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.羽色是表型多样性（phenotypic diversity）最引人注目的例证之一。该多样性既源自色调的差异，也源于不同羽毛区域中色素的存在与否。目前，调控羽毛中色素形成与缺失的分子机制尚未完全阐明。 本研究针对暗眼灯草鹀（Dark-eyed junco, *Junco hyemalis*）尾羽的差异性黑色素沉积展开基因表达谱表征分析——暗眼灯草鹀的尾羽是一类用于求偶及雄性间竞争的社会性羽毛装饰结构。该物种的尾羽同时存在白色无色素区域与深色黑色素沉积区域。 我们对发育中的尾羽白色与深色区域开展全转录组（transcriptome-wide）基因表达分析，以探究可能调控该羽毛装饰结构发育的调控通路。研究发现，白色与深色羽毛均表达黑色素细胞（melanocyte）标记基因，表明白色羽毛中存在具备色素合成能力的细胞；但仅深色区域的细胞表达与黑色素合成（melanin synthesis）相关的基因。我们还鉴定出了可能调控深色羽毛中黑色素细胞激活的差异表达基因。未来研究可通过实验验证这些基因在羽毛色素沉积差异形成中的作用。 总体实验设计：我们分析了7只暗眼灯草鹀（*Junco hyemalis*）发育中羽毛的基因表达，每只个体采集3至8枚羽毛。具体而言，我们对比了三类样本的基因表达：完全白色的外侧尾羽（第6枚尾羽，6th rectrix）、完全深色的内侧尾羽（第2枚尾羽，2nd rectrix），以及中间第4枚尾羽的白色与深色发育区域。