In silico determination of potential miRNAs encoded in wheat genome that target AvrSr35 in Puccinia graminis f. sp. tritici

Abstract

Wheat (Triticum aestivum L.) belonging to Poaceae family is a valuable staple food all over the world. Puccinia graminis f. sp. tritici is one of the major limiting factor in wheat production, causing stem rust disease. RNA interference (RNAi) is an effective technique for plant production against abiotic stresses. One of the most investigated RNAi molecules is microRNAs (miRNAs). It is well established that miRNAs play important role for the regulation of gene expression at post-transcriptional and pos-translational level. In the present study, wheat miRNAs-stem rust interactions were investigated by in silico methods. For this purpose, reference mature wheat miRNAs were retrieved from miRBase, and the sequences of avirulence gene (AvrSr35) in Puccinia graminis f. sp. tritici were obtained from NCBI. RNAhybrid algorithm was used to predict the relationships between miRNAs and avirulence gene targets. Moreover, a phylogenetic tree was constructed by using miRNAs via MEGA X. We determined that AvrSr35 gene was targeted by a total of 12 miRNAs including tae-miR9657a-3p, tae-miR9671-5p, tae-miR1122c-3p, tae-miR1130b-3p, tae-miR9678-3p, tae-miR9781, tae-miR9666b-3p, tae-miR531, tae-miR9773, tae-miR9778, tae-miR9677b and tae-miR10516. All miRNAs were separated into three major groups. All miRNAs showed close relationship. The first main group consisted of only tae-miR9778. Obtaining findings are expected to contribute roles of miRNAs in the interaction between disease-related miRNAs in plants and pathogens.