Transcriptome analysis of two rice genotypes with contrasting response to water stress at vegetative stage

To understand the diversity of physiological and molecular responses to drought in rice (Oryza sativa L.), transcript profiling was undertaken using 22K rice Oligoarray (Agilent technologies) in two contrasting genotypes namely, 1) Apo, and upland drought tolerant indica and 2) IR64, a popular high-yielding drought susceptible indica. Constitutively, the tolerant Apo was found to possess lower transpiration rate, lower stomatal conductance and upregulation of genes involved in cuticular wax and lignin biosynthesis. Under drought, the tolerant Apo showed a greater number of changes than IR64 and the two genotypes shared very few genes showing common behavior. Apo-specific upregulation included, genes involved in general stress response, osmoprotection, cell wall growth, lipid metabolism and signaling. In addition, Apo showed specific upregulation of several stress-related transcription factors carrying AP2, MYB, WRKY and NAC domains. Flavonoid biosynthesis and ROS scavening pathways were specifically upregulated in the sensitive IR64. The tolerant Apo had a greater number of genomic segments showing co-regulation of genes. Some of the RCEs (Region of Co-expression) on chromosome 1, 7 and 8 were found to co-localize within the boundary of reportd QTLs for drought tolerance, osmotic adjustment and cell membrane stability. Analysis of upstream cis-elements showed enrichment of ABRE and DREB elements in the genes specifically induced in Apo. To validate whether the loci obtained through microarray results are associated or tightly linked with the phenotypes grain yield, average height and days to flowering (DTF) under drought stress, forty Fsub3.5 progenies from the Apo/IR64 crosses with extreme performance against drought stress were genotyped using different SSR markers. Results revealed strong association of several microarray-identified genes to the phenotypes grain yield and DTF during drought stress. This study provides a genome wide transcriptional analysis of two well characterized rice genotypes differing in their drought tolerance under greenhouse conditions.