# Comparative Transcriptomics for Pepper (_Capsicum annuum_ L.) under Cold Stress and after Rewarming
###### Abstract  
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 malondialdehydedehyde, 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_ (Capanan2g003557) and _NAC7_ (Capanan07g002219) 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. p 2021 20  
hormones are also involved in response to cold stress [12]. Activating cold responsive (_COR_) genes, encoding cryoprotective proteins, protects plant cells from cold-induced damage [13]. Hormone components can activate _COR_ genes through C-repeat binding factor (CBF)-dependent or nondependent pathways to regulate chilling tolerance in plants [14]. In addition, DNA damage response (DDR) is the basis of the body's defense against various kinds of damage. It has been reported that after cold-triggered DNA damage in _Arabidopsis_ root stem cells, WEE1-mediated DDR can activate relevant signaling pathways to reduce cold damage to plants [15]. Transcriptome sequencing has developed as an important tool in genetic research to explain the molecular mechanisms of gene expression and improve the efficiency of identifying the genes of interest [16]. At present, comparative transcriptomics has been widely used to illustrate the complex genes regulatory networks of many plants under cold stress. Comparative transcriptome analysis in two peanut varieties with different cold-tolerant abilities showed that 445 TF genes were significantly differentially expressed under cold and revealed some possible mechanism in peanut cold tolerance [17]. The comparison transcriptome of the tea plant under cold found that 978 differentially expressed genes (DEGs) owned by the tolerant and sensitive plants were enriched in pathways of photosynthesis and hormone signal transduction, among others, and considered that the different expression of _Llca2_ and SNF1-related protein kinase 2 (_SnRK2_) are correlated with cold tolerance [18]. Comparative transcriptomics of _Poa patensis_ systematically reveals the changes in key genes and products of glycolysis and TCA cycle in response to cold stress [19]. Pepper (_Capsicum annuum_ L.) originating from tropical and subtropical areas is a warm season vegetable, and its optimal growth temperature ranges from 21 \({}^{\circ}\)C to 28 \({}^{\circ}\)C. Pepper plants lack mechanisms for cold acclimatization, making them very sensitive to low temperature [20]. Exposed to cold stress, pepper exhibit the reduction of nutritture and metabolic imbalances. Besides, cold stress impairs the function of the female organs and reduces the number of viable pollen grains per flower, which affects the growth, development, and productivity of pepper [21; 22; 23; 24].