RNA sequencing analysis in chicken spleen infected with Newcastle disease virus reveals genotype-specific immune response

Globally, the Newcastle disease virus (NDV) is a seriously important pathogen and results in substantial economic losses in the poultry industry. To mitigate this pathogen, the poultry industry has employed intensive breeding programs aimed at selecting genetic Lines that promote resistance and enhance immune response. Resistance to infection occurs at multiple levels and involves genotype-specific polymorphisms in the host. To date, the influence of genetic variations on the immune response within the same chicken Lines at the genotype-specific level is not fully understood. Therefore, it is important to understand the host genetic resistance that plays a role after NDV infection. This study aimed to investigate genotype-specific immune responses in chicken spleens following NDV infection at 7 days post-infection (7dpi), Samples were analyzed for differentially expressed genes (DEGs) using high-throughput RNA sequencing approaches. Twelve cDNA Libraries from LNH chicken spleens were compared with those of NDV-infected birds across the AA and GG genotypes. A total of 9886 genes were compared, of which 1348 were upregulated (833) and downregulated (515). Of these, 552 genes, with 415 upregulated and 137 downregulated genes, were differentially expressed (DE) between the two pairwise comparison groups: Control_AA vs. Immune_AA (AA group) and Control_GG vs. Immune_GG (GG group). Higher number of differentially expressed genes (407 DEGs), with 349 upregulated and 58 downregulated genes, were identified in chickens with the GG genotype, whereas 142 genes, with 63 upregulated and 79 downregulated genes, were observed in chickens with the AA genotype. In this study, a set of seven candidate genes (LECT1, MR1, MYH3, USH1C, NMU, BG8, and CCN3) was identified associated with the immune response in chickens. Further analysis revealed that DEGs in the spleen were enriched in various signaling pathways, such as neuroactive ligand-receptor interactions, tight junctions, and glycolysis/gluconeogenesis pathways, suggesting their potential role in immune resilience. RNA-seq analysis revealed immune-related genes and pathways involved in the immune response in the chicken spleen. The results indicate that chickens with the GG genotype exhibited higher levels of differentially expressed genes (DEGs), potentially linked to NDV responses. Our findings also offer valuable transcriptomic insights for the comparative analysis of molecular mechanisms underlying immune response in LNH chickens and have practical implications for enhancing chicken breeding programs.