Integrative transcriptomics and metabolomics analysis of body color formation in the common carp

The coloration of aquatic animals influences their adaptability to environment and economic values. The skin color of common carp (Cyprinus carpio) is various between different strains. Hebao red carp is famous for its bright red color, which is different from the brown skin color of wild-type common carp. To reveal the different components and molecular mechanism between skins with red and brown colors, LC-MS and transcript analysis were conducted. 614 significantly different metabolites (SDM) and 392 differentially expressed genes (DEG) were detected between skins of Hebao red carp (HB) and Yellow River carp (YR). There are 35 KEGG pathways shared by DEGs and SDMs, among which microbial metabolism in diverse environments (ko01120), carbon metabolism (ko01200) and metabolic pathways (ko01100) were significantly enriched by DEGs and SDMs. Pathways related to melanin synthesis and retinal metabolism were down-regulated in HB, such as adh8a, adh8b, cyp3a, dhrs3b, mart1, hgd, hpd and maiA, which may induce the disappear of melanocytes and accumulation of carotenoid. The content of lutein in HB skin was significantly higher than in YR. This study shows retinol and carotenoid metabolism is vital in the common carp body color formation, and will help understand the mechanism of color determination in common carp.