In-silico identification and validation of miRNAs in pearl millet [Pennisetum glaucum L.]

Abstract

Pearl millet [Pennisetum glaucum (L.) R. Br.] is an important C4 crop in the arid and semi-arid regions of Asian and African countries which is under cultivation for grain, forage and stover. Here, we report identification of the conserved miRNAs in pearl millet by mining publicly available data sets including expressed sequence tag (EST) sequences, genome survey sequences (GSS), and nucleotide sequences. Homology search of 7240 known mature miRNAs of plant species against 6014 Unigene sequences of pearl millet resulted in identification of 14 potential miRNAs belonging to 11 different families. The length of predicated precursor and mature miRNAs ranged from 60 to 109 nucleotides and 18–23 nucleotides, respectively. The negative minimal folding free energy of precursor miRNAs varied significantly between −13 to −41.73 kcal/mol. Five out of 14 predicted miRNAs were validated in root and leaf/shoot tissues of seedlings of two pearl millet genotypes (J2290 and 7042S) using quantitative real time polymerase chain reaction (qRT-PCR). The psRNATarget server predicted 33 potential target genes and their probable functions. Most of the pearl millet miRNA target genes were involved in stress response, transcriptional regulation, signal transduction, DNA replication proteins, male sterility, metabolic enzymes, plant growth and development. The results of the present study will help in the understanding of mechanism of miRNA functioning in pearl millet. Keywords: Expression, microRNA, Pearl millet, RT-PCR