Fish exhibit a broad spectrum of colors and patterns facilitated by specialized cells known as chromatophores. The vibrant coloration of fish, controlled by complex genetic and environmental interactions, serves critical roles in ecological functions such as mating, predation, and camouflage. This diversity not only makes fish an invaluable model for exploring the molecular mechanisms of pigmentation but also significantly impacts their economic value within the aquaculture industry, where color traits can drive marketability and breeding choices. This review delves into the sophisticated biological processes governing fish pigmentation and discusses their applications in enhancing aquaculture practices. By exploring the intersection of genetic regulation, environmental influences, and advanced breeding techniques, this review highlights both the scientific understanding and practical applications of fish coloration, providing a bridge between basic biological research and its application in commercial aquaculture.

Red tilapia is highly valued as a premium variety in Asia due to its vibrant red skin coloration. However, during aquaculture production, irregular black pigmentation (melanotic spots) frequently appears on the skin of some individuals, significantly reducing their economic value. Although epigenetic regulation is suspected to play a role, its involvement remains poorly understood. To uncover the molecular mechanisms underlying black spot formation, we employed Cleavage Under Targets and Tagmentation (CUT&Tag) to compare four key histone modifications (H3K4me3, H3K4me1, H3K27me3, and H3K27ac) between red and black pigmented skin regions. Integrated with transcriptomic analysis, our data indicated that red skin regions exhibited high expression of genes suppressing melanin synthesis, whereas melanotic spots likely resulted from localized derepression, allowing upregulation of melanin biosynthetic genes. Furthermore, by combining epigenomic chromatin state analysis and transcriptome data, we identified critical genes consistently active in melanotic spots and their corresponding potential cis-regulatory elements. Motif analysis of transcription factor binding sites upstream of these regulatory elements revealed that Ehf, Klf9, and Egr1 might facilitate melanin production in black regions, while Prdm1 and Sp5 could inhibit melanogenesis in red regions by repressing the Wnt signaling pathway. These findings provide valuable epigenetic insights into the mechanisms driving melanotic spot formation in red tilapia.