Transcriptome profiling of morphogenetic differences between contour and flight feathers in duck.

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) were identified in Heiwu and Nonghua duck respectively. Weighted gene co-expression network analysis (WGCNA) was used to construct a gene co-expression network of all DEGs and identify the key modules and hub genes associated with feather morphogenesis.4. Two key modules were enriched in many pathways involved in feather morphogenesis, such as the Wnt signalling pathway, anatomical structure morphogenesis, and focal adhesion. The CCNA2, TTK, NUF2, ECT2 and INCENP (in one module), and PRSS23, LAMC1, IGFBP3, SHISA5, and APLP2 (in another module) may be essential candidate genes for influencing feather morphology. Moreover, seven transcription factors (TFs) (UBP1, MBD2, ZNF512B, SMAD1, CAPN15, JDP2, KLF10, and MEF2A) were predicted to regulate the essential genes that contribute to feather morphogenesis.5. This work demonstrated gene expression changes of contour and flight feather follicles and is beneficial for further understanding of the complex structure of feathers.