Insights into the mechanism underlying feather pattern formation of sex-linked barring in Chinese native chickens

The sex-linked barring of chicken feather pattern is a fascinating trait, and it has great application value in chicken breeding by enabling autosexing. In this study, the transcriptome changes in skin follicle tissues from the back (SKs) and crown of the head (SKHs) were explored by RNA-seq in Wenshang Barred chickens during their feather pattern formation. The key genes and signaling pathways regulating sex-linked barring formation in chickens were analyzed. As a result, a total of 2291 and 4496 differentially expressed genes (DEGs) were found in SKs and SKHs, respectively, during barred feather formation. The expression pattern clusters of Profile 6 and Profile 7 were the important and mainstream expression trends of the DEGs. Melanogenesis KEGG pathway and GO terms of melanocyte differentiation, melanosome organization and melanin biosynthetic biological processes were significantly enriched in the DEGs, including the well-known TYR, TYRP1, EDNRB and PMEL genes, clustered in Profile 6 expression pattern. A series of DEGs, including CDKN2A, SFN, CDKN2B and CDK1, were significantly enriched in the cell cycle pathway and were mostly clustered in Profile 7. Protein‒protein interaction (PPI) network analysis revealed TYR, TYRP1, CDKN2A and SFN were the hub genes. It was speculated that CDKN2A may target SFN to regulate the melanocyte cycle arrest, causing the formation of white bands of sex-linked barring. TYR, TYRP1, EDNRB and PMEL genes may play important regulatory roles by melanogenesis pathway in the early growth of black feathers, as well as in the later formation of black stripes. The different expression patterns of SLC45A2, KIT, MC1R, ASIP, DCT and SOX10 in SKs and SKHs may contribute to the different formation processes of barred feather patterns on the head and the back. These results provide new insights into the regulation of sex-linked barred feather patterns in Chinese native chicken and provide a valuable theoretical foundation for future chicken breeding and related efforts.