Virtual Center for Analysis of Rice Genome Transcription

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As the international effort to sequence the rice genome is completed, it becomes essential to define each and every transcriptional unit (or gene) encoded in the rice genome. Computer assisted genome annotation suggests that there may be about 60,000 genes in the rice genome. However, it is estimated that the combination of all experimental data available provides expression validation for only approximately half of the predicted genes. Further, due to the high GC content in rice gene coding regions, existing gene prediction program will likely miss a significant fraction of the active genes. Thus there is an urgent need for experimental verification of all predicted genes and discovery of rice genes that were missed by current prediction programs.This project will attempt to discover all possible transcription units of the just completely sequenced Japonica rice. A high-density genome tiling oligonucleotide array produced with the Maskless Array Synthesizer (MAS) technology will be used, which permits reiteration of the oligo design for each subsequent array slide production. The workflow will be optimized first with rice chromosome 10 and then applied to all remaining chromosomes. Pooled probes derived from representative RNA samples from both normal grown rice and those subjected to various inductive treatments will be included to maximize transcription unit discovery. The data will be integrated into the current and ongoing genome annotation to test predicted gene models and to define structures of the novel transcription units. The raw data will be deposited in the MIAME compliant GEO database as soon as the results are subject to quality control. All the original data, including raw hybridization data as well as gene models, will be made available to the public through a project web site (www.plantgenomics.yale.edu) once they are quality controlled and verified. This web site will be online at the end of this first funding year (August 30, 2005) and the last data set will be made available by August 30, 2007. All the new or improved rice gene models created from this work be posted on our project web site and will also be forwarded to the NSF-supported rice genome annotation group at The Institute for Genome Research at bimonthly intervals for their incorporation into their public rice gene annotation web site. The full data set will be made available to TIGR and the public by the end of this project (August, 2007).Broader Impacts:The experimental identification of all Japonica rice transcription units will provide an essential foundation for rice functional genomics and proteomics research in the future and provide useful comparative data for other cereals. In the process of our proposed studies, a number of postdoctoral researchers and students (both graduate and undergraduate) will obtain training in plant genomics and informatics. The project will work with the Peabody Museum at Yale University to teach the general public and school children about the role of rice cultivation in cultures around the world, and on the potential benefits of rice genomic advances for society.