Comparative Transcriptomics for Pepper (Capsicum annuum L.) under Cold Stress and after Rewarming

Cold stress has become one of the main abiotic stresses in pepper, which severely limits the growth and development of pepper. In this study, the physiological indicators and transcriptome of a cold-tolerance (CT) inbred line A188 and a cold-sensitive (CS) inbred line A122 under cold–rewarm treatments were studied; the aim of this study was to determine the potential of the key factors in pepper response to cold stress. Compared with CT, CS wilts more seriously after cold stress, with poor resilience, higher content of malondialdehyde, and lower content of soluble sugar and total chlorophyll. Moreover, during cold treatment, 7333 and 5953 differentially expressed genes (DEGs) were observed for CT and CS, respectively. These DEGs were significantly enriched in pathways related to photosynthesis, plant hormone signal transduction, and DNA damage repair. Interestingly, in addition to the widely studied transcription factors related to cold, it was also found that 13 NAC transcription factors increased significantly in the T4 group; meanwhile, the NAC8 (Capana02g003557) and NAC72 (Capana07g002219) in CT were significantly higher than those in CS under rewarming for 1 h after 72 h cold treatment. Notably, weighted gene coexpression network analysis identified four positively correlated modules and eight hub genes, including zinc finger proteins, heat shock 70 kda protein, and cytochrome P450 family, which are related to cold tolerance. All of these pathways and genes may be responsible for the response to cold and even the cold tolerance in pepper.