Genome-wide association study reveals putative genetic determinants of longitudinal immune responses to avian influenza and Newcastle disease in chickens

Abstract

Abstract Background Avian Influenza virus (AIV) and Newcastle disease virus (NDV) are highly contagious immunosuppressive pathogens that cause high mortality rates and economic losses in the global poultry industry. Although vaccination to enhance the host antibody response remains the main control strategy, the genetic basis of this variation is poorly understood. In this study, we used a genome-wide association study (GWAS) to investigate the genetic architecture of the longitudinal antibody responses to AIV (subtypes H5, H7, and H9) and NDV in chickens. Results To identify the genomic regions and candidate genes associated with the longitudinal antibody response to AIV and NDV after immunization, we conducted a GWAS using 1,359,927 SNP markers in an advanced intercross line (AIL) of the F19 resource population. We found moderate heritability for both the traits. Based on these associations, we identified the genomic regions and candidate genes for both traits. Association analysis revealed two significant SNPs located on chromosome 3, rs316474025 near NFKBIE and SLC35B2 [rs316474025], and rs312870707 near ATG5 gene, that are associated with viral antibody titers against AIV subtypes H5 and H7, respectively. Additionally, one variant on chromosome 27, rs318005864 near DDK12 and RPL19 genes, was strongly linked to the antibody response associated with NDV at mid-phase (40 days post-immunization). Furthermore, another variant, rs737164663, near FRMD5 and GLCE genes, was strongly linked to the antibody titer associated with both AIV subtype H9 and NDV in the late phase (60 days post-immunization). Genes located in these regions may be responsible for the immune response in chickens. Before implementation in breeding programs, the efficacy and long-term persistence of selecting these antibody response traits should be validated in larger independent cohorts. Conclusions We confirmed the presence of genetic variability and identified SNPs significantly associated with antibody titer traits in F19 chickens. These findings highlight genomic regions contributing to variation in antibody responses and provide valuable information for improving antibody-related traits through selective breeding programs.