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Background: Fish muscular amino acids are a series of essential nutrients that embrace essential amino acids, branched-chain amino acids and flavorous amino acids. Previous studies have found that amino acids have important physiological effects on fish growth and development, as they are involved in maintaining nitrogen balance and in the formation of enzymes and hormones. Amino acids, such as aspartic acid, glutamic acid, glycine and alanine, that can have a significant effect on fish umami taste are called flavorous amino acids. Nevertheless, the studies on the genetic mechanisms of amino acid metabolism in the common carp (Cyprinus carpio) are still limited.Results: The purpose of this study was to examine the divergent patterns at the genomic, transcriptomic and epigenomic levels in fish with different amino acid contents. Genome-wide association analysis using 195 individuals of common carp was conducted, and 62 genes were identified to be associated with glycine, proline, and tyrosine content. RNA-Seq of samples with extreme contents of essential amino acids, branched-chain amino acids and flavorous amino acids was applied using brain, liver and muscle tissues, resulting in 1,643 differentially expressed genes. Whole-genome bisulfite sequencing identified 3,108 genes with differentially methylated promoters. Through the enrichment analysis of transcriptome and DNA methylation results, we screened out a series of enriched pathways associated with amino acid metabolism, including various categories of pathways spanning growth regulation, lipid metabolism, the citrate cycle and other signaling pathways. Integrated studies demonstrated prominent correlations between DGE and DMP for amino acid contents trait in brain and muscle tissues.Conclusions: In summary, the multi-omics data revealed candidate genes and pathways correlated with amino acid metabolism. These results will promote the process of the genomic selection and breeding strategy in muscular amino acid contents of fish. |
