Comparison of transcriptome and metabolome analysis revealed differences in cold resistant metabolic pathways in different apple cultivars under low temperature stress

Freezing injury in winter is an important abiotic stress that seriously affects plant growth and development. Deciduous fruit trees resist freezing injury by inducing dormancy. However, different cultivars of the same species have different cold resistance strategies. Little is known about the molecular mechanism of apple trees in response to freezing injury during winter dormancy. Therefore, in this study, 1-year-old branches of the cold-resistant cultivar ‘Hanfu’ (HF) and the cold-sensitive cultivar ‘Changfuji No. 2’ (CF) were used to explore their cold resistance through physiological, biochemical, transcriptomics, and metabolomics analyses. Combining physiological and biochemical data, we found that HF had a stronger osmotic regulation ability and antioxidant enzyme activity than CF, as well as stronger cold resistance. The functional enrichment analysis showed that both cultivars were significantly enriched in pathways related to signal transduction, hormone regulation, and sugar metabolism under freezing stress. In addition, the differentially expressed genes (DEGs) encoding galactinol synthase, raffinose synthase, and stachyose synthetase in raffinose family oligosaccharides (RFOs) metabolic pathways were upregulated in HF, and raffinose and stachyose were accumulated, while their contents in CF were lower. HF accumulated 4-aminobutyric acid, spermidine, and ascorbic acid to scavenge reactive oxygen species (ROS). While the contents of oxidized glutathione, vitamin C, glutathione, and spermidine in CF decreased under freezing stress, consequently, the ability to scavenge ROS was low. Furthermore, the transcription factors apetala 2/ethylene responsive factor (AP2/ERF) and WRKY were strongly induced under freezing stress. In summary, the difference in key metabolic components of HF and CF under freezing stress is the major factor affecting their difference in cold resistance. The obtained results deepen our understanding of the cold resistance mechanism in apple trees in response to freezing injury during dormancy.