Transcriptome analysis in gill reveals the adaptive mechanism of domesticated common carp to the high temperature in shallow rice paddies

Qingtian paddy field carp (PF-carp) is one of the core elements of the first Globally Important Agricultural Heritage System (GIAHS), Qingtian rice-fish coculture system, and might be the unique and most successful fish species domesticated under shallow rice paddy condition. It shows well adaptation to shallow water and high temperature in rice paddies. In order to reveal the mechanism of this kind of adaptation, we performed transcriptome sequencing and analyzed related enzyme activity indices in the gill tissues of PF-carp at different temperatures (28, 34 and 38 °C). A total of 2831 differentially expressed genes (DEGs) were identified by transcriptome sequencing analysis, and KEGG analysis revealed activation and involvement of DEGs in different pathways, including protein processing in endoplasmic reticulum, apoptosis and NF-κB signaling pathway. Among these pathways, key signaling factors such as HSP70, HSP90, gp78, Caspase 3, BAX, and IL-8 exhibited varying expression trends. Enzyme activity indicators showed no significant difference in CAT, GSH-Px and MDA at 34 °C and 38 °C within group. Our findings suggest that PF-carp primarily adapts to high temperature environment in rice paddies through the activation of protein processing in the endoplasmic reticulum to prevents protein misfolding and NF-κB signaling pathway activated by IL-8 and HIF-1β to enhance organism immunity, and the organism does not experience hypoxia and apoptosis when it is in high temperature environment. This study offers valuable insights into the adaptation mechanisms of this species to high temperature environments in rice paddies.