Transcription regulation network revealed the role of CBF3 gene in response to low-temperature stress of Cuphea hookeriana

This study focused on Cuphea hookeriana , which has ornamental, medicinal, and economic values, and aims to investigate its low-temperature response mechanism because its poor low-temperature tolerance limits its popularization in cold regions. Two-year-old cuttings were treated with low temperature at 5°C in an artificial climate chamber, and leaf samples were collected at 0 h (CK), 12 h (T1), 24 h (T2), 36 h (T3), and 48 h (T4). A number of physiological indices were measured, and it was found that low temperature stress resulted in an increase in malondialdehyde (MDA) content and conductivity, an increase and then a decrease in soluble protein and free proline content, and an increase and then a slight decrease in catalase (CAT) and superoxide dismutase (SOD) activities. The fatty acid analysis identified 35 fatty acid components, and identified palmitic acid and cis-9-octadecenoic acid as the key fatty acids. A total of 644.07 M high-quality reads were obtained from transcriptome sequencing, and 101,798 unigenes were assembled. 358 differentially co-expressed transcription factors were identified, and the AP2-EREBP family played a key role in the low-temperature response. Weighted gene co-expression network analysis (WGCNA) constructed gene co-expression networks and identified core genes in the ME turquoise module, including the ChCBF3 gene. When the ChCBF3 gene was cloned and transformed into Arabidopsis thaliana , the transgenic A. thaliana showed increased survival at low temperatures, decreased relative conductivity and MDA content, and increased soluble protein content and CAT activity, suggesting that the ChCBF3 gene enhances the cold hardiness of A. thaliana . This study provides a theoretical basis for the study of cold resistance mechanisms and the selection and breeding of cold-tolerant varieties of C. hookeriana and related plants. • Identified key fatty acids linked to Cuphea hookeriana cold stress response. • The CBF3 gene plays a potential role in cold tolerance in Cuphea hookeriana through regulatory pathways. • Built gene co-expression network; ME turquoise module key in cold response. • Validated CBF3 function in Arabidopsis thaliana , showing increased cold resilience.