Development of Rice Genome Tiling Microarray
Computer assisted genome annotation suggests that there are about 60,000 genes in the rice genome. However, it is estimated that the combination of all experimental data available (such as those from MPSS, SAGE, EST and full-length cDNA analyses) can only provide expression validation for about 50% of the predicted genes. Thus there is need for experimental verification of all predicted genes to discover rice genes that were missed by current prediction programs.
Led by Dr. Xing Wang Deng (Yale), the project is constructing a whole genome oligonucleotide tiling microarray approach to empirically determine all transcribed units of the japonica genome. A comprehensive inventory of rice transcription units will become available through this work. This will set the stage for next phase studies of the complete rice full-length ORFeome, proteomics and functional genomics to determine functions of all genes in the rice genome. It will also help train a new generation of researchers with hand-on experiences in both bench and computational skills, and enhance the public awareness of the NSF supported genomic research and their impact on crop improvement.
Jiao Y, Jia P, Wang X, Su N, Yu S, Zhang D, Ma L, Feng Q, Jin Z, Li L, Xue Y, Cheng Z, Zhao H, Han B, Deng XW. 2005. A Tiling Microarray Expression Analysis of Rice Chromosome 4 Suggests a Chromosome-Level Regulation of Transcription. Plant Cell. 2005 17:1641.
