Low-temperature stress severely limits early-spring melon (Cucumis melo L.) production. However, the regulatory roles of NAC transcription factors in melon responses to abiotic stress remain insufficiently understood. In this study, the melon cultivar ‘Xizhoumi No. 17’ was used as the experimental material, and an Agrobacterium-mediated root transformation system was employed to generate CmNAC29-overexpressing and empty-vector control plants. Phenotypic analysis, physiological measurements, transcriptome sequencing, and molecular interaction assays were performed to systematically investigate the regulatory mechanism by which CmNAC29 mediates chilling tolerance in melon roots. The results showed that CmNAC29 overexpression significantly alleviated cold stress-induced growth inhibition in melon seedlings, reduced membrane lipid peroxidation, and enhanced antioxidant enzyme activities and proline accumulation. Transcriptome analysis revealed that differentially expressed genes associated with CmNAC29 overexpression were significantly enriched in functional categories related to oxidoreductase activity. Further validation showed that CmNAC29 upregulated the expression of antioxidant enzyme genes, the key proline biosynthesis gene CmP5CS1, and core components of the Inducer of CBF Expression–C-repeat Binding Factor–Cold-Regulated pathway. Molecular assays confirmed that CmNAC29 possesses transcriptional activation activity and directly binds to the promoters of CmP5CS1-1 and CmCOR413 by recognizing NAC-binding sites, thereby activating their transcription. Taken together, these findings demonstrate that CmNAC29 positively regulates chilling tolerance in melon seedlings by coordinately enhancing antioxidant defense, osmotic adjustment, and cold signal transduction. This study provides an important genetic resource and theoretical basis for the molecular breeding of cold-tolerant melon cultivars.

Salt stress severely restricts pepper growth and productivity. Although AP2/ERF transcription factors are widely involved in plant responses to environmental stress, their functions in salt tolerance in pepper remain largely unknown. In this study, transcriptome-based screening identified CaERF3 (Capana07g002313) as a primary-candidate salt-responsive ERF transcription factor. Functional analyses of CaERF3 knockout (KOERF3) and overexpression (OEERF3) lines demonstrated that CaERF3 positively regulated both seedling growth and salt tolerance. Under salt stress, OEERF3 plants exhibited higher SOD, POD, and CAT activities, lower TBARS accumulation, and a more favorable Na⁺/K⁺ balance, whereas KOERF3 plants showed the opposite phenotype. Integrated metabolomic and transcriptomic analyses indicated that CaERF3-mediated salt tolerance was associated with amino sugar and nucleotide sugar metabolism and galactose metabolism. The knockout of CaERF3 reduced the expression of the galactinol synthase genes CaGolS1-1 and CaGolS1-2, accompanied by decreased galactinol and stachyose accumulation, suggesting impaired raffinose-family oligosaccharide biosynthesis. In addition, genes associated with Golgi function, vesicle trafficking, and cell wall modification (CaLAC, CaVSR, CaUNC-1, and CaCHIEP3-1) were coordinately downregulated. Furthermore, CaERF3 functioned as a nuclear transcriptional activator and directly activated the endochitinase gene CaCHIEP3-1 by binding the GCC-box in its promoter. These findings establish CaERF3 as a positive regulator of salt tolerance in pepper and provide new insights into the transcriptional regulation of carbohydrate metabolism and glycan biosynthesis during salt stress.