Multi-Omics Analysis Reveals Impacts of SCARB1, TYR, and TYRP1 Knockouts on Pigmentation and Metabolic Pathways in Oujiang Color Common Carp

Abstract

Gene knockout (KO) techniques are important for understanding gene function and their impact on organismal traits. This study investigates the effects of targeted KO of SCARB1, TYR, and TYRP1 genes in Oujiang Color common carp, focusing on pigmentation changes, metabolic dysregulation, and host-microbiome interactions. Our multi-omics approach revealed that SCARB1 KO led to complete loss of red pigmentation, while TYR and TYRP1 KOs resulted in hypopigmentation and altered pigmentation patterns. Transcriptomic analysis identified seven key genes (PLA2G4, C3, F2, ERN1, UGP2, purA, and GRIN2A), linked to major pathways: glycerophospholipid metabolism, biosynthesis of cofactors, autophagy, and neuroactive ligand-receptor interaction. Notably, we observed significant upregulation of phosphatidylethanolamine (PE) and disruptions in glycolysis and tyrosine metabolism. Histological analysis showed reductions in epithelial and goblet cells, and microbiome profiling indicated shifts in microbial diversity, including significant changes in Firmicutes, Bacteroidetes, and genera such as Pseudomonas, Rhodobacter, Bacillus, and ZOR0006. These findings uncover pigmentation genes as pivotal players in regulating pigmentation, cellular stress, metabolism, and the microbiota. This study improves our understanding of pigmentation regulation in common carp and provides potential molecular targets for color trait improvement in aquaculture species.