Multi-omics Study On Muscular Amino Acid And Fatty Acid Content And Regulation Of Trim25 Gene Expression In The Yellow River Carp

Common carp(Cyprinus carpio)is one of the most widely cultured freshwater fish all over the world.Most C.carpio are cultured in China,with an annual production of around three million tons.There are a variety of populations of C.carpio in China,such as Yellow River carp,Songpu mirror carp,Hebao red carp,Xingguo red carp,Oujiang color carp and many hybrid strains.Among these,the Yellow River carp occupies an important position due to its high nutritional value.The composition and content of amino acids and highly unsaturated fatty acids are the key factors affecting the nutritional value and taste of the Yellow River carp.However,the genetic mechanism of muscle amino acid and high unsaturated fatty acid content of carp is still unclear.First,genome-wide association analysis using 195 individuals of Yellow River 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 1643 differentially expressed genes.Whole-genome bisulfite sequencing identified 3108 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.GWAS was performed on 40 first-year-old Yellow River carp and 96 third-year Yellow River carp.The first batch of samples screened 239 genes related to ARA,DHA and EPA,and the second batch screened 31 genes related to ARA,DHA and EPA.The samples with the highest 1/4 and lowest 1/4 contents of ARA,DHA and EPA in the first batch of sample were collected for RNA-seq.There were 4433 genes related to ARA traits,5453 genes related to DHA traits and 237 genes related to EPA.Through the KEGG enrichment analysis,"fatty acid degradation","pyruvate metabolism","glycerophospholipid metabolism","unsaturated fatty acid biosynthesis","PPAR signaling pathway","fatty acid elongation" and other pathways were enriched.The innate immune system is the main defense system against virus infection in teleost fish.As an important part of the innate immune system,the TRIM protein family participates in the regulation of immune network during virus infection,among which TRIM25 has been reported to play an important role in the immune response in many types of fish.There are 16 copies of TRIM25 sequences in Cyprinus carpio,but the specific differences among these sequences are not clear.In this study,16 copies of the trim25 gene in Cyprinus carpio were compared with other species by phylogenetic and syntenic analysis.Functional domain structures for 16 copies of TRIM25 protein were predicted,and the expression and cis-regulatory network of each gene copy in tissues were compared.Sequence alignment and phylogenetic analysis showed that the TRIM25 protein structure of Cyprinus carpio was highly similar to that of Spinibarbus auratus and Danio rerio,but distinct from that of other species beyond the Cyprinidae species.The results of gene synteny indicated that the upstream and downstream genes of the trim25 gene were relatively conservative in the evolution of different species.The structural analysis of TRIM25 protein showed that 6 copies had complete functional domains among the 16 copies of common carp,of which 5 copies were highly expressed in the liver and brain tissues,respectively.In the eQTL regulatory network for trim25,5 and 17 SNPs were identified regulating trim25 expression in liver and brain tissues,respectively.In summary,GWAS,RNA-seq and methylation sequencing analysis were used to analyze the amino acid and fatty acid content traits of Yellow River carp in this study,revealing the potential mechanism of amino acid metabolism and fatty acid metabolism in Yellow River carp.The differences among different copies of TRIM25 sequences in Cyprinus carpio were compared,and the SNP sites affecting TRIM25 expression were screened out from the eQTL regulatory network established by our research group.