An RNA-Seq transcriptome analysis of rice genes in response to soil-water deficiencies and the identification of OsPhyB-mediating novel regulatory pathway for drought tolerance in root. Oryza sativa

To improve our understanding of soil moisture stress, we performed RNA-Seq analysis using roots from four-week-old rice seedlings grown in soil that had been subjected o drought conditions for 2 to 3 d. From the upregulated genes, we found a T-DNA insertional mutant of rice phytochrome B (OsPhyB) that negatively regulates plant’s degree of tolerance to water deficiencies through its control of ascorbate peroxidase and catalase mediating ROS processing machinery besides the control of total leaf area and stomatal density as previously reported. Overall design: Four weeks old rice seedlings were given drought stress for two and three days. Well watered plants of the same growth stage were used as control. Root samples from control and drought treated plants were used for generating paired end RNASeq data. Total six samples with two biological replicates were used.