Comparative transcriptome analysis of Rosa chinensis 'Slater's crimson China' provides insights into the crucial factors and signaling pathways in heat stress response.

Heat stress limits the growth of roses and adversely affects the yield and the quality of the rose cut-flowers. To investigate the heat stress response (HSR) mechanisms of rose, we compared the transcriptome profiling generated from Rosa chinensis 'Slater's crimson China' exposed to heat stress for five different time duration (0, 0.5, 2, 6, 12 h). Overall, 6175 differentially expressed genes (DGEs) were identified and exhibited different temporal expression patterns. Up-regulated genes related to chaperone-mediated protein folding, signal transduction and ROS scavenging were rapidly induced after 0.5-2 h of heat treatment, which provides evidence for the early adjustments of heat stress response in R. chinensis. While the down-regulated genes related to light reaction, sucrose biosynthesis, starch biosynthesis and cell wall biosynthesis were identified after as short as 6 h of heat stress, which indicated the ongoing negative effects on the physiology of R. chinensis. Using weighted gene co-expression network analysis, we found that different heat stress stages could be delineated by several modules. Based on integrating the transcription factors with upstream enriched DNA motifs of co-expressed genes in these modules, the gene regulation networks were predicted and several regulators of HSR were identified. Of particular importance was the discovery of the module associated with rapid sensing and signal transduction, in which numerous co-expressed genes related to chaperones, Ca signaling pathways and transcription factors were identified. The results of this study provided an important resource for further dissecting the role of candidate genes governing the transcriptional regulatory network of HSR in Rose.