动物体色的性二态现象（sexual dichromatism）作为最重要的生物多样性模式之一，广泛存在于鸟类中。鸟类的羽色丰富多彩，黑色素、类胡萝卜素等多种色素的沉积以及羽毛微结构的特征是形成多样羽色的基础。一般认为雌雄羽色的分化受到性选择和自然选择驱动，同时与体型、社会行为、分布及生活史特征有关。除去羽色所受的外在选择压力，雌雄羽色的演化还受到自身遗传的限制，相关机制的研究到近年才有所突破，即便如此，此前对于鸟类羽色性二态遗传机制的认识大多来源于对两性个体性腺表达基因差异的研究，且多聚焦于特定色型的驯化个体，限制了对羽色性二态遗传机制的理解。

红腹锦鸡（Chrysolophus pictus）具有鲜明的羽色性二态。成年雄鸟羽色绚丽，其胸腹部呈现出鲜艳的红色，与呈现出暗淡羽色的雌鸟和亚成雄鸟相区别。本研究对红腹锦鸡的基因组进行了高质量的测序和组装，进而选择其具有代表性的胸部羽毛作为研究对象，采用多种方法量化了成年雄鸟、亚成雄鸟与雌鸟之间羽色表型特征的差异，并基于转录组分析比较了不同性别和年龄个体间羽毛发生过程中基因表达水平的差异，从表型特征和遗传机制两个方面揭示了红腹锦鸡羽色性二态的形成基础。主要研究结果如下：

1.红腹锦鸡成年雄鸟胸羽的着色模式与雌鸟及亚成雄鸟呈现显著差异，其羽色性二态由多种色素与微结构差异共同塑造，并且亚成雄鸟与雌鸟具有更相似的羽色特征。基于反射光谱法和鸟类视觉模型对羽色信号的分析结果表明，成年雄鸟与雌鸟存在明显羽色性二态，而亚成雄鸟和雌鸟间的羽色差异不易区分。在对胸羽着色基础的分析中，类胡萝卜素仅沉积于成年雄鸟的胸羽，而在亚成雄鸟和雌鸟中均无沉积；成年雄鸟胸部羽毛的末端具有松散稀疏的特征，其微结构特征显著区别于雌鸟与亚成雄鸟，而亚成雄鸟羽毛的微结构与雌鸟更相似。

2. 利用10×Genomics技术，测序组装获得了高质量的红腹锦鸡基因组。基因组大小为1.13 Gb，Scaffold N50为26.65 Mb。对成年雄鸟、亚成雄鸟和雌鸟共9只红腹锦鸡的胸羽毛囊样品进行转录组测序，并进行基因差异表达水平分析，结果表明，两性别间羽色基因与角蛋白基因的差异表达是决定性二态的主要遗传基础。雌鸟和亚成雄鸟具有更相似的基因表达谱，而与成年雄鸟存在差异。对成年雄鸟与雌鸟的差异表达基因（DEGs）进行GO分析，黑色素合成相关基因被显著富集。通过不同年龄和性别间的差异表达基因进行组间比较筛选，发现TYR, MC1R等与黑色素着色有关的基因在成年雄鸟中相比雌鸟和亚成雄鸟显著上调，且性激素受体基因GPER1和ADRA2C在成年雄鸟的胸羽毛囊中的表达量也存在显著上调；与羽毛角蛋白合成有关的基因（例如：LOC107055225，LOC107055419，LOC431320和LOC431321）在成年雄鸟中显著下调。

本研究通过对红腹锦鸡成年雄鸟、亚成雄鸟与雌鸟的羽色表型进行多尺度的量化，系统揭示了其羽色性二态的表型特征与形成基础，结合高质量的de novo基因组，比较了不同性别、年龄个体间羽毛毛囊基因表达水平的差异，确定了与红腹锦鸡羽色性二态有关的多个备选基因，为深入理解鸟类羽色性二态的形成基础与遗传机制提供了新的认识。

As one of the most important patterns of biodiversity, sexual dichromatism is widespread in birds. The deposition of various pigments such as melanin and carotenoids and the microstructure of feather are the basis for the formation of vivid feather colors. It is generally believed that the diversity of feather color between sexes is driven by natural selection and sexual selection, and is also related to the body shape, social behavior, species distribution and life history of birds. In addition to the external selection pressure of feather color, the evolution of integument coloration between sexes is still limited by bird's own genetics, and related studies has made breakthroughs in recent years. Even so, most of the previous studies on the genetic mechanism of sexual dichromatism focused on the DEGs in the gonads between sexes, and only focused on domesticated individuals with specific color types, which limits the understanding of the genetic mechanism of sexual dichromatism.

The golden pheasant (Chrysolophus pictus) has a distinctive sexual dichromatism of plumage coloration. The adult male has a gorgeous color, and its breast and abdomen show a bright red color, which is different from the female and juvenile male that show a dim color. In this study, I have quantified the phenotype of the breast coloration of three groups of golden pheasant (adult male, juvenile male and female), and have performed de novo sequencing of genome and transcriptome data of breast feather follicles, aimed to reveal the formation mechanism of the sexual dimorphism of golden pheasant from the phenotype to gene expression. The main findings of this study are as follows:

1. The color pattern of golden pheasant are different between different sexes and ages. There are significant differences in pigment deposition and microstructure between adult male and female, and the breast feather color of juvenile male is more similar to female. The results of reflectance spectra and bird visual model analysis show that golden pheasant is not easy to distinguish the color between juvenile male and female breast feathers, but they can distinguish the difference of color between male and the other two groups well (color distances > 3 JND); The results of HPLC analysis shows that carotenoids are only deposited in the feathers of adult males. Scanning electron microscopy (SEM) result indicate that adult male has loose and sparse phenotype of end of breast feather. The shape of the breast feathers of juvenile male is more similar to female. The barbules at the base and the end of the breast feather are almost the same distance between female and juvenile male, and their barbules at the end are denser than the base. For the adult male, the distance between the end barbules is larger which resulted in an incompact phenotype of breast feather. Therefore, golden pheasant shows a very significant sexual dichromatism between adult male and female in terms of pigment deposition and microstructure of breast feather.

2.We sequenced and assembled a high-quality de novo genome from a male golden pheasant, the genome size is 1.13 Gb and the Scaffold N50 is 26.65 Mb. We also sequenced transcriptome of breast follicles from nine golden pheasants including adult males, juvenile males and females. The result of hierarchical clustering shows that the expression profiles of different genes are consistent in each group. Female and juvenile males are clustered first, and then clustered with adult male birds; GO analysis of adult male and female birds showed that the significant enrichment results were related to the process of melanin synthesis. For the DEG analysis for adult males, juvenile males and females, we selected genes with the same regulatory trend in the two comparison groups of "adult male vs female" and "adult male vs juvenile male", and have found that adult male birds have several up-regulated genes related to melanin coloration, such as TYR, MC1R, in addition to, two sex hormone receptor genes GPER1 and ADRA2C are up-regulated in adult male. The down-regulated genes in adult male birds are related to feather keratin, including LOC107055225, LOC107055419, LOC431320 and LOC431321, which may contribute to the different microstructure of breast feather between sexes.

In this study, the phenotype characteristics of feather color from golden pheasant was quantified at multiple levels, and the formation basis of feather color dichromatism were systematically revealed. Combined with high-quality de novo genome and transcriptome of the growing follicles, DEG analysis of 3 groups has revealed important genes that may play important roles in shaping sexual dichromatism of golden pheasant, which may provide a new understanding of the formation basis and genetic mechanism of dichromatism.