Identification of micronutrient deficiency related miRNA and their targets in Triticum aestivum using bioinformatics approach

Abstract

Identification of miRNAs and their target proteins infer their functions to understand the biological processes of miRNAs and their involvement in plant growth and development. The homology-based approach (BLAST suite) was used for the identification of miRNA related to Zn and Cu deficiency in the bread wheat genome. Calculated the coding potential for the precursor miRNA and then predicted their secondary structure through RNAfold. PmiREN online server identified the miRNA target wheat protein. Further, STRING database predicted the biological relevance of the target protein. This in-silico study has identified the 3 miRNAs of the respective family of miR528, miR397, and miR168 of Triticum aestivum related to Cu and Zn deficiency. Out of the 42 targets for tae-miR397c; one of the targets is MFS domain-containing protein that contributes to “electron transfer” between photosystem700 and the “cytochrome b6-f complex” in photosystem and rest of the targets are laccase protein; involved in cell wall ligning deposition. Tae-miR528c has 6 targets; four are uncategorized proteins and the remaining two targets viz. GRF-type domain-containing protein and phytocyanin domain-containing protein are responsible for Zn ion binding and participate in electron transfer activity. The protein-protein interactions (PPIs) have found the various proteins that are associated with these identified miRNAs (tae-miR397c and tae-miR528c) target the protein that could be annotated further for their role in plant growth and development. The current computational hypothesis has developed a fast and robust pipeline to identify plant miRNAs and their targets compared to other used approaches.