Transcriptomic dynamics and immune-associated SNP discovery in Monopterus albus infected with Chinese rice-field eel rhabdovirus

Viral infections represent a significant challenge to the health and productivity of Chinese rice-field eel (Monopterus albus) aquaculture. In this study, a 108-h preliminary experiment identified the critical immune response window between 24 and 48 h post-infection (hpi) with Chinese rice-field eel rhabdovirus (CrERV). Based on this, kidney and spleen tissues were sampled at 24 and 48 hpi for histopathological analysis using hematoxylin and eosin staining. Marked hemorrhage and tissue destruction were observed in the kidneys at 48 hpi, indicating progressive pathological damage during later stages of infection. To investigate molecular responses, transcriptome sequencing of kidney tissues at 0, 24, and 48 hpi was performed. Functional enrichment via GO and KEGG analysis revealed significant activation of immune-related pathways, such as NF-κB signaling, Toll-like receptor signaling, and cytokine-cytokine receptor interactions. The reliability of the transcriptomic data was validated using quantitative real-time PCR (qRT-PCR). A total of 77 immune-related differentially expressed genes (DEGs) were identified and subjected to protein-protein interaction network analysis, identifying 15 hub DEGs as key immune regulators. Tissue-specific expression profiling revealed high expression of these genes in the kidney and spleen, highlighting their central roles in antiviral defense. Among the key genes, LAMR was found to harbor functional SNPs and was further analyzed. small interfering RNA-mediated knockdown of LAMR, followed by viral challenge using CrERV, significantly delayed median lethal time and improved survival, suggesting a protective role potentially through inhibition of viral entry or replication. In addition, several SNPs within immune-related genes were identified, some of which may influence gene function or expression, offering potential molecular markers for selective breeding. Overall, this study presents a comprehensive analysis of the immune dynamics and genetic responses to viral infection in M. albus, providing valuable insights and molecular resources for disease prevention.