High-SNP-density genes and functional pathway analysis reveal key regulators of feed conversion ratio in broiler chickens

Feed conversion ratio (FCR) is a critical economic trait in broiler production, influencing both productivity and sustainability. In this study, an initial set of 2272 peak SNP records associated with FCR was retrieved from the Animal QTL Database and, following filtering and removal of duplicate/redundant records, 513 unique, non-redundant SNPs were retained for functional annotation using the Ensembl Variant Effect Predictor (VEP). These SNPs were mapped to 543 genes, allowing a detailed analysis of their genomic distribution and functional effects. The majority of SNPs were intron variants (54.0%), followed by downstream (17.7%), upstream (10.2%), and synonymous variants (6.5%). Missense variants (1.4%) were identified in biologically relevant genes such as ST3GAL6 , NOX4 , and TGFBR3 , while 2.5% of SNPs were located in regulatory regions. Biotype classification showed that most variants (93.7%) occurred in protein-coding regions, with smaller proportions in lncRNA, enhancer, and miRNA regions. SNP clustering revealed potential genomic hotspots, with ST3GAL6 and DGKZ exhibiting exceptionally high densities, suggesting roles in FCR-related regulatory pathways. Functional enrichment analysis via g:Profiler identified significant associations with transcription factor binding motifs, including PU.1, NF-E4, and MAFA, as well as enrichment of catalytic activity and phosphatase-related complexes. These findings highlight potential genetic targets, such as ST3GAL6 and DGKZ , and regulatory networks, including catalytic activity (GO:0003824), that may influence FCR.