Background: Although many genes have been found to be associated with skin pigmentation,the characteristics of global gene expression is still not well understood at early stage of skin pigmentation in mammals.Here we reported a rare natural group of goat(Youzhou dark skin goat)featuring the dark skin of body including the visible mucous membranes,which may be an exclusive kind of mammalian species with this special phenotype so far.Using two goat groups with different skin colors as the models,we investigated the global gene expression in the fetal skin at gestation of 100 days in goats by deep RNA-sequencing method.Results: With a computational pipeline,we identified 1616 novel transcripts with certain protein coding potential but differing from the catalog of lncRNA in goat genome.According to their annotation,these novel transcripts were classified into two distinct groups,especially large differences observed in TEs density and position bias near TSS in their gene sequences.Moreover,we identified a large amount of alternative splicing(AS)events in the present study.Especially,there were AS events in the differentially expressed(DE)genes between the two groups of goat with different skin colors,such as ASIP,TYRP1,DCT,and RAB27A,which are well-known genes associated with pigmentation.Subsequent functional enrichment analysis of the DE genes demonstrated that 7 terms relative to(hyper)pigmentation and one KEGG pathway associated with melanogenesis were most overrepresented in our analyses.In addition,ASIP and TYRP1 were also significantly enriched in a kind of OMIM_DISEASE in human.These findings above provide the considerable evidence underlying a diversity of dermal colors in goats at global level of gene expression.Conclusion: There are obvious differences in the characteristics of fetal skin transcriptome between hyperpigmented and normal skin of goats.Our findings can not only contribute to elucidate the mystery of skin pigmentation at early stage of development,but contribute to the annotation of the goat genome.The Youzhou dark-skin goat can also be used as an ideal animal model for human diseases associated with pigment,such as skin melanopathy,melanosis coli,mucosal melanosis,etc.