Identification of Resistance Loci to Avian Leukosis via Genome-Wide Association Analysis in Chengkou Mountain Chickens

Avian leukosis (AL), a major vertically transmitted infectious disease, poses a significant challenge to the conservation and industrial development of indigenous chicken breeds in China. In this study, Chengkou mountain chickens were used as a model to systematically identify genetic markers associated with resistance to avian leukosis virus subgroup J (ALV-J) through a genome-wide association study (GWAS). Genomic DNA was extracted from 500 hens at 300 days of age, and cloacal swabs, plasma, and egg white samples were collected to assess the ALV-J infection status. A total of 325 ALV-positive (ALV+) and 175 ALV-negative (ALV-) individuals were identified. Based on 10× whole-genome resequencing and stringent quality control, 12,644,463 high-quality SNPs were obtained. GWAS revealed a significant enrichment of SNPs on chromosome 6 (Chr6), from which 218 SNPs significantly associated with ALV-J resistance and 49 candidate genes were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that many of these genes, including <i>PTPN13</i>, <i>TTF2</i>, <i>TIAL1</i>, <i>DLG2</i>, <i>FBXL7</i>, <i>CDH5</i>, and <i>CDH11</i>, are involved in tumorigenesis and immunosuppression through the JAK/STAT signaling pathway and cell adhesion molecule pathways. Additionally, candidate genes, such as <i>ANKH</i>, <i>SLC4A7</i>, and <i>SLC5A1</i>, were found to potentially regulate ALV-J infection by modulating membrane transport and inflammatory responses. This study is the first to identify ALV-J resistance-associated genetic markers in Chengkou mountain chickens, revealing key genes related to immune regulation, membrane function, and tumor development. The findings provide a foundational molecular basis for disease-resistant breeding in poultry.