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Research Note: Genome-wide association study identifies a 1.03-Mb resistance-associated haplotype on chromosome 12 associated with avian leukosis virus susceptibility in Wuhua yellow chickens
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DOI：10.1016/j.psj.2026.107246.png)
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Abstract
En 中文
Avian leukosis virus (ALV) causes immunosuppression and tumors, resulting in considerable economic losses in the poultry industry. However, the genetic basis of ALV susceptibility in indigenous breeds remains elusive. Herein, we conducted a genome-wide association study for ALV susceptibility in 259 Wuhua yellow chickens, an indigenous Chinese breed with known disease resistance. ALV infection status was determined by p27 antigen ELISA at 46 weeks of age, with 10 individuals (3.9%) classified as positive. We identified 58 significant SNPs, all located on chromosome 12 and concentrated within a 1.03-Mb region (12.19–13.22 Mb), using SAIGE to account for extreme case‑control imbalance. Gene annotation demonstrated 11 candidate genes, among which FHIT accounted for 44 of the 58 significant SNPs (76%). Additionally, PDHB, PTPRG, FAM3D, and FAM107A were identified as potential candidate genes associated with ALV susceptibility. Notably, conditional analysis confirmed that the lead SNP in FHIT (chr12:12,650,715) is the main driver of this cluster, given that its inclusion as a covariate eliminated all neighboring signals. Functional enrichment showed the citrate cycle as the most considerably enriched pathway, highlighted by PDHB, alongside pyruvate and carbon metabolism. The convergence of tumor suppression (FHIT, FAM107A), metabolic reprogramming (PDHB), and immune/signaling (PTPRG, FAM3D) genes within a single genomic region suggests a potential resistance-associated haplotype block. Our study provides promising candidate genetic markers for breeding ALV-resistant lines and offers novel insights into host–retrovirus interactions beyond traditional immune signaling.
Keywords:
Genome-wide association study
Avian leukosis virus
Wuhua yellow chicken
Genetic susceptibility
Novel candidate gene
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