Transcript profile analysis suggests marker genes to distinguish between Phase 0 and Phase 1 responses of Arabidopsis to salt stress

Most physiological and molecular mechanisms of salinity stress are researched based on salt shock conditions. However, salt shock doesn’t occur in agricultural practice or natural ecosystem. In the fields, salts accumulate gradually through high salt or sodium irrigation water and poor managements that allow ground water to rise to soil surface. Therefore, it is more reasonable to research salinity stress in a mild way (stepwise salt addition). The objective of this study is to select marker genes to differentiate between salt shock (Phase 0) and salt stress (Phase 1). Three replicates were used for all RNA-Seq experiments conducted on control, Phase 0 and Phase 1 samples in Arabidopsis thaliana. Phase 0 samples (rosette leaves) were harvested 1 hour later from 105 mM NaCl salt shock treatment; Phase 1 samples (rosette leaves) were harvested 2 days later after reaching 90 mM NaCl by a stepwise addition (15 mM NaCl per day). Three replicates were used for all RNA-Seq experiments conducted on control, Phase 0 and Phase 1 samples in Arabidopsis thaliana.