Integrative GWAS and RNA-seq identify MYL9 as a key regulator of pullorum disease resistance in chickens

Pullorum disease, caused by Salmonella Pullorum, is a significant avian disease that poses a serious threat to poultry health. To elucidate the host immune response characteristics and key regulatory gene mechanisms during infection, this study investigated 2,100 White Plymouth Rock hens at 100 days of age. A rapid plate agglutination (RPA) test was conducted for screening, identifying 175 individuals as strongly positive and 42 as weakly positive. Immune factor levels in peripheral blood were measured in 375 birds, revealing that the expression levels of IgG, IL-6, and IL-8 were significantly higher in the positive group than in the negative group, indicating that Salmonella Pullorum infection induces the release of immune factors.Whole-genome resequencing (WGS) of the 375 samples identified 72 SNPs significantly associated with the agglutination phenotype through genome-wide association study (GWAS), and 289 candidate genes were screened. Transcription sequencing (RNA-seq) analysis identified 536 differential expressed genes (DEGs), which were enriched in pathways related to Salmonella infection, calcium signaling, and immune responses. Integrated analysis of the GWAS and RNA-seq results revealed five overlapping genes: MYL9, SYT1, KLHL38, C11orf87, and KCNH4. Among them, MYL9 was enriched in the Salmonella infection pathway and occupied a central node in the protein-protein interaction (PPI) network. Functional validation of MYL9 in HD11 cells showed that MYL9 significantly promoted the expression of IL-2, IL-3, IL-6, IFN-α, IFN-β, and TNF-α, and increased the protein levels of IFN-α, TNF-α, and IgG in HD11 cells. It indicates that MYL9 plays a role in Salmonella Pullorum by upregulating immune factors.