Transcriptome Analysis Reveals the Potential Key Genes in Nutritional Deposition in the Common Carp (Cyprinus carpio)

Simple Summary: The common carp (Cyprinus carpio) is a significant aquaculture species in China. This study sought to identify the critical genes and signaling pathways that regulate muscle nutritional composition by analyzing muscle nutritional content and transcriptome data from liver and muscle tissues across three different carp varieties. The results revealed that among the three varieties, FFRC carp exhibited the highest levels of crude fat, total n-3 polyunsaturated fatty acids, and total n-6 polyunsaturated fatty acids in its muscle tissue. This was associated with the significant upregulation of genes in the liver involved in the activation and transportation of fatty acid as well as biosynthesis and elongation of long-chain unsaturated fatty acids. Additionally, Huanghe carp demonstrated the highest muscle crude protein and amino acid content. This was correlated with significant changes in the expression of genes related to amino acid metabolism. This research lays a theoretical groundwork for the genetic enhancement of carp, aimed at optimizing its nutritional composition. The common carp (Cyprinus carpio) is one of the most important aquaculture species in China, known for its remarkable adaptability and nutritional profile. However, the specific molecular response mechanisms regulating the nutritional deposition of carp remain inadequately elucidated. This study conducted a comprehensive analysis of muscle nutritional content and transcriptome data from liver and muscle tissues of three distinct carp varieties. The aim was to elucidate the key genes and signaling pathways that regulate muscle nutritional composition in carp. The findings revealed that FFRC carp (FFRC) exhibited significantly higher levels of crude fat, total n-3 polyunsaturated fatty acids, and total n-6 polyunsaturated fatty acids in muscle tissue compared to Ying carp (YC) and Huanghe carp (HC) (p < 0.05). Transcriptomic analyses correlated these elevated levels with a marked upregulation of genes involved in the activation and transportation of fatty acid (fabp7, acsl5, acsbg2) as well as biosynthesis and elongation of long-chain unsaturated fatty acids (elovl2, fads2) within the liver. Furthermore, the flavor amino acid, essential amino acids, and crude protein content in the muscle of HC were significantly higher than in FFRC and YC (p < 0.05). Transcriptomic analyses indicated that this was associated with significant changes in the expression of genes related to amino acid metabolism (asns, alt, ldha, glul, setd, prodh, l3hypdh, hoga1) within their muscle tissue. This research provides a theoretical foundation for the precise modulation of the muscle nutritional composition in carp.