Identification of miRNAs and their target genes in Trachyspermum ammi

MicroRNAs are main groups of small, non-coding molecules that regulate gene expression in animals and plants. Ajwain (Trachyspermum ammi) is plants known for their medicinal properties. To date, no miRNAs have beenidentified in T. ammi. Therefore, in the present study, a computational approach based on homology search through Blastx algorithm against mirbase database was used to predict miRNA and their target genes. The parameters of GC percentage, minimum folding free energy, minimum folding free energy index and secondary structure were determined and the sequences of miRNA precursor candidate were identified. In order to investigate the expression of selected genes using Real time PCR, an experiment was performed in a completely randomized design on the ajwain Arak ecotype at three levels of 0, 12 and 24 hours after methyl jasmonate application. A total of nine miRNAs including miR156, miR160, miR166, miR168, miR171, miR172, miR396, miR477 and miR827 were identified. It was estimated that they regulate 931 of T. ammi genes, which belong to several gene families with different biological functions. Jasmonate and its derivatives are plant signaling molecules. Therefore, miR160 and miR166 expression was evaluated by Real time PCR technique. The results showed that pri-miR160 and pri-miR166 was up-regulated in response to methyl jasmonate treatment, that indicated pri-miR160 and pri-miR166 were associated with hormone transfer.