In silico analysis of salt responsive survival associated motifs in rice promoter

In stressed condition, several specific transcription factors bind to corresponding regulatory elements or motifs resulting in the expression of appropriate genes, which helps the plant to survive in that condition. Till now, several motifs have been identified though computationally validating those motifs is a major research concern. Considering this, we present an in silico method to validate the presence of such motifs in the promoter of rice genes, which could be associated with the survival of rice in saline environments. For this, we present a statistical approach that consists of three consecutive steps: finding overrepresented oligomers in sensitive variety, identifying the potential motif from the overrepresented oligomers and validating oligomers in the promoters of up regulated genes of tolerant variety using the motif of the sensitive one. In our experiment, we have initially identified 5 potential pentamers and then the most represented one (ACGAC) was used to validate previously described motifs overrepresented in promoters of genes in different abiotic stress tolerant rice to justify their association with survival. Ultimately, our method has shown promises to better identify motifs in promoters of genes up regulated during salt stress according to their likelihood to be associated with the plant survival.