Comparative transcriptome analysis reveals potential candidate genes for resistance to <i>Edwardsiella tarda</i> in turbot (<i>Scophthalmus maximus</i>)

Turbot (Scophthalmus maximus) is one of the most important marine aquaculture species worldwide. However, with the continuous expansion of farming scale, disease outbreaks have become a major constraint to the development of the industry. Among the pathogens, Edwardsiella tarda is recognized as one of the primary causative agents. Identifying resistance-related genes and applying marker-assisted selection present promising strategies for breeding E. tarda-resistant turbot strains. In this study, two families with the highest and lowest average breeding values were selected as resistant and susceptible groups, respectively. Transcriptomic analyses were conducted on spleen and head kidney tissues before and after E. tarda infection. The objective was to identify key genes associated with resistance to E. tarda in turbot. Among all comparison groups, the highest number of differentially expressed genes (DEGs) was observed in spleen tissue from sensitive families before and after infection (NiS vs. InS), with 866 significant DEGs. In contrast, the resistant group (NiR vs. InR) exhibited the fewest DEGs, with only 290 identified. Based on GO annotation and KEGG pathway enrichment, 26 significant DEGs were identified, including 7 upregulated genes (gdf10a, tnfsf12, tat) and 19 downregulated genes (jun, relb, fosab). In the KEGG pathway enrichment analysis, significant enrichment was observed in immune-related pathways, including the MAPK signalling pathway, cytokine-cytokine receptor interaction, toll-like receptor signalling pathway, as well as metabolic pathways such as starch and sucrose metabolism, glycolysis/gluconeogenesis and phenylalanine metabolism. Further analysis revealed that 21 of these genes were enriched in the MAPK signalling pathway and cytokine-cytokine receptor interaction pathway, both of which are closely related to immune and inflammatory responses in fish. To verify the reliability of transcriptome data, four genes (egfra, fosab, gdf10a and si_ch211-79 m20.1) were selected for real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) validation. The results showed consistent expression trends with transcriptomic data, confirming the credibility of the identified DEGs. In conclusion, this study identified several candidate genes associated with resistance to E. tarda in turbot, enhancing our understanding of its immune response mechanisms and providing a theoretical basis for future genetic selection and molecular breeding efforts.