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Salinity stress is one of the most important environmental stresses that decrease crop growth and yield. Barley is an important crop known as the salt-tolerant plant in cereals. In this study, the salt stress-responsive root transcriptome of tolerant (Afzal) and susceptible (Yusef) cultivars was investigated. The sequencing of mRNA transcripts (termed RNA-Seq) was performed using the Illumina HiSeq platform after filtering for RNA with 3' polyadenylated tails to include only mRNA. The Tuxedo pipeline was used to identify the altered expression of transcripts. Sequencing results showed that, after initial trimming of the reads, more than 20 million reads (92%) remained for all samples, of which 88% were aligned with the barley genome. Bioinformatics analysis showed the altered genes expressions in various processes such as membrane antiporter and transporter activity, an antioxidant, wide range of kinase and phosphatase cascades, internal signal transduction, metabolism of carbohydrates, amino acids, and lipids, binding processes, response to plant hormones, catalytic activity, and cell wall organization. Gene network analysis revealed that key genes, including proteins involved in systemic acquired resistance, peroxidase family proteins, cyclin-dependent protein kinase, phosphatidylinositol kinase, auxin-carrying proteins, mannose 6 phosphate isomerase, helicases and transcription factors play an important role in salt tolerance. These data can be used as a valuable source in future studies for genetic manipulation of barley and development of salinity tolerant cultivars.

Keywords: Gene network, Gene ontology, RNA-Seq, Salinity tolerance.

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