Integrating GWAS and transcriptomics to identify candidate genes associated with the crest trait in Yongshun crested duck

The Yongshun crested duck (YCD) is a newly discovered ornamental duck breed characterized by a cluster of spherical feathers on the head. However, the genetic mechanisms underlying the crest trait in YCD remain unclear. In this study, we integrated whole-genome resequencing and transcriptomic analyses to identify candidate genes and regulatory pathways associated with the crest trait. A total of 175 YCD individuals (76 crested and 99 non-crested) were subjected to genome-wide association study (GWAS). Population genetic analyses revealed sufficient genetic recombination and no obvious population stratification, supporting the suitability of this population for association analysis. GWAS identified significant association signals on chromosome 1, and highlighted two prominent association peaks. Candidate genes within the associated region included MFAP5, APOBEC1, SLC2A3, NANOG, and A2ML1, which were mainly related to extracellular matrix organization, metabolic regulation, and developmental processes. To further characterize transcriptional changes associated with crest formation, RNA sequencing was performed on scalp tissues from five crested and five non-crested ducklings. A total of 660 differentially expressed genes (DEGs) were identified, including multiple HOX family genes (HOXA7, HOXB4, HOXB6, HOXA5, HOXB5, HOXC5, HOXC8, and HOXC10) and lipid metabolism-related genes (PNPLA2, PPARG, and CD36). Functional enrichment analysis revealed that these DEGs were mainly involved in extracellular matrix organization, cell adhesion, Wnt, TGF-β, MAPK signaling pathways, and lipid metabolism. Notably, C3AR1, a GWAS candidate gene, was also differentially expressed in crest-associated scalp tissues, providing convergent genomic and transcriptomic evidence for its potential involvement in the crest trait. Collectively, our findings suggest that the crest trait in YCD is associated with genetic variation on chromosome 1 and distinct transcriptional patterns involving cranial skin development, extracellular matrix remodeling, HOX-mediated developmental regulation, and lipid metabolism. This study provides new insights into the genetic architecture associated with avian crest traits and offers valuable information for the conservation and molecular breeding of ornamental ducks.