Identify Candidate Genes Associated with the Weight and Egg Quality Traits in Wenshui Green Shell-Laying Chickens by the Copy Number Variation-Based Genome-Wide Association Study

Simple Summary The Wenshui green shell-laying chicken is an improved breed crossed from the Wenshang reed-feather chicken and Xinyang green shell-laying chicken, whose major characteristics are reed feathers, green-shelled eggs, a high egg-laying number, and excellent egg quality. The study of body weight and egg quality traits in Wenshui green shell-laying chickens is important for chicken-related breeding work. In this paper, we performed a copy number variation regions (CNVRs)-based genome-wide association study (GWAS) in Wenshui green shell-laying chickens to identify variations and candidate genes associated with their weight and egg quality traits. Finally, we identified important genes associated with body weight and egg quality traits. This study can provide a basic reference for the genetic improvement of chickens' body weight and egg quality traits.Abstract Copy number variation (CNV), as an essential source of genetic variation, can have an impact on gene expression, genetic diversity, disease susceptibility, and species evolution in animals. To better understand the weight and egg quality traits of chickens, this paper aimed to detect CNVs in Wenshui green shell-laying chickens and conduct a copy number variation regions (CNVRs)-based genome-wide association study (GWAS) to identify variants and candidate genes associated with their weight and egg quality traits to support related breeding efforts. In our paper, we identified 11,035 CNVRs in Wenshui green shell-laying chickens, which collectively spanned a length of 13.1 Mb, representing approximately 1.4% of its autosomal genome. Out of these CNVRs, there were 10,446 loss types, 491 gain types, and 98 mixed types. Notably, two CNVRs showed significant correlations with egg quality, while four CNVRs exhibited significant associations with body weight. These significant CNVRs are located on chromosome 4. Further analysis identified potential candidate genes that influence weight and egg quality traits, including FAM184B, MED28, LAP3, ATOH8, ST3GAL5, LDB2, and SORCS2. In this paper, the CNV map of the Wenshui green shell-laying chicken genome was constructed for the first time through population genotyping. Additionally, CNVRs can be employed as molecular markers to genetically improve chickens' weight and egg quality traits.