Insights into the Rice Responsive Transcriptome Against Twelve Abiotic Stress and Plant Hormone Treatments

Plant have the ability to adapt various growing conditions. To understand the genes and its regulatory networks responsible for the adaptation, we performed a time-course transcriptome analysis of rice reference cultivar (Oryza sativa L. ssp. japonica cv. Nipponbare) under ten abiotic stresses (high salinity, high-, low-phosphate, high-, low-, very-low-cadmium, drought, osmotic, cold and flood) and two plant hormone treatment conditions (abscisic acids and jasmonic acids) using RNA-Seq. A large number of abiotic stress responsive genes, including previously unannotated genes predicted with the RNA-Seq data, were detected. A hierarchical clustering analysis revealed similarities in responsive transcriptome among environmental, nutrient, heavy-metal stresses and plant hormone treatments. Furthermore, tissue-specific and dose-dependent responsive profiles were also observed. A number of responsive genes encode transcription factors that likely control responsive transcriptome profiles, however the timing of induction of the genes were different. In addition, we found that a number of cis-regulatory elements significantly enriched in the promoter regions of responsive genes were shared between different conditions. Taken together, these results suggested that rice responsive transcriptome against various abiotic stresses and plant hormone treatments was regulated by transcriptional networks and a considerable number of components are shared between different stress signaling pathways. All resources (gene annotation, expression profiles, co-expressed genes, cis-regulatory elements, etc.) were available in the TENOR (Transcriptome ENcyclopedia Of Rice) database.