Responses of rice plant to multiple abiotic stresses revealed by transcriptome meta-analysis and identification of novel genetic factors.

Plant responses to abiotic stresses have a complex polygenic nature including main and epistatic genetic factors. Several tolerant rice varieties were subjected to drought, salt and cold stresses and their transcriptomic responses were evaluated using affymetrix probe set. Meta-analysis of standardized microarray data was conducted to identify specific and common genes responding to multiple abiotic stresses. 375 and 298 genes were up- and downregulated under drought stress, 281 and 313 genes were up- and downregulated under salt stress, and 1,273 and 2,996 genes were up- and downregulated under cold stress. In addition to many specific genes for each stress condition, common genes were identified for response to drought and salt (n=91), drought and cold (n=121), and salt and cold (n=108), while 14 genes were common for response to all 3 stresses. 12 out of 14 genes were downregulated under the 3 stresses; however, only 2 upregulated genes (including an auxin-responsive protein and a LRR protein) were common among the 3 stresses. One of the common downregulated genes is a non-ABC transporter belonging to proton-dependent oligopeptide transport (POT) family protein which is novel and has a vital role in uptake of nutrients, particularly nitrate, and in recognizing plant defense compounds and hormones. In addition, two other non-ABC transporters (OsAAP7C and OsGT1) were identified which were downregulated under drought, salinity and cold stresses. This finding can explain why and how the uptake of necessary nutrients for growth and development of plants decreases under these oxidative stresses. Another novel downregulated gene under the 3 stresses is a TraB-related protein with vital role for normal mitochondrial function. These results open new insights into genetic engineering and molecular breeding of plants for tolerance to abiotic stresses.