Whole-genome resequencing to explore genome‑wide single nucleotide polymorphisms and genes associated with avian leukosis virus subgroup J infection in chicken.

Abstract

Avian leukosis virus subgroup J (ALV-J) is an oncogenic virus that causes serious economic loss in the poultry industry. Currently, no effective vaccine or drug is available against this virus. Therefore, it is imperative to explore and understand the molecular regulatory mechanisms underlying ALV-J infection. In this study, blood samples from 21 ALV-J-infected and 22 ALV-J-uninfected (DZ) chickens (JZ) were analyzed by whole-genome resequencing (WGR). By combining the fixation index (FST) with the nucleotide diversity (π) ratio based on WGR data, 425 candidate genes were identified. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed the top 20 enriched pathways, among which 9 pathways were significantly associated with diseases, including endometrial cancer, Chagas disease, PD-L1 expression and PD-1 checkpoint pathway in cancer, colorectal cancer, endocrine resistance, fluid shear stress, atherosclerosis, basal cell carcinoma, non-small cell lung cancer, and melanoma. Fourteen single nucleotide polymorphisms related to twelve genes showed a notable difference between DZ and JZ group chickens. The genes included COMMD3, PPP1CB, VEGFA, GTF2H1, NOTCH2, ITPR1, FGFR4, GNAS, NECTIN1, WNT2B, PPP1CC, and MRC2. These findings may provide a valuable foundation for further exploration of the pathogenesis of ALV-J in chickens.