Genome-wide methylation and transcriptome analysis in koi carp (Cyprinus carpio var. koi): Uncovering novel molecular mechanisms in skin color differentiation and pigmentation

Koi carp (Cyprinus carpio var. koi) are popular ornamental fish, and their complex mottling and patterning are ideal models for studying the regulatory mechanisms of pigmentation. However, there are few studies addressing the influence of epigenetics, especially DNA methylation on koi coloration and phenotype formation. In this study, we focused on three phenotypes of Kohaku offspring, namely the Rs group (all red-skinned), the Rw group (red-white-skinned) and the Ws group (all white-skinned), each of which underwent DNA methylation and transcriptome sequencing. A comprehensive analysis revealed that the genes in the differentially methylated regions and the differentially expressed genes (DEGs) were significantly enriched in pathways such as retinol metabolism and melanogenesis. The highest number of DEGs was observed in the Rs and Rw groups, while key genes involved in color differentiation, such as mitf, gch2 and bco1, were hypermethylated and regulated in the Rs group. Vivo experiments also showed that inhibition of methylation led to a significant increase in the expression of genes related to the retinol and pteridine pathway (e.g. pnp4a, gch2 and bco2) in the dorsal skin but not in the ventral skin. The results of in situ hybridization of carotenoid metabolism genes (bco1 and bco2) also suggest that DNA methylation is involved in the regulation of different color phenotypes and coloration in various parts of the body. These findings could deepen the understanding of the dynamic changes in DNA methylation that are crucial for the differentiation and variation of skin color in koi, thus revealing the potential influence of epigenetics on pigmentation.