Identification of pigment genes (melanin, carotenoid and pteridine) associated with skin color variant in red tilapia using transcriptome analysis

Red tilapia (Oreochromis spp.) is an inter-specific hybridization between two tilapia strains by directional breeding. It is favored by consumers due to the color and market value. However, the skin color of red tilapia is unstable and phenotypic segregation with irregular black dots may appear in their offsprings, which is harmful to red tilapia aquaculture industry. To elucidate the mechanisms underlying differential pigmentation in red tilapia, four typical phenotypes were collected for comparative transcriptome analysis. Differentially expressed genes (DEGs) were categorized into three aspects, including melanin, carotenoid and pteridine. The Gene Ontology and KEGG pathways analysis were also done afterwards. We identified candidate genes related to the regulation of pigment synthesis and deposition and the distribution of chromatophores. The genes relevant to melanin synthesis (e.g., pmel, oca2, tyrp1, bmp2, vps11, edn3, ednrb and wnt6) have the higher expression in whole black red tilapia. The genes with the elevated expression level in whole pink tilapia were involved in carotenoid transport and deposition cooperated with lipid metabolism (e.g., scarb1, plin2, stard5, stard10, rbp7, pnpla2, apod and rdh12, etc.), xanthophore formation (e.g., pax7 and gch1). This research would be useful for future genetic studies on the pigmentation of the skin color variation in red tilapia, and it provides a theoretical basis for achieving genetic improvement of red tilapia body-color stability and consistency in red tilapia aquacluture industry.