expression profiles of coding and non-coding RNAs from white and black skin samples obtained from individual Wuzhishan pigs

Coat color is readily observable, can be used to distinguish different species, breeds, or individuals, and has long been a subject of fascination. However, the underlying genetic mechanisms of pigmentation are often difficult to decipher. Most studies have focused mainly on polymorphisms of candidate genes, while limited information is available on how coat color phenotypes may be regulated at the transcriptional level, especially in Chinese indigenous breeds such as Wuzhishan pigs, which have black backs and white abdomens. In this study, we used high-throughput RNA sequencing to compare expression profiles of coding and non-coding RNAs from white and black skin samples obtained from individual Wuzhishan pigs. Expression profiling revealed that 194 lncRNAs, 189 mRNAs, and 162 miRNAs had significantly different levels of expression (|log2 fold-change|>1, P-value<0.05) in white and black skin. Relative to RNA levels in black skin, white skin had higher expression of 185 lncRNAs, 181 mRNAs, and 23 miRNAs, and lower expression of 9 lncRNAs, 8 mRNAs, and 139 miRNAs. Functional analysis suggested that the differentially expressed transcripts are involved in biological processes such as melanin biosynthetic, pigmentation, and tyrosine metabolism. Several key genes involved in melanogenesis, including MLANA, PMEL, TYR, TYRP1, DTC, TRPM1, and CAMK2A had significantly different expression in the two skin tissues. Potential lncRNA-miRNA-gene interactions were also examined. 15 lncRNAs, 11 miRNAs, and 7 genes formed 23 lncRNA-miRNA-gene pairs, suggesting that complex regulatory networks of coding and non-coding genes underlie the coat color trait in Wuzhishan pigs. The lncRNA-miRNA-gene interaction networks were constructed for the first time contributes to elucidate the complex molecular mechanisms underlying skin physiology and melanogenesis in pig.