Molecular responses of paddy field carp (Cyprinus carpio) in the agricultural heritage to major environmental factors in paddy fields

As a core element of the Globally Important Agricultural Heritage System (GIAHS), the Qingtian paddy field carp (Cyprinus carpio, PF-carp) has been domesticated for over 1200 years in paddy field environments. This species has successfully adapted to shallow-water conditions in paddy fields. To reveal the adaptation mechanism, we conducted transcriptome sequencing on the hepatopancreas of PF-carp under two temperature conditions (28 °C and 38 °C) and concurrently analysed RNA-seq data from hypoxic conditions in the same tissue. By analysing high-temperature transcriptome data, 3154 differentially expressed genes (DEGs) were identified. KEGG analysis indicated that DEGs involved various pathways, including protein processing in endoplasmic reticulum, circadian rhythm, and HIF-1 signaling pathway. Notably, protein processing in endoplasmic reticulum was significantly enriched with key genes such as HSP70, HSP90, HSP40, CNX, CRT, and Bip. Through concurrent analysis of RNA-seq data from hypoxic conditions, we found that PF-carp regulate their metabolism through multiple pathways and produce almost opposite metabolic regulation to adapt to high temperature and hypoxic environments. The opposite activation state observed in the HIF-1 signaling pathway is particularly intriguing. In conclusion, PF-carp appear to rely on protein processing in endoplasmic reticulum to maintain cell homeostasis at high temperatures. The HIF-1 signaling pathway may emerged as a key player in adapting PF-carps to paddy fields. This study provides valuable insights into the adaptive mechanisms of domesticated fish in paddy fields.