Genomic Data Reveals Key Candidate Genes Underlying Chicken Comb Morphology

Comb morphology is a salient chicken trait of biological and breeding interest. We analyzed whole-genome data from 228 birds representing 10 breeds, including Hetian (HTC) and Xiangdong (XDC)-the only two Chinese breeds with carnation combs-to investigate population structure, diversity, and genomic correlates of comb type. Population analyses revealed clear breed stratification, with clustering that partly tracked comb type; breeds subjected to strong artificial selection or bottlenecks showed reduced genetic diversity. The integrated fixation index (F _ST) and genome-wide association study (GWAS) approach highlighted multiple regions differentiating carnation- from non-carnation-comb birds, with the strongest, most consistent signal at HSF5. Additional associated loci included EDN3, ITGB8, PDE4B, SDK1, MC1R, CDKL5, NRXN1, and STAG3. Gene-set enrichment pointed to pathways involved in vascular development and embryogenesis, processes plausibly contributing to comb morphogenesis. Notably, while HTC and XDC maintained distinct global genomic backgrounds, they exhibited high similarity within the major candidate genes influencing the carnation comb phenotype, suggesting that independent breed differentiation occurred alongside a shared genetic basis for this trait. While causative variants were not established, these results nominate tractable candidates and pathways for functional validation and inform marker development for conservation and selection in indigenous breeds.