High nutritional value and the development of efficient biotechnological methods of controlled production have made black porgy (Acanthopagrus schlegelii) an economically important fish in Chinese aquaculture in recent years. However, aquaculture production of the species faces multiple issues associated with reduced growth rate, low reproduction ability, and high mortality during production, which are associated with the species’ limited tolerance to low temperatures. To date, comprehensive information on the genetic-based mechanisms of cold tolerance and adaptation to low temperature in the species are still unavailable. In this study, the HiSeq™2500 (Illumina) sequencing platform was used to analyze the transcriptomic profile of the liver tissue in the black porgy subjected to different extents of cold shock, including a control temperature group (AS, T = 15 °C), an intermediate temperature group (AL1, T = 10 °C), and an acute low-temperature stress group (AL2, T = 5 °C). For this purpose, three standardized cDNA libraries of AS, AL1, and AL2 were established. We obtained 43,258,908, 48,239,072, and 38,983,833 clean reads from the AS group, AL1 group, and AL2 group, respectively. After pairwise comparison, 70 differentially expressed genes (DEGs) were identified in the examined fish groups. Among them, 60 genes were found to be significantly differentially expressed after trend analysis. GO annotation and enrichment results showed that they were mainly enriched into three categories: biological processes (12 subcategories), molecular functions (7 subcategories), and cellular components (7 subcategories). KEGG analysis results indicated that all significantly differentially expressed genes were annotated to 102 signaling pathways, including biological rhythm, cholesterol metabolism, glycerolipid metabolism, animal autophagy, FoxO signaling pathway, steroid biosynthesis, and regulation of adipocyte lipolysis and apoptosis. Four of them, namely: G6PC, GPX1, GCK, and HSPE1 were randomly selected for further qRT-PCR verification of data reliability obtained by RNA-Seq technology. In this study, we found that environmental acute cold stress mainly affected the black porgy’s biological processes related to metabolism, apoptosis, and signal transduction. The data that we have reported provides baseline information for further studies concerning the genetic responses of the black porgy under cold stress conditions, the improvement of its aquaculture production, and other economically important matters regarding their limited tolerance to cold shock.

Black porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate SNPs (Single Nucleotide Polymorphism) were screened out and genotyped through GATK4 (Genome Analysis ToolKit) software and MALDI-TOF MS (Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry). The experimental results showed that a total of sixty SNPs were successfully genotyped, with a success rate of 98.36%. The results of principal component analysis and correlation analysis of growth traits showed that body weight was the first principal component, with a cumulative contribution rate of 74%. There were significant correlations (p < 0.05) or extremely significant correlations (p < 0.01) between different growth traits. The results of genetic parameter analysis and association analysis showed that scaffold12-12716321, scaffold13-4787950, scaffold2-13687576 and scaffold290-11890 were four SNPs that met the requirement of polymorphic information content and conformed to the Hardy–Weinberg equilibrium. There were significant differences between their genotype and the phenotype of growth traits. The four SNP molecular markers developed in this research will lay a foundation for further exploration of molecular markers related to the growth traits of black porgy and will provide a scientific reference for the further study of its growth mechanisms. At the same time, these molecular markers can be applied to the production practices of black porgy, so as to realize selective breeding at the molecular level and speed up the breeding process.

In this study, the complete cDNA sequence (1552bp) of the cold-inducible RNA binding protein gene (cirbp gene) was successfully cloned from the liver in Acanthopagrus schlegelii (initial weight: 15.02.3g). Results showed that Ascirbp (cirbp gene from A. schlegelii) gene has 24 phosphorylation sites, no signal peptide, and no transmembrane helix structure. AsCIRBP, with a molecular weight of 18.84ku and an isoelectric point of 9.04 was a stable protein that encodes 182 amino acids. Subcellular localization analysis of this protein showed that it was located in the nucleus. Sequence alignment results showed that the AsCIRBP amino acid sequences of various fishes including black porgy were highly conserved, especially the RNA recognition motif (RRM). Those results of real-time quantitative PCR (qRT-PCR) demonstrated that Ascirbp gene was specifically expressed in the liver tissue of black porgy and its expression was significantly increased under cold stress or cold acclimation. The RNA interference experiment results showed that Ascirbp-dsRNA could suppress the expression of Ascirbp gene in the liver of black porgy through intraperitoneal injection. After silencing the expression of Ascirbp gene, RNAi groups were more severely damaged in the structure of the liver tissue and more prone to apoptosis under cold stress than control groups. The results of the study on the linkage between Ascirbp gene expression and mitochondrial apoptosis pathways showed that changes in the expression of the Ascirbp gene had a significant effect on the expression of key genes of apoptosis. The most striking result from silencing the expression of the Ascirbp gene was that expressions of the bcl-2 and apaf-1 gene in the liver of black porgy decreased significantly, which can block the normal apoptotic process. After the disruption of the normal apoptotic process, the expressions of p53, bax, cyto-c, caspase-9, caspase-3, diablo, and caspase-1 gene were significantly affected. These results suggest that Ascirbp gene can inhibit apoptosis and protect tissue structure in the liver tissue of black porgy at low temperatures.