Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in Two Egyptian Rice Varieties with Different Tolerance Levels

The response of rice to salt stress (200 mmol/L NaCl) was investigated at the transcription level in Egyptian varieties Giza 177 (salt sensitive variety) and Giza 178 (salt tolerant variety). We applied a genome-wide RNA-Seq transcriptome study at 21-day-old seedlings of both varieties, exposed or not to salt stress for 24 h. Most differentially expressed genes (DEGs) between the two varieties in response to salt stress were related to the expression of genes active at the cell wall (CW) level, including wall modification, hemicellulose/cellulose synthesis and transcripts of the peroxidase family activated in response to oxidative stress/oxidation reduction, which were significantly more represented in Giza 178. Consistently, Gene Ontology (GO) analysis showed differentially expressed transcripts, involved in response to oxidative stress and chemical stimulus, directly implicated in salt stress response and up-regulated in Giza 178, as well as oxidoreductase, peroxidase and antioxidant activities. When the two varieties were directly compared in exposed or not to salt stress conditions, Giza 177 showed a higher number of differentially expressed and unique loci than Giza 178, including transposable elements (TE). However, Giza 178 showed a higher number of transcription factors (TF) expressed, mostly involving myeloblastosis (MYB) family members and bZIP elements, with annotated elements including zinc finger domain, kinase, expansin, cellulose, sucrose synthase, peroxidase precursor, dehalogenase-like hydrolase, and sodium/ calcium exchanger protein.