice genome by using the gene expression monitoring technique" (commonly called as "the Microarray project") started in 1999 to identify useful genes by microarray system. Microarray is the powerful tool for understanding comprehensive gene expression at genome-wide level (for details, refer to the Technical Background Section). By using this system, it has become possible to isolate the genes quickly that confer resistances or are responsive to cold temperature, drought, unsuitable soil condition, insect pest and disease, etc.
It has become possible by using this system to begin to quickly isolate the genes that confer such resistance. Also it has become possible to isolate which genes are expressed in particular tissues and organs. In 1999, there were 42 research groups that were taking part in the project. The number had increase to 64 groups in the year 2000. The groups can be divided into those that were responsible for setting up the microarray system for this project (the Microarray Center) and those that utilize the microarray technique to isolate useful genes. The former group consists of two organizations: 1) the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (hereafter referred to as STAFF) which is part of the Corporate Center for the Promotion of Advanced Technology in Agriculture, Forestry and Fisheries, and 2) theLaboratory of Gene Expression in the Department of Molecular Genetics of the National Institute of Agrobiological Resources. The latter group that utilizes microarrays consists of the research laboratories of the Japanese Ministry of Agriculture, Forestry and Fisheries and also, universities, and private companies.
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■ The role of the Microarray Center
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The role of the Microarray Center was to set up the microarray systems for the project members and to contribute services during the projects. The following figure shows the organizational structure. The essential element in the system provided by the center is the contract with Asmersham Pharmacia for providing the MTAP system (Microarray Technology Access Program). At the present time there has been a large amount of cDNA clones isolated and analyzed as EST clones from the initial period of the rice genome project. In addition, other members who are not part of the rice project also use the arrays for the clones of their respective organizations (zinnia, beans, sweet potato, citrus, apples, etc.)
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