Multi-Omics Data Reveal Amino Acids Related Genes in the Common Carp Cyprinus carpio

Abstract

Amino acids have important physiological effects on fish growth and development and are essential nutrition for humans. Flavor-related amino acids, such as glutamic acid and glycine, could have a significant effect on the taste of fish flesh. However, studies on the genetic mechanisms of amino acid metabolism in common carp (Cyprinus carpio) are still limited. This study identified divergent patterns on the genomic, transcriptomic and epigenomic levels in two groups of common carp with different amino acid contents. After genome-wide association analysis, a total of 62 genes was found to be associated with glycine, proline and tyrosine content. Transcriptome analysis of essential amino acids, branched-chain amino acids and flavor-related amino acids were performed using brain, liver and muscle tissues, resulting in 1643 differentially expressed genes (DEGs). Whole-genome bisulfite sequencing identified 3108 genes with differentially methylated promoters (DMPs). After the enrichment analysis, a series of pathways associated with amino acid metabolism, including growth regulation, lipid metabolism and the citrate cycle, was revealed. Integrated studies showed a strong correlation between DEGs and DMPs for amino acid contents in brain and muscle tissues. These multi-omics data revealed candidate genes and pathways related to amino acid metabolism in C. carpio.