Abiotic Stress Related Genes Screening And Promoter Analysis In Rice With Microarray Data

Rice yield and quality can be greatly affected by abiotic stresses such as drought, salt, heat and cold. DNA Microarray is the best tool to investigate gene expression on transcriptome level. The Gene Expression Omnibus (GEO) database has cumulated huge amount of gene expression data. How to integrate these data and mine the abiotic stress responsive genes and regulatory cis-acting element in the rice genome is the aim of this research.Fourteen experiments employing GPL2025platform were screened out from253rice related datasets in GEO database for quality assessment. Differentially expressed probes were identified in6drought,4salt,1heat and1cold datasets respectively. The drought and salt datasets which have multiple experiments were combined for clustering. Gene Ontology classification and enrichment analysis was performed base on clusters. The key regulatory genes responding to drought, salt, heat and cold were found. ERF, HSF, MYB, WRKY, bZIP family transcription factors were found responding drought stress. ERF, bZIP, WRKY, HSF family transcripton factors were found responding salt stress. Cytochrome P450family genes and serine/threonine protein kinase were found responding heat stress. ERF, WRKY family transcription factors were found responding cold stress.Thirty six new regulatory cis-acting elements were predicted by GimmeMotif base on clusters. There are12new elements predicted in drought,12in salt,6in heat and6in cold. The consensus sequences of dAgm2and dCgm4in drought, sCgm4in salt, hDgml and hUgm3in heat was simliar to ABI4which is related to sugar and light responsive pathway. The consensus squences of dCgm10in drought, sCgm9and sCgm12in salt, hUgm2in heat, cDgml and cDgm2in cold was similar to E2F1which is cell-cycling regulation related. Cis-acting element co-occurring analysis system was built to investigate the enrichment and co-occurence of known elements with the motif information provided by PlantCARE. Known elements co-occurring networks were constructed for each cluster in four abiotic stresses. Statistical analysis was performed on part of the most significant co-occurring elements for the element distribution on the promoter region and co-occurring distance. The light-induced ACE, ABA responsive CE3, root specific Motif Ⅰ and GCCCG-motif which function is unknown significantly enriched in drought, salt and cold stresses. ABRE, CE3, ACE, Motif Ⅰ, TGA-box, GCCCG-motif were found in the core of most co-occurring networks. The significantly co-occuring elements prefer to concentrate at ATG upstream-500bp. The co-occurring distance could be co-occurring at a certain distance, multiple distances and no specific distance.