Copy number variation (CNV) represents a key form of genetic diversity that can influence gene regulation, phenotypic variability, disease predisposition, and evolutionary processes in animals. To gain deeper insights into the weight and egg quality characteristics of chickens, this study aimed to detect CNVs in Wenshui green-shelled laying chickens and perform a genome-wide association study (GWAS) based on copy number variation regions (CNVRs). The goal was to identify genetic variants and candidate genes correlated with weight and egg quality traits to aid breeding improvements. In total, 11,035 CNVRs were identified in Wenshui green-shelled laying chickens, covering 13.1 Mb, approximately 1.4% of the autosomal genome. Among these CNVRs, 10,446 were of the loss type, 491 were gains, and 98 were mixed types. Notably, two CNVRs were significantly linked to egg quality, while four showed associations with body weight, all located on chromosome 4. Candidate genes potentially related to these traits included FAM184B, MED28, LAP3, ATOH8, ST3GAL5, LDB2, and SORCS2. This study constructed the first CNV map of the Wenshui green-shelled chicken genome using population genotyping, suggesting that CNVRs can serve as molecular markers to enhance weight and egg quality traits in chicken breeding.
