Comparison of muscle nutritional composition, texture quality, carotenoid metabolites and transcriptome to underling muscle quality difference between wild-caught and pond-cultured Yellow River carp (Cyprinus carpio haematopterus)

The common carp is one of the most important freshwater aquaculture fish. The quality is an emerging concern for aquatic animals, and wild-caught fish is considered to exhibit better quality compared with cultured fish in some species. In present study, muscle nutritional composition, flesh quality index, scale and fins color, carotenoid metabolites, and RNA-sequencing were compared between wild-caught carp (WCC) and pond-cultured carp (PCC) to elucidate their quality difference. Results showed that WCC showed higher moisture, EPA, DHA, and EAA/TAA compared with PCC (P < 0.05). However, PCC showed higher muscle protein and lipid content, and mono-unsaturated fatty acids (MUFA). Hardness, chewiness, and shear force were significantly higher in WCC compared with PCC. The WCC showed higher a* and b*values in back and caudal fin (P < 0.05). Targeted metabolomics of carotenoids analysis showed that 4 carotenoid metabolites in scale and 6 carotenoid metabolites in fins showed significant difference between WCC and PCC. Furthermore, transcriptome analysis showed that a total of 8624 differentially expressed genes (DEGs) were identified in WCC vs. PCC. Gene function enrichment demonstrated that up-regulated DEGs were mainly in response to cell cycle, immunology regulation, and inositol phosphates metabolism, whereas, down-regulation genes were mainly in response in RNA transport, carbohydrate metabolism, protein and lipid metabolism. The study provided a comprehensive view of nutritional and texture difference between WCC and PCC, and which could provide reference for improving nutritional and texture quality in farmed carp.