Cnaphalocrocis medinalis granulovirus (CnmeGV) is a potential biocontrol agent for C. medinalis which is a major rice pest. However, its insecticidal efficacy is slow due to cell apoptosis. This study investigated the role of miRNAs in CnmeGV-mediated apoptosis. Small RNA sequencing and qRT-PCR identified miRNAs tca-miR-3885-5p and tca-miR-3897-3p, which initially increased and then decreased post-infection, but remained higher than controls. This trend was opposite to the changes in midgut apoptosis levels detected using terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) and DNA ladder assays. Compared to the group treated with CnmeGV alone, agomirs increased the CnmeGV-induced larval mortality, reduced midgut apoptosis, whereas antagomirs had the opposite effects. We found that the upregulation of CnmeGV replication induced by agomirs initially increased and then decreased, while the apoptosis inducer PAC-1 compensated for the weakening trend of CnmeGV replication upregulation induced by agomirs in the later stages of infection. Results indicated the virus hijacks these miRNAs to inhibit early apoptosis, later requiring apoptosis for systemic infection from the midgut. Agomirs treatment and dual-luciferase assays showed these miRNAs functioned via apoptosis-inducing factor 1 (AIF1) and apoptosis-stimulating protein of p53 1 (ASPP1) mRNA expression. This study highlights the role of these miRNAs in infection and provides insights for developing viral insecticide enhancers.
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