Genes expression analysis of rice under salinity stress and identification of promoter’s cis-elements role of TPC1 gene responsible for long-distance signaling in salinity tolerance

Soil salinity is one of the major limitations of rice production worldwide, especially in coastal areas. Sensitivity or tolerance of rice to salinity depends on the coordinated function of stress-responsive genes. In order to investigate the genes related to stress response, expressed sequence tags from salinity tolerant and sensitive rice libraries with 4571 and 3823 EST sequences from the Harvard University database were analyzed.  EST sequences were assembled using EGassembler software to find similarities between the two libraries. The unigenes were analyzed using X-blast by CLCbio software against non-redundant gene bank proteins. IDEG6 statistical software and Audic-Claverie statistics were used to identify differential expression genes between libraries. The GoMapMan comparative classification tool was used to classify the functional catalogs. Statistically significant differences were observed between the genes of the two libraries in 9 functional groups. The results indicate the importance of genes involved in the three key functional groups, transport, components of the long-distance signaling pathway and epigenetic regulation in salinity tolerant cultivars, introducing TPC1 as a possible candidate for molecular modification of salinity-sensitive rice genotypes. The function of the cis-acting elements in the promoter region of this gene determines the regulatory network of salinity stress response mechanisms that will be necessary to better understand stress management in plant salinity tolerance to cope with the consequences of climate change and other environmental challenges. Improving the stress response systems and adaptation to them in plants can contribute to achieving sustainable agricultural goals and food security around the world.