Transcriptome analysis revealed molecular basis of cold response in Prunus mume.

Japanese apricot (Prunus mume Sieb. et Zucc.) is a traditional woody flower and fruit tree restrictedly cultivated in northern area due to its inability to survive harsh winters and early springs. In the current study, RNA-seq and physiological assay were used to study the cold response of P. mume 'Xuemei'. A total of 4705 genes were identified as differentially expressed genes (DEGs) in the 21 pairwise comparisons among seven time points under 0 °C cold treatment, and 3678 of them showed differential levels compared with control at normal temperature. The gene expression profiles indicated that the number of upregulated genes increased with prolongation of treatment time throughout the whole 48 h. Hierarchical clustering suggested three obvious phases of the gene expression profiles. Gene ontology (GO) analysis of the 4705 DEGs resulted in 102 significantly enriched GO items in which the transcription activity was dominant. 225 DEGs were predicted to encode transcription factor (TF) genes. Some important TFs (ERF, CBF, WRKY, NAC, MYB, bHLH) were strongly induced during the whole cold treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that plant signal transduction pathways such as plant hormone and calcium (Ca2+) were notable. Metabolic pathways such as sugar metabolism, especially RFOs (raffinose family oligosaccharides) were activated, which was accompanied by the accumulation of soluble sugars. SOD and POD enzyme activities coupled with reactive oxygen species (ROS)-related gene expression profile implied a gradually induced ROS scavenging system under cold treatment. These results might shed light on the sensitivity to cold stress in Japanese apricot and provide new insights into hardiness studies in P. mume and its related species. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01376-2.