Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

in silico Screening Of Stress Response Genes In Common Wheat

Yasunari Ogihara¹ , Kanako Kawaura¹ , Etsuo Shimosaka² , Keiichi Mochida³

¹  Laboratory of Genetic Engineering, Graduate School of Agriculture, Kyoto Prefectural University, Hangi-cho 1-5, Shimogamo Kyoto 606-8522, Japan

²  Laboratory of Plant Genecology, Hokkaido National Agricultural Experiment Station, Hitsuji-ga-oka 1, Sapporo, 062-8555, Japan

³  Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga 526-0829, Japan

In order to characterize wheat genes expressed in response to abiotic stresses, we virtually displayed gene expression patterns by computing abundantly expressed sequence tags (ESTs) from six of 21 cDNA libraries. Six cDNA libraries were constructed from the stress-treated tissues of common wheat such as cold acclimations, heat shock, drought, abscisic acid (ABA) treatment. ESTs from six cDNA libraries were grouped into 5676 contigs with the phrap method. These contigs were grouped into six major clusters based on their expression profiles. Simultaneously, correlated expression patterns of genes across the stress-treated tissues were monitored. Multi-dimensional analysis of EST data is analogous to the microarray experiments. As an example, genes specifically induced and/or suppressed by cold-acclimation and heat shock treatments were selected in silico. 490 genes showing five-fold induction or 218 genes for suppression in comparison to the control expression level were selected. These selected genes were annotated with the BLAST search. Furthermore, gene ontology was conducted for these genes with the InterPro search. Since typical genes detected in temperature-sensitive treatments as well as genes with unknown-functions were successfully selected and this method is applicable to other stress-treated tissues, in silico selection of genes should provide a powerful tool for functional genomics.