Computational Analysis of Responsive Transcription Factors Involved in Drought and Salt Stress in Rice

Document Type : Original Article


Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran


Introduction: Rice is one of the most important crops to more than half the world's population. The reduction of rice yield has been severely influenced by drought and salt stress. The main purpose of this survey was to detect Transcription Factors (TFs) involved in drought and salt stress in rice.
Materials and Methods: In this study, microarray data in PlnTFDB and DRTF were taken to evaluate the expression of responsive TFs to drought and salt stress in the growth stages. A comprehensive analysis of responsive TFs were performed containing gene network, expression analysis in different tissues, and detection of Transcription Factor Binding (TFBs) sites.
Results: A total of 80 TFs were found differentially expressed (DEGs) under drought and salt stress in rice. Gene Ontology (GO) revealed that biological processes included transcription, regulation of transcription, regulation of RNA metabolic, and RNA metabolic. In addition, some molecular functions such as organic cyclic compound binding, heterocyclic compound binding, DNA binding, and cellular component are enriched in intracellular and nucleus. To survey selection pressure in responsive TFs under drought and salt conditions, Tajima’s and Fu test analysis revealed balancing selection. Analysis of TFBs illustrated that several TFBs namely AP2, bZIP, and MYB/SANT act as basic TFBs linked to abiotic stress responses as well as different growth stages in rice. The current study revealed that most TFs related to histone modification were up-regulated whereas, TFs associated with the regulation of repression/ activation transcription were down-regulated.
Conclusions: Our results can provide an insight into the regulatory mechanisms involved in response to drought and salt stress which can aid to improve rice varieties.