Skin transcriptome profiles associated with coat color in goat

Capra hircus, an economically important livestock, plays an indispensable role in the world animal fiber industry. To identify additional genes that may play important roles in coat color regulation, Illumina/Solexa high throughput sequencing technology was used to catalog the global gene expression profiles in the skin of three different coat colors goat (Lubei white goat (white), Jining gray goat (gray) and Jianyang big ear goat (brown)). The RNA-Seq analysis generated 83174342, 70222592 and 52091212 clean reads in white skin, gray skin and brown skin, respectively, which provided abundant data for further analysis. A total of 91 genes were differentially expressed between the gray skin and white skin libraries, with 74 upregulated and 17 genes downregulated. Between the brown skin and white skin libraries, there were 23 upregulated genes and 44 downregulated genes, while there were 33 upregulated genes and 121 downregulated genes between the brown skin and gray skin libraries. To our surprise, and showed no significant difference in the skin of three different coat colors and the expression of was only detected in white skin and not in gray and brown skins. The expression of , , , and was validated by real-time quantitative polymerase chain reaction (qPCR) and the results of the qPCR were consistent with the RNA-seq except the expression of between the gray skin and white skin libraries. This study provides several candidate genes that may be associated with the development of diferent coat colors goat skin. More importantly, the fact that the gene was only detected in the white skin and not in the other dark skins and the gene showed no significant difference in expression between the three different coat colors goat is of particular interest for future studies that aim to elucidate theirs functional role in the regulation of skin color. These results will expand our understanding of the complex molecular mechanisms of skin physiology and melanogenesis in goat and provide a foundation for future studies.