Back and thigh skin of chickens showed significant differences in the thickness and the feather follicle density and size, which are important traits for slaughtered chickens' appearance. In the present study, global gene expression profiling was conducted in the back and thigh skin of chickens using Microarray technology. The results showed that 676 genes were differentially expressed between back and thigh skin. The expression of the differentially expressed genes (DEGs), including PPP1R3C, IGF1, PTCHD1, HOXB6, FGF9, CAMK4, SHH, BMP8B, FOXN1 and PTGER2, was validated by real-time quantitative polymerase chain reaction (RT-qPCR), and the results were consistent with microarray results. Functional analysis revealed that the DEGs were significantly involved in cell proliferation, differentiation, apoptosis, adhesion and transport process, and the pathways were significantly mapped into the ECM-receptor interaction, peroxisome, focal adhesion, Hedgehog and PPAR signalling pathways. Protein-protein interaction network analysis suggested that signalling pathways related to feathers morphogenesis and development, such as Wnt, FGF, MAPK, SHH and BMP signalling pathways, occupied important positions in the network. Genes involved in these signalling pathways and adhesion molecules might play a vital role in skin and feather follicle development. Further single nucleotide polymorphism (SNP) association analysis of Wnt3A showed that the AC genotype of SNP g.255361 C>A significantly increased the feather follicle density of thigh skin. Our findings may provide new insights on candidate genes and pathways related to skin and feather follicle formation of chickens.

中文翻译：

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鸡皮毛囊性状候选基因及分子通路的基因共表达网络分析

鸡的背部和大腿皮肤在厚度和毛囊密度和大小方面表现出显着差异，这是屠宰鸡外观的重要特征。在本研究中，使用微阵列技术在鸡的背部和大腿皮肤中进行了全局基因表达谱分析。结果显示676个基因在背部和大腿皮肤之间差异表达。通过实时定量聚合酶链反应 (RT-qPCR) 验证差异表达基因 (DEG) 的表达，包括 PPP1R3C、IGF1、PTCHD1、HOXB6、FGF9、CAMK4、SHH、BMP8B、FOXN1 和 PTGER2，并且结果与微阵列结果一致。功能分析表明，DEGs显着参与细胞增殖、分化、凋亡、粘附和转运过程，并且这些通路被显着地映射到 ECM 受体相互作用、过氧化物酶体、粘着斑、刺猬和 PPAR 信号通路。蛋白质-蛋白质相互作用网络分析表明，与羽毛形态发生和发育相关的信号通路，如Wnt、FGF、MAPK、SHH和BMP信号通路，在网络中占有重要地位。参与这些信号通路和粘附分子的基因可能在皮肤和羽毛毛囊发育中发挥重要作用。Wnt3A的进一步单核苷酸多态性（SNP）关联分析表明，SNP g.255361 C>A的AC基因型显着增加了大腿皮肤的羽毛毛囊密度。我们的发现可能为与鸡皮肤和羽毛毛囊形成相关的候选基因和途径提供新的见解。