Identification of Differentially Expressed Genes and SNPs Linked to Vibrio mimicus Resistance in Yellow Catfish (Pelteobagrus fulvidraco)

Vibrio mimicus infection poses a severe threat to the sustainable aquaculture of yellow catfish (Pelteobagrus fulvidraco), a commercially important freshwater species of the order Siluriformes. To reveal the genetic mechanisms underlying the resistance to this pathogen, we established an infection model and integrated genome-wide association study (GWAS) and transcriptomics to identify key resistance loci and genes. Firstly, from whole-genome re-sequencing (WGRS) and high-quality genotypic data, six SNP loci significantly associated with resistance to V. mimicus were identified, which were annotated to 17 immune-related candidate genes. Notably, the rac2 gene associated with the locus Chr15:3,227,652 exhibited significantly differential expression in skin tissue. Through transcriptomic analysis, 6684 and 6616 differentially expressed genes were identified from the skin and muscle tissues, respectively. Functional enrichment analysis revealed that the skin, as the first line of defense against pathogens, prioritizes the activation of immune defense mechanisms, whereas muscle tissue responds to infection-induced stress primarily by regulating metabolic processes. Quantitative real-time PCR (qRT-PCR) validated that rac2 enhances the antibacterial capacity of yellow catfish in skin tissue by regulating the expression of NADPH oxidase complex subunits ncf1 and ncf4. This study reveals, for the first time, the core functional genes of yellow catfish associated with resistance to V. mimicus infection, providing theoretical support for disease-resistant breeding of this species.