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Updated: Jan 13, 2026

Reverse Genetic Approach to Identify Regulators of Pigmentation using Zebrafish
Published on: March 1, 2022
Integrative Methylome and Transcriptome Analysis Reveals Epigenetic Regulation of Pigmentation in Oujiang Color
Wenqi Zhao1, Xiaowen Chen1, Ayesha Arif1
1Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
Abstract:
Oujiang color common carp display four striking varieties of pigmentation, but their epigenetic basis is unclear. We integrated genome-wide DNA methylation (MBD-seq) and transcriptomes (RNA-seq) from dorsal skin of four Oujiang color common carp varieties with three biological replicates. Black-spotted groups (RB, WB) showed approximately 6% higher global methylation than non-black-spotted groups (WR, WW), with differential methylation enriched in introns (>23%) and intergenic regions (>47%). Integrative analyses revealed a strong inverse association between promoter methylation and gene expression; 96 pigmentation-related genes were identified, spotlighting genes such as ASIP and frmA as key epigenetically silenced regulators in black-spotted carp. RT-qPCR confirmed directional concordance with RNA-seq for ASIP, frmA, DGAT2, SCARB1, and FOSB. Pathway enrichment implicated melanogenesis metabolism, tyrosine metabolism, lipid metabolism, and fatty acid metabolism, suggesting an interplay between pigment deposition and metabolic regulation. Collectively, the findings present an exploratory view of epigenetic control of coloration and underscore promoter methylation as a core layer influencing color diversity in Oujiang color common carp.
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