Supplementary Material for: Transcriptome Profile Analysis of Mechanisms of Black and White Plumage Determination in Black-Bone Chicken

<b><i>Background/Aims:</i></b> Melanin is a major and ubiquitous component of plumage colouration, and patterns of melanin pigmentation in birds are extremely varied. However, the molecular mechanism of pigmentation in avian plumage is still largely unknown. <b><i>Methods:</i></b> To elucidate the molecular mechanisms involved in the formation of black and white plumage, this study takes advantage of high-throughput sequencing technology to compare differences in the transcriptome between black and white chicken feather bulbs. In total, we constructed six cDNA libraries from black (Group B) and white (Group W) feather bulbs in the dorsal plumage of Muchuan black-boned chickens. <b><i>Results:</i></b> A comparison between Groups B and W revealed 61 differentially expressed genes, with 47 displaying higher, and 14 displaying lower, levels of expression in white feather bulbs. Our results revealed a set of candidate genes and two potential metabolic pathways involved in black-bone chicken plumage melanogenesis. These include four homeobox genes (HOXB9, HOXC8, HOXA9, and HOXC 9), two glutathione (GSH) metabolism-related genes (CHAC1 and GPX3), and the transforming growth factor beta (TGF-β) signalling pathway. Two known genes, TYR and MITF, were also shown to play a role in melanin formation. <b><i>Conclusion:</i></b> our data provide a valuable resource for discovering genes important in plumage melanin formation and will help further elucidate the molecular mechanisms for black and white plumage.

***背景与目的：*** 黑色素（Melanin）是羽毛着色的主要且广泛存在的组成成分，鸟类的黑色素沉着模式极为多样。然而，鸟类羽毛着色的分子机制在很大程度上仍未明确。
***方法：*** 为阐明参与黑白羽毛形成的分子机制，本研究采用高通量测序技术，对比黑白鸡羽毛毛囊的转录组（transcriptome）差异。本研究共计从沐川乌骨鸡背部羽毛的黑色（B组）与白色（W组）羽毛毛囊中构建了6个cDNA文库。
***结果：*** 对B组与W组的对比分析显示，共存在61个差异表达基因（differentially expressed genes），其中白色羽毛毛囊中有47个基因表达上调、14个基因表达下调。本研究结果鉴定出一批参与乌骨鸡羽毛黑色素生成的候选基因与两条潜在代谢通路，包括4个同源框基因（homeobox genes）：HOXB9、HOXC8、HOXA9及HOXC9，2个谷胱甘肽（GSH）代谢相关基因：CHAC1与GPX3，以及转化生长因子β（TGF-β）信号通路。此外，酪氨酸酶（TYR）与小眼畸形相关转录因子（MITF）这两个已知基因也被证实参与黑色素形成。
***结论：*** 本研究的数据为发掘与羽毛黑色素形成相关的关键基因提供了宝贵资源，同时将有助于进一步阐明黑白羽毛形成的分子机制。