Transcriptome profiling of Prunus persica branches reveals candidate genes potentially involved in freezing tolerance

Abstract Peach (Prunus persica var.) is an important fruit tree species. Dingjiaba Liguangtao is an excellent cold-tolerant variety of peach. To understand the cold-adaptive mechanism of this peach variety, we analyzed the physiochemical and transcriptomic changes of this cultivar under different low temperature conditions. The results showed that cold stress induced the accumulation of soluble sugar, soluble protein and proline. The increased contents of these compounds enhanced the cold tolerance of Dingjiaba Liguangtao, as indicated by the relatively lower and stable levels of electrolyte leakage index (ELI) and malondialdehyde (MDA) (regardless of the higher value of MDA at −20 °C) before the temperature was decreased to below −25 °C. Meanwhile, the antioxidant enzymes peroxidase (POD) and superoxide dismutase (SOD) also play a role in mitigating the damage caused by cold stress in Dingjiaba Liguangtao. Transcriptomes of samples treated at −5 °C, −15 °C, −25 °C and −35 °C, respectively, were generated and characterized. In total, 890 differentially expressed genes (DEGs) were identified, including 693 upregulated genes and 197 downregulated genes. These genes were enriched in 38 Gene Ontology (GO) terms and 24 clusters of orthologous groups (COG) involved in 64 Kyoto Encyclopedia of Genes and Genomes (KEGG)-defined pathways. DEGs related to signal transduction, carbohydrates and lipid metabolism were significantly enriched. In total, 124 transcription factors belonging to 24 families were found to be cold-responsive. Notably, the largest gene family was the AP2/ERF gene family followed by MYB and NAC. Taken together, these results provide a better understanding of the cold-adaptive mechanism functioning in this excellent cold-tolerant peach species. The unique DEGs identified in this study provide useful information for further study on cold response mechanisms and genetic enhancement of cold resistance in Prunus persica.