Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

Gene Expression Analysis And Data Mining For The Gene Network Analysis Derived From Drought Stress Treatments In Rice

Kouji Satoh¹ , Koji Doi¹ , Toshifumi Nagata¹ , Aeni Hosaka¹ , Kohji Suzuki² , Xumei Ji² , Muturajan Raveendran³ , Ramil Mauleon³ , John Bennett³ , Hei Leung³ , Richard Bruskiewich³ , Shoshi Kikuchi¹

¹  Plant Genome Research Unit Division of Genome and Biodiversity Research National Institute of Agrobilogical Sciences (NIAS) Kan'non dai 2-1-2 Tsukuba Ibaraki 305-8602 Japan

²  Hitachi Software Engineerings,Co.,Ltd., 6-81 Onoe-cho, Naka-ku, Yokohama 231-0015, Japan

³  International Rice Research Institute (IRRI) DAPO Box 7777, Metro Manila, Philippines

To elucidate global responses to drought stress in rice, a 60 mer oligomer microarray covering 22K unique genes based on the sequence of full-length cDNA clones was used to profile gene expression changes at the seedlings, using Apo and IR64 and in the peduncle at heading using IR64. As reported by Ji et al. (2005) Plant Mol Biol. 59:945-964, peduncle elongation in rice is inhibited by drought stress. Cluster analysis of genes up- and down-regulated by drought stress in these two different growth stages revealed the possible combination of the transcription factors and their down-streamers and stage-specific gene expression profiles. Gene expression analysis using the metabolic pathway data in Rice Cyc (http://www.gramene.org/pathway/) showed that genes encoding many enzymes of sugar metabolism, such as degradation of sucrose, glucose and galatose, are down-regulated, along with genes encoding enzymes of cell-wall biosynthetic, while genes encoding enzymes of some amino acid biosynthetic pathways are up-regulated. Drought-induced ABA is clearly involved in antagonizing GA-dependent events underlying peduncle elongation, but the biosynthetic genes related to these hormones are not clearly affected by the drought stress treatment. Among 613 differentially expressed transcription factor-related genes, the C3H, AP2-EREBP, bHLH, NAC, MYB and WRKY types of TF-related genes showed differential expression during drought stress treatment and re-watering treatment. Finally, the promoter regions (1kb upstream sequence) of the genes clustered after microarray experiments were examined using a newly developed cis-element analysis tool; the results of this analysis will also be discussed. Data mining using gene annotation data (ex. GO term), pathway data, and genome mapping data suggests the existence of transcription network of drought stress-responsive genes.