Deep transcriptome sequencing reveals the expression of key functional and regulatory genes involved in the abiotic stress signaling pathways in rice

Drought, salt and cold are the major abiotic stresses that limit the rice production. Identification of the key functional and regulatory genes in the abiotic stress signaling pathways is important for understanding the molecular basis of abiotic stress tolerance. In this study, we investigated the transcriptomes of rice leaves and roots under cold, drought, and salt stresses using the massively parallel signature sequencing (MPSS) and sequencing by synthesis (SBS) technologies. About 1.8 to 2.6 million individual signatures were obtained from the seven abiotic-stressed and control libraries of the japonica cultivar Nipponbare. A total of 102,630 and 1,414,788 distinct signatures were obtained from the MPSS and SBS libraries, respectively. Clustering analysis identified many up- and down-regulated genes specifically and commonly expressed in the cold, drought and salt-treated plant leaves and roots. Data mining revealed the expression patterns of key functional and regulatory genes that were involved in different abiotic stress signaling pathways. Highly conserved cis-regulatory elements in the promoter of the up-regulated genes were identified. Our comprehensive and deep survey of abiotic stress transcriptome of rice has provided candidate genes for further understanding the molecular basis of abiotic stress tolerance in rice.