1. This study examined the transcriptomic profiles of contour and flight feather follicles from two duck breeds to determine the molecular network and the candidate genes associated with contour and flight feather morphogenesis. 2. High-throughput RNA sequencing was performed to compare differences in feather follicles between contour and flight feathers in two duck breeds (Heiwu and Nonghua duck). 3. Comparing the contour feather follicles with flight feather follicles, 4,757 and 4,820 differentially expressed genes (DEGs)...