A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio.

Docosahexaenoic acid (DHA) is an essential nutrient for humans and plays a critical role in human development and health. Freshwater fish, such as the common carp (Cyprinus carpio), have a certain degree of DHA biosynthesis ability and could be a supplemental source of human DHA needs. The elongase of very-long-chain fatty acid 5 (Elovl5) is an important enzyme affecting polyunsaturated fatty acid (PUFA) biosynthesis. However, the function and regulatory mechanism of the elovl5 gene related to DHA synthesis in freshwater fish is not clear yet. Previous studies have found that there are two copies of the elovl5 gene, elovl5a and elovl5b, which have different functions. Our research group found significant DHA content differences among individuals in Yellow River carp (Cyprinus carpio var.), and four candidate genes were found to be related to DHA synthesis through screening. In this study, the expression level of elovl5a is decreased in the high-DHA group compared to the low-DHA group, which indicated the down-regulation of elovl5a in the DHA synthesis pathways of Yellow River carp. In addition, using a dual-luciferase reporter gene assay, we found that by targeting the 3’UTR region of elovl5a, miR-26a-5p could regulate DHA synthesis in common carp. After CRISPR/Cas9 disruption of elovl5a, the DHA content in the disrupted group was significantly higher than in the wildtype group; meanwhile, the expression level of elovl5a in the disrupted group was significantly reduced compared with the wildtype group. These results suggest that elovl5a may be down-regulating DHA synthesis in Yellow River carp. This study could provide useful information for future research on the genes and pathways that affect DHA synthesis.

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.