Transcriptomic profiles of melanin pigmentation in a plumage ornament

Feather coloration is one of the most extraordinary examples of phenotypic diversity. This diversity results both from the variation in hue as well as from the presence/absence of pigment in distinct feather regions. The mechanisms that drive presence/absence of pigmentation in feathers are not yet fully understood. Here we characterize the gene expression profiles associated with differential melanin pigmentation in Dark-eyed junco (Junco hyemalis) tails, a social feather ornament used in courtship and male-male competition. Junco tail feathers contain both white apigmented regions as well as dark melanin-pigmented regions. We compared the transcriptome-wide gene expression in developing white and dark regions of tail feathers to understand the regulatory pathways that may regulate the development of this feather ornament. We show that both white and dark feathers express melanocyte markers, indicating that white feathers contain cells capable of producing pigment. However, only dark cells express genes associated with melanin synthesis. We identify differences in expression of genes that may regulate melanocyte activation in dark feathers. Future studies should experimentally test the role of these genes in driving differences in feather pigmentation. Overall design: We analyzed gene expression in developing feathers from 7 Dark-eyed junco (Junco hyemalis) individuals, sampling 3 to 8 feathers from each bird. Specifically, we contrast gene expression in the completely white outer tail feathers (6th rectrix), completely dark inner feathers (2nd rectrix), and the white and dark developing portions of the intermediate 4th rectrix.