ABSTRACT: Hypoxia has become one of the most critical factors limiting the development of aquaculture. Crucian carp (Carassius auratus) is widely consumed fish in China, with excellent tolerance to hypoxic environment. However, the molecular mechanisms underlying hypoxia adaptation and tolerance in crucian carp remain unclear. In this study, we detected the changes of biochemical parameters after hypoxia stress (3 h (H3h), H12h, and H24h) and reoxygenation (reoxygenation for 3 h after hypoxia 24 h (R3h)), mRNA and miRNA expression profiles under H12h compared to the control, and key hypoxia-related genes expression patterns in the liver of crucian carp through biochemical methods, RNA-seq, and qRT-PCR. Compared with the control, increased T-SOD, CAT, GSH-Px, T-AOC, ALT, and AST activities and MDA, TCHO, and TG contents, and decreased TP and ATP contents were observed after hypoxia stress, and LDH activity increased only in the H12h and H24h groups. Based on RNA-seq, 2479 differentially expressed (DE) mRNAs and 60 DE miRNAs were identified, and numerous DE mRNAs involved in HIF signaling pathway (hif-1α, epo, vegfa, and ho), anaerobic metabolism (hk1/hk2, pfk, gapdh, pk, and ldh) and immune response (nlrc3, nlrp12, cxcr1, cxcr4, ccr9, and cxcl12) were significantly upregulated after hypoxia exposure. Integrated analysis found that ho, igfbp1, hsp70, and hk2 were predicted to be regulated by novel_867, dre-miR-125c-3p/novel_173, dre-miR-181b-5p, and dre-miR-338-5p/dre-miR-128-3p, respectively, and targets of DE miRNAs were significantly enriched in MAPK signaling pathway, FoxO signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, NOD−like receptor signaling pathway, and cytokine-cytokine receptor interaction. Expression analysis showed that the mRNA levels of vegfa, epo, ho, hsp70, hsp90aa.1, igfbp1, ldh, hk1, pfk, pk, and gapdh exhibited a remarkable increase, whereas sdh and mdh were downregulated in the H3h, H12h, and H24h groups compared with the control. These results contribute to our understanding of the molecular mechanisms of hypoxia tolerance in crucian carp, which are of great significance for genetics and breeding of other fishes tolerant to hypoxia.
