Sexually Dimorphic Sail Feathers in the Mandarin Duck: A Model for Lifelong Developmental Modulation [RNA-seq]

Developmental processes extend beyond embryogenesis to support lifelong tissue adaptations. Avian feather follicles, with their resident stem cells and capacity for cyclic regeneration, provide a dynamic model for postnatal tissue remodeling. Here, we propose the Mandarin duck (Aix galericulata) as an ideal model to study lifelong developmental modulation, focusing on the sexually dimorphic “sail feather”—a secondary flight feather in males that undergoes seasonal transformation into a strikingly asymmetric, ornamented phenotype during the breeding season. We identified asymmetric morphogen expression in regenerating male sail feathers and used transcriptome and H3K27ac ChIP-seq to uncover male and female signaling pathways and regulatory elements. Comparative epigenomic profiling reveals enriched estrogen receptor binding motifs in females. Hormone profiling shows seasonal variation, with a marked rise in female estrogen levels preceding the mating season. These results imply Mandarin duck sail feathers integrate local morphogenetic programs, epigenetic regulation, and systemic hormonal cues to orchestrate sexually dimorphic and seasonally dynamic feather morphogenesis. This work establishes a framework for further mechanistic study of the interplay between regeneration, regional identity, and hormonal plasticity in a vertebrate integumentary system. Overall design: We performed bulk RNA-seq to profile gene expression in regenerating Mandarin duck (Aix galericulata) sail feather follicles during early growth in the breeding season (“in season”). Feathers were dissected to separate pulp (mesenchymal) and epithelium (epidermal) compartments from the lateral blue and medial brown vanes of male sail feathers. In total, eight libraries were generated: blue sail feather pulp (Chuong-152, Rep 1; Chuong-251, Rep 2), brown sail feather pulp (Chuong-151, Rep 1; Chuong-248, Rep 2), blue sail feather epithelium (Chuong-150, Rep 1; Chuong-250, Rep 2), and brown sail feather epithelium (Chuong-149, Rep 1; Chuong-247, Rep 2). Each sample represents an independent biological replicate, enabling differential expression analysis between tissue compartments (pulp vs. epithelium) and feather vane identities (blue vs. brown). This design allowed us to identify gene expression programs associated with asymmetry and pigmentation in sexually dimorphic sail feather morphogenesis.