Genome-wide association study reveals loci associated with cytokine levels in chicken serum.

Cytokine-mediated immune responses constitute a critical line of defense that protects chickens from invasion of viruses, bacteria, parasites and other pathogens. Accordingly, the present study aimed to identify genomic variants and candidate genes linked to serum cytokine concentrations in chickens, with the long-term objective of uncovering potential molecular markers to support selective breeding for improved immune traits in chickens. For this purpose, a total of 206 ten-week-old Qiandongnan Xiaoxiang chickens were selected as experimental animals. Serum concentrations of six key cytokines-interferon gamma (IFN‑γ), interleukin‑1β (IL‑1β), interleukin‑6 (IL‑6), interleukin‑17 (IL‑17), interleukin‑22 (IL‑22), and tumor necrosis factor alpha (TNF‑α)-were quantified and regarded as immune-related phenotypic traits. Subsequently, genome-wide resequencing data were analyzed using the FarmCPU model implemented in the rMVP package to conduct genome-wide association studies (GWAS), enabling the identification of critical loci significantly associated with the measured immune phenotypes. Importantly, the GWAS identified 58 loci significantly associated with serum cytokine traits; these loci reside in or near 20 candidate genes such as SCRN1, GALT-CNTFR, and MESDC1-MESDC2. Overall, this research delineates the population variation patterns of major serum cytokines in Qiandongnan Xiaoxiang chickens. These loci and candidate genes can be used to screen molecular markers for immune traits.