Identification and profiling of micro RNA s associated with white and black plumage pigmentation in the white and black feather bulbs of ducks by RNA sequencing

Summary Micro RNA s (mi RNA s) play important roles in many biological processes by regulating gene expression at the post‐transcriptional level. However, the mechanism by which specific mi RNA s may regulate plumage pigmentation has remained largely elusive. In this study, we sequenced mi RNA s using S olexa sequencing and then performed a detailed analysis of their expression profiles between the black and white feather bulbs of ducks from C ui H ei, K aiya, L iancheng pure breeds and a K aiya‐ L iancheng F 2 population. mirdeep 2 software identified 121 conserved and eight novel mi RNA s. Five differentially expressed mi RNA s between the two tissues types were also identified by degseq software. Notably, mi R ‐204 was predominantly expressed in black feather bulbs. To further validate the sequencing data, we applied stem‐loop quantitative PCR of ten known mi RNA s based on the identified sequences. Furthermore, in exploring the temporal expression pattern of mi R ‐204, we performed profiling in nine duck tissues. The targets of these mi RNA s were predicted using a PITA algorithm and were later grouped based on G ene O ntology and KEGG pathway analysis using the DAVID website. The melanogenesis pathway was among the identified signalling pathways, implying key roles of these mi RNA s in plumage pigmentation. Expression analysis of the target genes in the melanogenesis pathways was also performed. This study provides the foundation for subsequent studies on the prospective practical role for such mi RNA s in post‐transcriptional gene regulation linked to plumage pigmentation.