Differential Transcriptional Regulation of Drought Stress Revealed by Comparative RNA-seq Analysis of Contrasting indica Rice from North East India

Indica rice varieties especially from North East India show a broad variation in drought tolerance due to the rich biodiversity of the region. In this study, genome-wide analysis of drought-responsive regulons was performed by comparing the stress-tolerant, Tampha and stress-sensitive, Chandan, indica rice genotypes. The results showed that drought stress induces greater number of differentially expressed transcripts in the Tampha as compared to Chandan. Sixty-one drought-regulated transcripts showed higher expression level in Tampha and these included dehydrins, glycosyltransferases, DnaK molecular chaperones and several transcription factors. The drought-responsive transcripts formed co-expression gene modules and were majorly associated with redox pathways and carbohydrate metabolism. The gene regulation was coordinated by transcription factors and miRNAs. The Tampha transcriptome also exhibited significant changes in ASE under drought stress. Therefore, the results demonstrate that substantial differences in both transcriptional variations and post-transcriptional regulations determine the transcriptome profiles to regulate the plant response to drought stress in varieties.