In silico Analysis of miRNAs Targeting Sugarcane Mosaic Virus and Identification of Their Target Genes and Host Responses in Sugarcane (Saccharum officinarum)

Sugarcane mosaic virus (SCMV) is recognized as one of the most destructive pathogens in sugarcane. In response to pathogen attacks on a host plant, the expression of miRNAs is modified, leading to changes in the expression of downstream target genes. This study aimed to bioinformatically evaluate the potential interactions between sugarcane-encoded miRNA sequences and the genome of the virus isolate, and to identify their target genes and pathways in response to SCMV. The in-silico analysis identified sof-miR159e as the common effective candidate, capable of targeting the HC-Pro in the SCMV genome and affecting 165 target genes in sugarcane. Singular enrichment analysis of the target genes with enrichment determined using FDR with a P-value cutoff of 0.05 revealed 25 significant gene ontology (GO) terms in sugarcane. According to GO analysis, the pathways of biological process were related to growth and development, response to stimulus, organelle organization, reproductive-related processes, and cellular and metabolic processes. In addition, mitochondria, intracellular membrane-bounded organelles, and cytoplasmic and intracellular parts were identified as key cellular components. Furthermore, the molecular functions were primarily associated with catalytic and oxidoreductase activities. The top six enriched Kyoto encyclopedia of genes and genomes (KEGG) pathways included transcriptional regulation, plant hormone signal transduction, mitogen-activated protein kinase signaling pathway, plant-pathogen interaction, ethylene signaling, and biosynthesis of secondary metabolites, with the latter having the highest rich factor. These findings identified the key miRNA involved in the binding to the viral genome, the host target genes, and the associated pathways affected by sof-miR159e, which may provide valuable insights into the relationship between miRNAs and SCMV infection dynamics.