Cyprinid herpesvirus 3 (CyHV-3) is a pathogen that causes high mortality in common carp (Cyprinus carpio) and koi. Common carp breeding lines with different genetic backgrounds exhibit different resistance levels to viral pathogens. This study aimed to determine the differences in CyHV-3 disease resistance performance between the hybrid offspring (Y × M and M × Y) of the mirror carp ‘Longke 11’ (resistant to CyHV-3) and Yellow River carp, as well as the self-crossed offspring (M and Y). The M, Y × M, M × Y and Y groups were infected with CyHV-3 by immersion. The order of mortality and the duration of death for the four groups of carp were as follows: Y group > Y × M group > M × Y group > M group. Throughout the entire infection stage, the mRNA expression levels of the viral factors thymidine kinase (TK) and open reading frame 72 (ORF72) in the four groups of carp tended to first increase but then decrease. The viral factor expression evaluated on days 30 and 31 post-infection (p.i.), which was the peak of infection mortality, was the highest in the Y group and the lowest in the M group, and compared with the Y × M group, the M × Y group had considerably lower viral gene expression (p < 0.05). The immune-related enzyme activity and content levels of the four carp groups matched the patterns of viral gene expression. On day 29 p.i., a time point with high mortality, the levels of alkaline phosphatase (AKP), glutathione peroxidase (GSH-Px) and total antioxidant capacity (T-AOC) were significantly the lowest in the Y group and significantly the highest in the M group, while the Y × M group showed a significant decrease compared to the M × Y group (p < 0.05). Quantitative real-time (q-PCR) analysis revealed that interleukin-21 receptor (IL21R), interferon regulatory factor 9 (IRF9), interferon type I (IFN-I), interleukin-6 (IL-6) and microtubule-associated protein light chain 3 (LC3), exhibited an initial increase followed by a decrease among the four experimental groups of common carp. In the peak mortality period of carp in the four groups (30 days post-infection), the expression levels of IL21R, IRF9, LC3, and IFN-I were significantly the highest in the M group and significantly the lowest in the Y group, with the mRNA expression of these genes in the M × Y group being significantly higher than that in the Y × M group (p < 0.05). In contrast, IL-6 expression levels exhibited the opposite trend. In this study, the M group exhibited the greatest resistance to CyHV-3, followed by the M × Y group, whose resistance was greater than that of the Y × M group, with the Y group showing the lowest disease resistance. Our findings demonstrate that hybridization modulates resistance to CyHV-3. Furthermore, we identified conserved immune signatures common to both susceptible and resistant carp, including the activation of nonspecific immunity and the upregulation of immune-associated genes.

Tumor necrosis factor receptor-associated factors (TRAFs) are key signal transduction molecules in innate immunity and are involved in multiple immune pathways, such as TNF receptor and Toll-like receptor signaling. In this study, 16 CcTRAFs were identified from the common carp genome, assigned to six subfamilies (TRAF1/2/3/4/6/7), with no TRAF5 found. Significant paralogous expansion was observed in the TRAF2/4 subfamilies. All CcTRAF proteins were predicted to be unstable and hydrophilic by ProtParam analysis; most contain conserved RING, TRAF and MATH domains, whereas CcTRAF7 carries seven WD40 domains. Gene structure and conserved motif analysis revealed high conservation of exon numbers and motif compositions within each subfamily, while the TRAF7 subfamily displayed distinct characteristics. Collinearity analysis further indicated that segmental duplication promotes CcTRAF family expansion. qRT-PCR showed that CcTRAF genes have tissue-specific expression patterns and are preferentially expressed in the liver, spleen, and kidney. Under CyHV-3 infection, the expression levels of CcTRAF3/6/7 in these tissues first increased and then decreased, peaking at 48 h post-challenge. In summary, CcTRAF genes, especially CcTRAF3/6/7, play important roles in the immune response of common carp against CyHV-3. This study provides a molecular basis for understanding innate immune regulation in teleost fish and the functional roles of TRAF genes.