Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China.
Hubei Livestock and Poultry Breeding Centre, Wuhan 430070, China.
Genomics. 2020 Mar;112(2):1853-1860. doi: 10.1016/j.ygeno.2019.10.019. Epub 2019 Oct 31.
To increase the current understanding of the gene-expression profiles in different skin regions associated with different coat colors and identify key genes for the regulation of color patterns in goats, we used the Illumina RNA-Seq method to compare the skin transcriptomes of the black- and white-coated regions containing hair follicles from the Boer and Macheng Black crossbred goat, which has a black head and a white body. Six cDNA libraries derived from skin samples of the white-coated region (n = 3) and black-coated region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for skin samples from black- and white-coated regions, respectively, of which 75.39% and 76.05% were covered in the genome database. A total of 165 differentially expressed genes (DEGs) were detected between these two color regions, among which 110 were upregulated and 55 were downregulated in the skin samples of white- vs. black-coated regions. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that some of these DEGs may play an important role in controlling the pigmentation of skin or hair follicles. We identified three key DEGs, i.e., Agouti, DCT, and TYRP1, in the pathway related to melanogenesis in the different skin regions of the crossbred goat. DCT and TYRP1 were downregulated and Agouti was upregulated in the skin of the white-coated region, suggesting a lack of mature melanocytes in this region and that Agouti might play a key developmental role in color-pattern formation. All data sets (Gene Expression Omnibus) are available via public repositories. In addition, MC1R was genotyped in 200 crossbred goats with a black head and neck. Loss-of-function mutations in MC1R as well as homozygosity for the mutant alleles were widely found in this population. The MC1R gene did not seem to play a major role in determining the black head and neck in our crossbred goats. Our study provides insights into the transcriptional regulation of two distinct coat colors, which might serve as a key resource for understanding coat color pigmentation in goats. The region-specific expression of Agouti may be associated with the distribution of pigments across the body in Boer and Macheng Black crossbred goats.
为了提高对与不同毛色相关的不同皮肤区域的基因表达谱的现有认识，并确定调控山羊毛色模式的关键基因，我们使用 Illumina RNA-Seq 方法比较了含有博尔和麻城黑杂交山羊毛囊的黑色和白色被毛区域的皮肤转录组，该山羊具有黑色头部和白色身体。从三头全同胞山羊的白色被毛区域（n=3）和黑色被毛区域（n=3）皮肤样本中构建了六个 cDNA 文库。平均而言，我们分别从黑色和白色被毛区域的皮肤样本中获得了约 7650 万和 7350 万条reads，其中 75.39%和 76.05%被基因组数据库覆盖。在这两个颜色区域之间共检测到 165 个差异表达基因（DEGs），其中 110 个在白色 vs. 黑色被毛区域的皮肤样本中上调，55 个下调。GO 和京都基因与基因组百科全书富集分析的结果表明，其中一些 DEGs 可能在控制皮肤或毛囊的色素沉着中发挥重要作用。我们在杂交山羊不同皮肤区域的黑素生成相关途径中鉴定出三个关键 DEGs，即 Agouti、DCT 和 TYRP1。在白色被毛区域的皮肤中，DCT 和 TYRP1 下调，Agouti 上调，表明该区域缺乏成熟的黑色素细胞，Agouti 可能在颜色图案形成中发挥关键发育作用。所有数据集（Gene Expression Omnibus）均可通过公共数据库获取。此外，还对 200 头具有黑色头部和颈部的杂交山羊进行了 MC1R 基因分型。在该群体中广泛发现 MC1R 的功能丧失突变以及突变等位基因的纯合性。MC1R 基因似乎在决定我们的杂交山羊的黑色头部和颈部方面没有起主要作用。我们的研究提供了对两种不同毛色的转录调控的见解，这可能是理解山羊毛色色素沉着的关键资源。Agouti 的区域特异性表达可能与博尔和麻城黑杂交山羊体内色素的分布有关。
