Genomic analysis reveals potential involvement of the brain-retina axis in regulating chicken feeding behavior

Feeding behavior is a fundamental biological process closely linked to development, growth, metabolism, and immune regulation in animals. In livestock production, it serves as both an indicator of health status and a selection criterion for breeding programs aimed at improving feed efficiency and adaptive behavior. However, the genetic basis and regulatory mechanisms governing these traits remain poorly understood. In this study, we investigated the genomic architecture of feeding behavior in 205 slow-growing yellow broilers using whole-genome sequencing and high-resolution behavioral phenotyping recorded by automated feeders. Six feeding behavior traits - average daily feed intake, number of daily visits, daily feeding duration, feeding duration per visit, feed intake per visit, and feeding rate - along with 17 production traits in 205 slow-growing yellow broilers were analyzed. SNP-based heritability estimates ranged from 0.30 to 0.69, indicating moderate to high genetic control. Phenotypic and genetic correlations showed significant positive correlations with residual feed intake, suggesting their potential as breeding indicators of feed efficiency. Genome-wide association studies (GWAS) identified seven single nucleotide polymorphisms (SNPs) and three structural variants (SVs) significantly associated with time-related and intake-related feeding traits. Functional annotation and regulatory element prediction highlighted candidate genes, including SMARCC1, SLC15A2, SEMA5B, LRIG1, ARHGAP39, HSPBAP1, and MAPK15, which, based on public databases, were expressed across multiple tissues but showed relatively higher levels in neuro-related tissues, with the retina emerging as a common site of high expression. These genes are involved in chromatin remodeling, neuropeptide transport, retinal development, and stress response, supporting a potential regulatory role of the brain-retina axis in feeding behavior. Together, our findings identify candidate genomic loci and biological pathways associated with feeding behavior, providing new insights into the neural regulation of appetite and valuable molecular targets for genetic improvement of feed efficiency and animal welfare in poultry breeding.