Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Deep Transcriptional Profiling Of Rice Using Signature Sequencing

Kan Nobuta¹ , Venu R Channarayappa² , Kalyan Vemeraju ¹ , Mayumi Nakano¹ , Kevin McCormick ¹ , Maria Bellizzi ² , Eric Stahlberg ³ , Huameng Li² , Guo-liang Wang ² , Blake C Meyers¹

¹  Delaware Biotechnology Institute, Univeristy of Delaware, Newark, DE, 19711, USA

²  Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA

³  Ohio Supercomputer Center, Columbus OH 43210, USA

We have generated MPSS (Massively Parallel Signature Sequencing) data for 22 rice libraries that include diverse untreated tissues and tissues treated with abiotic stress. These data include 121,581 distinct signatures that matched the genome and passed our filters. A comparison of these signatures to the annotated genes demonstrates that at least 22,504 genes are transcribed. This complexity is consistent with and not substantially higher than that of Arabidopsis. In addition, thousands of signatures were identified that suggest the existence of alternatively transcribed and novel (intergenic) transcripts. We are in the process of confirming these potential transcripts with microarrays and RACE PCR. Additional experiments focus on the analysis of genotype-specific gene expression in comparisons of the indica and japonica haplotypes and an F1 hybrid of the two subspecies. The rice MPSS data are available through our MPSS web-interface (http://mpss.udel.edu/rice); these data will facilitate gene discovery, functional analyses and permit "electronic Northern" analyses of specific genes of interest.