Biochemical, physiological and molecular responses of rice to terminal drought stress: transcriptome profiling of leaf and root reveals the key stress-responsive genes

Drought stress has been known to adversely affect growth, development, and productivity of plants to varying extent. Being a multifaceted trait, drought tolerance involves interaction of an array of genes, pathways, and mechanisms. A unique regulatory scheme is adopted by different plants, which provides tolerance to drought stress in association with biochemical and physiological mechanisms. Transcriptome analysis of a drought tolerant [Nagina 22 (N-22)] and drought sensitive (IR-64) cultivars provides insights into the genes/pathways/mechanisms involved in terminal drought stress tolerance. In the present study, comparative physio-biochemical analyses of the rice cultivars under terminal drought stress substantiated their performance. Whole transcriptome analysis of leaf and root from the rice cultivars exposed to terminal drought stress revealed 6077 and 10,050 differentially expressed genes (DEGs) in leaf of N-22 and IR-64, respectively, under drought stress. A maximum of 2682 genes were up-regulated exclusively in N-22 while 7198 genes were down-regulated exclusively in leaf of IR-64. Interestingly, the highest number (2594) of genes was down-regulated exclusively in roots of IR-64, while only 1497 gene were up-regulated exclusively in root of N-22. Differential expression of OsNAC10, OsbZIP23, OsABA8ox1, OsCPK4, OsLEA3, and OsNCED4 along with the GO terms enriched with up-regulated genes for transcription factors (TFs), redox homeostasis, and ABA signaling in N-22 under terminal drought stress play crucial roles in stress tolerance. The stress-responsive genes for transcription factors, redox homeostasis, and ABA signaling up-regulated in N-22 were mainly responsible for terminal drought tolerance. These stress-associated genes can be utilized for genetic improvement of rice for drought tolerance.