Integrative genome-wide association study and transcriptomic analysis to identify candidate genes and pathways for...

Enhancing disease resistance is one of the primary objectives of the poultry industry through breeding. The heterophil to lymphocyte ratio (H/L ratio) represents a critical indicator of stress and immune status in chickens. However, the essential genetic networks and functional genes governing the H/L ratio remain uncharacterized. In this study, by combining genomic and transcriptomic data, we aimed to identify functional variants and key genes regulating the H/L ratio in white-feathered broilers. Using a genome-wide association study (GWAS) analysis of 218 birds, we identified single-nucleotide polymorphisms (SNPs) significantly associated with H/L ratio and H count, respectively. These SNPs were annotated to several candidate genes, including MYO16, AKT3, RBM34, SMOC2, and TOMM20. Functional enrichment analysis revealed that candidate genes were involved in FoxO signalling pathway, mTOR signalling pathway, and other immune-related pathways. Fine-mapping analysis identified potential causal variants at multiple sites, specifically chr1:138395826, chr3:34663003, chr3:34663053, and chr3:34663073. Additionally, through integrating transcriptomic and immune-related phenotypic data using weighted gene co-expression network analysis, key hub genes were identified in the bursa and thymus, respectively. Moreover, combined analysis of candidate and hub genes from the GWAS and transcriptomic analyses, respectively, illustrated that these genes were co-enriched in functionally important pathways, including mTOR, FoxO, and MAPK signaling pathways. In summary, our results indicated that MYO16 and AKT3 may represent potential causal genes associated with H/L ratio, and that multiple immune signaling pathways regulate the balance between heterophil and lymphocyte immune cells in chickens. These findings provide new insights into the genetic architecture of immune-related traits in poultry. Moreover, it is crucial to confirm the biological function of these candidate genes and variants by conducting further verification in larger populations with genetic diversity.