Multi-omics analysis unravels the underlying mechanisms of the escape response of the common strain black carp

Abstract

Abstract Reducing the escape response of fish during the aquaculture has important economic value and ecological safety significance. This study takes the common strain black carp (Cyprinus carpio var. baisenensis), which is known for its low-escape response, as the main research object. Through a simulated flood experiment, the common strain black carps were divided into the low-escape (BL) group and the high-escape (BH) group. Multi-omics techniques:transcriptome sequencing, LS-MS/MS detection, and 16s sequencing were used to analyze the differences in brain gene transcription levels, liver metabolites, and intestinal microbiota composition between the two groups. In addition, in order to reduce false positives generated by transcriptome experiments, Jian carps (Cyprinus carpio var. Jian) were also grouped into the low-escape (JL) group and the high-escape (JH) group and subjected to transcriptome analysis. According to the differentially expressed genes (DEGs) analysis, 18 DEGs were obtained from both the common strain black carp and Jian carp. Except for the MAP6 gene, which was significantly highly expressed, the remaining 17 genes showed significantly low expression in the BL group, which were almost related to signal transduction, and brain tissue and neuronal development. The results of KEGG signaling pathway annotation, KOG functional annotation, and topGO enrichment analysis showed that there were significant differences in signal transduction between the BL and BH groups, especially in the gama aminobutyric acid (GABA) signaling pathway. The detection of liver metabolites showed that there were differences in tryptophan metabolism between the BL and BH groups of the common strain black carp, with higher tryptophan content in the liver of the BL group fish. This study suggests that the brain activity and development of low-escape fish may be lower than that of high-escape fish. Meanwhile, differences in the brain's GABA signaling pathway and the liver's tryptophan metabolismmay also affect fish's escape response. This study accumulates experimental foundation of fish escape response, and provides a new insight into breeding low-escape fish and developing novel strategies to reduce escape responses during aquaculture.