Transcriptomic analyses of regenerating adult feathers in chicken

Abstract

Background: Feathers have diverse forms with hierarchical branching patterns and are an excellent model for studying the development and evolution of morphological traits. The complex structure of feathers allows for various types of morphological changes to occur. The genetic basis of the structural differences between different parts of a feather and between different types of feather is a fundamental question in the study of feather diversity, yet there is only limited relevant information for gene expression during feather development.

Results: We conducted transcriptomic analysis of five zones of feather morphologies from two feather types at different times during their regeneration after plucking. The expression profiles of genes associated with the development of feather structure were examined. We compared the gene expression patterns in different types of feathers and different portions of a feather and identified morphotype-specific gene expression patterns. Many candidate genes were identified for growth control, morphogenesis, or the differentiation of specific structures of different feather types.

Conclusion: This study laid the ground work for studying the evolutionary origin and diversification of feathers as abundant data were produced for the study of feather morphogenesis. It significantly increased our understanding of the complex molecular and cellular events in feather development processes and provided a foundation for future studies on the development of other skin appendages.

Fig. 1

Principal component analysis of gene expression profiles. (a) Morphology of body (left) and flight feathers (right). (b) Principal Component Analysis (PCA) of gene expression profile. The results were obtained by analyzing 12,608 genes with FPKM >0.1 in all libraries. cEB, early body feather of chicken (pennaceous); cLB, late body feather (plumulaceous); cEF, early primary flight feather; cMF, middle primary flight feather; cLF, late primary flight feather (calamus)

Fig. 2

Gene ontology (GO) annotation for top 3,000 transcripts that were highly expressed in feather epithelium

Fig. 3

Venn diagram showing the genes expressed in each of the five feather tissue types. Among these genes, 9,638 are expressed at all five samples, 10,001 are co-expressed in cEB and cLB, 10,173 are co-expressed in cEB and cEF, 11,283 are co-expressed in cEF and cMF, and 11,132 are co-expressed in cMF and cLF. The GO enrichment analysis showed that the specifically expressed genes of the body feather (cEB and cLB) are not significantly enriched for any known functions, whereas those of the flight feather (cEF, cMF, and cLF) are significantly enriched for several functions indicated in the figure

Fig. 4

Gene expression level in five comparisons. X-axis and Y-axis plots gene expression counts after FPKM quantification in comparison. (a) cEB vs. cLB, (b) cEB vs. cEF, (c) cEF vs. cMF, and (d) cMF vs. cLF. The red points indicate significantly differentially expressed genes

Fig. 5

IPA Canonical Pathway analysis of differentially expressed genes. (a) cEB vs. cLB, (b) cEB vs. cEF, (c) cEF vs. cMF, and (d) cMF vs. cLF