Transcriptome analysis reveals the genetic basis of crest cushion formation in duck

The Chinese crested duck is a unique duck breed having a bulbous feather shape on its duck head. However, the mechanisms involved in its formation and development are unclear. In the present study, RNA sequencing analysis was performed on the crested tissues of 6 Chinese crested ducks and the scalp tissues of 6 cherry valley ducks (CVs) from 2 developmental stages. This study identified 261 differentially expressed genes (DEGs), 122 upregulated and 139 downregulated, in the E28 stage and 361 DEGs, 154 upregulated and 207 downregulated in the D42 stage between CC and CV ducks. The subsequent results of weighted gene co-expression network analysis (WGCNA) revealed that the turquoise and cyan modules were associated with the crest trait in the D42 stage, meanwhile, the green, brown, and pink modules were associated with the crest trait in the E28 stage. Venn analysis of the DEGs and WGCNA showed that 145 and 45 genes are associated between the D42 and E28 stages, respectively. The expression of WNT16, BMP2, SLC35F2, SLC6A15, APOBEC2, ABHD6, TNNC2, MYL1, and TNNI2 were verified by real-time quantitative PCR. This study provides an approach to reveal the molecular mechanisms underlying the crested trait development.