Comparative Transcriptomics of Feather Follicles Reveals Potential Candidate Genes for Duck Feather Type Differentiation

Down feathers and contour feathers are two distinct feather types with vastly different structures and functions coexisting in the same individual. However, the molecular mechanism underlying these differences remains unclear. In this study, skin tissue containing intact feather follicles was collected from four anatomically defined regions of healthy Beijing ducks (Anas platyrhynchos domesticus) for transcriptomic sequencing: the breast and abdomen, which generate down feathers, and the wingtips and rump, which produce contour feathers. To mitigate bias arising from site-specific effects, we established paired comparisons between contour feathers and down feathers across different regions. Across all comparisons, 36 core differentially expressed genes (DEGs) were consistently identified. These encompassed nine HOX family transcription factors across three paralogous clusters, ZIC family members (ZIC1 and ZIC4), WNT4, TBX4, BMP5, cytoskeletal and sarcomeric genes (MYOZ2, ACTN2, DES, SMPX), extracellular matrix regulators (ASPN, MGP, FMOD), and lipid metabolism-related genes (MOGAT2, PNPLA2), among others. Pathway enrichment analysis revealed that transcriptomic variations in different feather follicles involve gene modules functioning in positional identity, cytoskeletal organization, extracellular matrix remodeling and lipid metabolism, with potential neuroendocrine modulation. The transcriptomic dataset established here facilitates future studies on the molecular mechanisms of feather differentiation and offers a reference for molecular breeding to enhance down feather yield and quality of Beijing ducks.