Investigating transcriptomics and metabolomics differences offers insights into the mechanisms of muscular fat deposition in common carp (Cyprinus carpio)

With the global population increasing and lifestyle improving, the demand for high-quality nutritional aquatic foods has been rising. Muscle fat is a crucial nutritional index for evaluating the quality of fish flesh. However, the comprehensive and systematic understanding of the molecular mechanism underlying differences in muscle fat deposition remains insufficient. In this study, we integrated transcriptomics and metabolomics of selected samples with extremely high and low muscle fat in common carp (Cyprinus carpio), the major freshwater aquaculture fish in Asia, to identify critical genes, metabolites and metabolic pathways. We totally identified 204 differentially expressed genes (DEGs) and 1528 differentially accumulated metabolites (DAMs). Glycerolipid, glycerophospholipid and glyoxylate and dicarboxylate metabolisms were enriched through both transcriptomics and metabolomics. These lipid metabolism pathways may be regulated by some critical signal transduction pathways, including Extracellular matrix [ECM]-receptor interaction, mTOR signaling pathway and FoxO signaling pathway. Combined with the validation of gene expression and biochemical indices, a supposed regulatory network was established. To our knowledge, it is the first study to apply a multi-omics approach in fish with naturally different muscle fat to comprehensively elucidate the mechanism. This study could deepen our understanding of the molecular mechanism of muscle fat deposition and be helpful for improving the quality of fish.