The molecular basis underlying the differential development of immune organs between Huaifu and Cherry Valley ducks during early growth

Production experience has shown that local meat duck breeds possess stronger immune capacities than commercial breeds. However, systematic comparisons of their immune differences remain insufficient, and the molecular basis underlying these differences is still unclear. In this study, we compared body weight, serum immune molecule levels (IgA, IgM, IgG, IFN-γ, IL-6, and IL-10), and immune organ indices during early growth stages (1, 14, and 28 days of age [D]) between Huaifu meat ducks (HF) and Cherry Valley ducks (CV). The results showed that no significant differences were observed in these parameters at 1 and 14 D. At 28 D, the body weight of CV was significantly higher than that of HF. Meanwhile, ELISA results showed significantly higher levels of serum IgA, IgM, IL-6, and IL-10 in HF. In addition, the thymus index of HF was significantly greater. Furthermore, transcriptome sequencing (RNA-seq) was performed on immune organs at 28 D. Subsequent analysis identified 443, 451, and 449 differentially expressed genes (DEGs) in the thymus, spleen, and bursa of Fabricius (BF), respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified six, five, and two immune-related pathways in the thymus, spleen, and BF. IL6, CCR9, IL10, IL12A, RIPK2, RNASEL, SPP1, TLR5, and CASR, which were enriched in these pathways, might play key regulatory roles. Then, we performed Spearman correlation analysis between them and the DEGs in their corresponding tissues and constructed gene sets based on the results. A protein–protein interaction (PPI) network was further established for the gene sets from the three tissues. Functional enrichment analysis revealed that these genes were primarily associated with metabolism. In summary, 28 D represented a critical stage for the growth and immune system development of HF and CV. The genes IL6, CCR9, IL10, IL12A, RIPK2, RNASEL, SPP1, TLR5, and CASR were identified as key candidates, which might participate in essential metabolic processes, collectively influencing immune organ development with particularly pronounced effects on the thymus. In addition, serum levels of IgA, IgM, IL-6, and IL-10 appeared to be coordinately regulated by the thymus and spleen. These findings provided the molecular basis for subsequent disease-resistant breeding.