Exploring the Potential of Oryza sativa derived Candidate miRNAs to Target Rice Tungro Bacilliform Virus (RTBV) Genome

Abstract

Background: Rice tungro disease (RTD) poses a serious threat to global rice cultivation, primarily afflicted by Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV) strains. This challenge demands innovative approaches presenting a computational procedure to identify potential candidate miRNAs from Oryza sativa based mirBase repository that can predict target sites in RTBV and RTSV genome. Results: Through our insilico based analysis utilizing different target prediction algorithms, five potential rice derived miRNAs were screened with maximum potential to target the RTBV genome. The candidate miRNAs include osa-miR166a-5p, osa-miR156g-3p, osa-miR413, osa-miR426, and osa-miR160a-5p. Additionally, seven miRNAs were predicted to explore their potential to target the RTSV genome i.e., osa-miR530-3p, osa-miR414, osa-miR390-5p, osa-miR156h-3p, osa-miR164b, osa-miR166c-3p, and osa-miR160a-5p. These miRNAs underwent effective evaluation, including free energy estimation and secondary structures were determined to ensure their efficacy in genome silencing. Moreover, site conservation analysis revealed conserved domains inside target sites. The screened miRNAs underscoring their immense potential to trigger robust mRNA intervention in viral genome. Furthermore, phylogenetic trees were also constructed to interpret the evolutionary relationships among closely related species providing valuable insights into the evolutionary standing of RTBV and RTSV. This study presents a holistic computational framework exploring potential candidate miRNAs derived from Oryza sativa with good capability to target RTBV and RTSV genomes. Conclusion: These findings hold considerable promise for the development of RNA-based strategies aimed at mitigating the impact of rice tungro disease, thereby contributing to sustainable rice production and global food security.