Analysis of the transcriptomes of salt tolerant and susceptible cultivars of indica rice by microarray

Over the years, many traditional rice varietites of India were sourced and studied owing to their ability to withstand abiotic pressures like excessive salinity in the soil and water. These cultivars growing in specific areas of the country represent a rich gene pool from where a deeper understanding of the processes underlying tolerance to abiotic stress can be gained. Indigenous varieties like Nonabokra and Pokkali are known salt tolerant varieties and are being studied in great detail. In the present study, we have analyzed the transcriptomes of the contrasting cultivars; Nonabokra (tolerant), Pokkali (tolerant) and IR29 (susceptible) in order to decipher the differences in their responses to salinity stress by utilizing microarray. Seedlings of Nonabokra, Pokkali and IR29 were grown hydropnically for seven days and then subjected to salinity stress by placing them in 200 mM NaCl solution under light for 3 h and 6 h at 28±1oC. For control samples, seedlings were kept in RGM (root growth medium) for 6 h at 28±1oC. RNA extracted from each sample was hybridized on rice Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. Overall, twenty seven samples were analyzed representing control, 3 h and 6 h of salinity stress for each cultivar (Nonabokra, Pokkali and IR29).