Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice



Shuchi Smita1, 2, Amit Katiyar1, 2, Dev Mani Pandey2, Viswanathan Chinnusamy3, Sunil Archak1 & Kailash Chander Bansal1*



1National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi-110012, India; 2Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi-835215, Jharkhand, India; 3Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi-110012, India.


Email; *Corresponding author


Article Type




Received December 07, 2012; Revised December 22, 2012; Accepted November 23, 2012; Published January 18, 2013



Identification of genes that are coexpressed across various tissues and environmental stresses is biologically interesting, since they may play coordinated role in similar biological processes. Genes with correlated expression patterns can be best identified by using coexpression network analysis of transcriptome data. In the present study, we analyzed the temporal-spatial coordination of gene expression in root, leaf and panicle of rice under drought stress and constructed network using WGCNA and Cytoscape. Total of 2199 differentially expressed genes (DEGs) were identified in at least three or more tissues, wherein 88 genes have coordinated expression profile among all the six tissues under drought stress. These 88 highly coordinated genes were further subjected to module identification in the coexpression network. Based on chief topological properties we identified 18 hub genes such as ABC transporter, ATP-binding protein, dehydrin, protein phosphatase 2C, LTPL153 - Protease inhibitor, phosphatidylethanolamine-binding protein, lactose permease-related, NADP-dependent malic enzyme, etc. Motif enrichment analysis showed the presence of ABRE cis-elements in the promoters of > 62% of the coordinately expressed genes. Our results suggest that drought stress mediated upregulated gene expression was coordinated through an ABA-dependent signaling pathway across tissues, at least for the subset of genes identified in this study, while down regulation appears to be regulated by tissue specific pathways in rice. 



Coexpression, Drought stress, Hub gene, Rice, Transcriptome, WGCNA.



Smita  et al  Bioinformation 9(2): 072-078 (2013)


Edited by

P Kangueane






Biomedical Informatics



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