Embarking on rice functional genomics via cDNA microarray: use of 3' UTR probes for specific gene expression analysis

Because rice is the major source of food for half of the world population, a comprehensive understanding of its genome will have a tremendous impact on the status of agriculture in the Twenty-first Century. The Rice Genome Research Program (RGP) has undertaken an extensive rice genome analysis since its initial launching in 1991 that has resulted in the establishment of a catalog of rice genes, a high-density linkage map, and a YAC-based physical map. An enormous collection of expressed sequence tags (ESTs) was generated from large-scale cDNA sequencing using cDNA libraries derived from rice callus cultured in different media and tissues such as root, shoot, leaf and panicle. This included more than 9000 partial cDNA sequences corresponding to unique genes have been identified. Based on the results of large-scale cDNA analysis, microarray can be used to monitor gene expression profiles and to initiate functional analysis of the rice genome. We initiated a rice cDNA microarray project beginning in April 1999 that aims to elucidate the function of all genes in rice using a gene expression monitoring system. The National Institute of Agrobiological Resources (NIAR) and the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF) are jointly conducting this project in collaboration with 64 research institutions all over Japan. The research areas and investigator/institutions involved in this collaboration are listed in http://microarray.rice.dna.affrc.go.jp/. Homology search of all ESTs was performed by BLASTN and about over 9000 clones with high similarity were clustered. Clustered clones were analyzed for sequence similarity against public protein and nucleic acid databases. Then BLASTN and BLASTX were performed and clones with high similarity were identified putatively. One