Integration of physiological, miRNA‐mRNA interaction and functional analysis reveals the molecular mechanism underlying hypoxia stress tolerance in crucian carp (Carassius auratus)

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. 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. 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 (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‐17a‐3p, respectively, and targets of DE miRNAs were significantly enriched in MAPK signaling pathway, FoxO signaling pathway, and glycolysis/gluconeogenesis. 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. Furthermore, research found that hk2 is a target of dre‐miR‐17a‐3p, overexpression of dre‐miR‐17a‐3p significantly decreased the expression level of hk2, while the opposite results were obtained after dre‐miR‐17a‐3p silencing. These results contribute to our understanding of the molecular mechanisms of hypoxia tolerance in crucian carp. Crucian carp (Carassius auratus), as an economically important freshwater fish in China, displays a substantial tolerance for hypoxia. Under hypoxia stress, we found that antioxidant capacity and anaerobic metabolism were enhanced, and aerobic metabolism was weakened in the liver of crucian carp. Based on RNA‐seq data, numerous hypoxia‐related miRNA‐mRNA pairs and pathways were identified. Functional studies revealed that dre‐miR‐17a‐3p can play a regulatory role in hypoxia stress by regulating hk2.