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

Abstract

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.

Keywords: Cyprinus carpio; amino acid; nutritional deposition; transcriptome; unsaturated fatty acids.

Figure 1

Comparison of differential gene expression in the different carps of liver and muscle samples. Bar graphs (A) (liver) and (B) (muscle) show different comparisons of upregulated and downregulated genes.

Figure 2

Illustration of the GO pathways in the different carps of liver and muscle samples. (A–C) represent the results of pairwise comparisons between the liver tissues of groups YC, FFRC, and HC, while (D–F) represent the results of pairwise comparisons between muscle tissues of groups YC, FFRC, and HC. The horizontal axes in the graphs display the names of the GO entries, and the vertical axes indicate the −log10 p values.

Figure 3

KEGG bubble plots representing the different carps of liver and muscle samples. (A–C) present the results of two-by-two comparisons between the liver tissues of groups YC, FFRC, and HC, while (D–F) show the outcomes of similar comparisons between the muscle tissues of groups YC, FFRC, and HC. The horizontal axes in the graphs represent the enrichment scores, where larger bubbles indicate higher numbers of differentially protein-coding genes within that entry. The bubble color transitions from green to white and then to brown with smaller enrichment p-values indicate greater statistical significance values.

Figure 4

Heatmaps illustrating the changes in gene expression related to (A) fatty acid metabolism in the liver and (B) amino acid metabolism in the muscle. The FPKM value of each gene was used to plot the heatmaps. Upregulated genes are visually represented in red, whereas downregulated genes are represented in blue.

Figure 5

Relative expressions of DEGs detected by qPCR and RNA-Seq. The left y-axes represent the relative expression results obtained via qPCR. The right y-axes show the gene expression levels in FMPK obtained through RNA-Seq. (A–D) correspond to the four validated genes in the liver tissues while (E–H) represent the four validated genes in the muscle tissues. Different lowercase letters represent significant differences (p < 0.05), and the letters apply only to the comparison of qPCR data.