Transcriptome and resequencing reveal immune-related genes and molecular markers associated with Aeromonas salmonicida resistance in Salmo trutta fario

Understanding the molecular mechanisms underlying disease resistance in Salmo trutta fario is of fundamental importance for enhancing the health and sustainability of salmonid aquaculture. In this study, we performed an integrative multi-omics analysis combining transcriptome sequencing and whole-genome resequencing to systematically identify immune-related genes and single-nucleotide polymorphisms (SNPs) associated with resistance to Aeromonas salmonicida infection. Transcriptomic profiling identified multiple differentially expressed genes involved in immune and signaling pathways, including interferon-induced protein 44-like (IFI44L), PI3K family members (PIK3R2, PIK3R5), and NF-κB inhibitors (NFKBIA, NFKBIAA). These genes were significantly enriched in key immune regulatory pathways such as chemokine, PI3K-AKT, and NF-κB signaling, indicating their potential roles in modulating host defense responses. The integration of transcriptome and whole-genome resequencing data further revealed 104 SNPs distributed across immune-related genes that effectively differentiated resistant (R) and susceptible (S) populations. Among these, six candidate SNP loci were validated by PCR and demonstrated strong discriminatory power for resistant individuals, with multiplex PCR (MPCR) achieving an overall identification accuracy of 88.33%. The proportion of resistant genotypes within the population reached 14.82%, suggesting the progressive formation of a disease-resistant S. trutta fario strain. Overall, our findings provide novel and comprehensive insights into the genetic and transcriptional regulation of disease resistance in S. trutta fario. The identified immune-related genes and SNP markers represent valuable molecular resources for selective breeding and the development of health-oriented aquaculture strategies in salmonids.