Differentially expressed genes in sensitive and tolerant rice varieties in response to salt-stress

Soil salinity is a major constraint to rice production worldwide; hence intensive efforts are on to identify genes that make rice varieties tolerant to the salt stress. In this study, four rice varieties differing in tolerance to salinity were studied for differential gene expression through microarray analysis of RNA extracted from rice seedlings grown under control and salt stress conditions. Overall 1,696 gene probes in the tolerant and 2,220 gene probes in the sensitive varieties showed significant differential expression under salt stress as compared to control plants, but only 72 of these were common between the tolerant and susceptible variety groups. Fifty highest responsive genes in the tolerant and sensitive variety groups included some of the well known salt responsive genes, e. g. basic proline-rich protein, zinc finger protein and late embryogenesis abundant protein. We identified 6 genes that were commonly differentially expressed under salt stress in all the four varieties studied and hence could be the nodal points for transcriptional regulation under salt stress. These included genes for FACT complex subunit SSRP1-A, ORM1, abscisic stress ripening protein, photosystem II 10 kDa protein, negative transcription regulator-like protein and purple acid phosphatase. Expression patterns of the 6 genes were similar in the four genotypes except that all of these were down regulated in the salt tolerant variety CSR 27 under salt stress, while one gene was uniquely over expressed in highly salt sensitive variety VSR 156. These lists may contain the probable candidate genes for salt tolerance.