Transcriptome and Metabolome Analyses Reveal Molecular Responses of Two Pepper (Capsicum annuum L.) Cultivars to Cold Stress

Abstract

Low temperature is a significant factor affecting field-grown pepper. The molecular mechanisms behind peppers’ response to cold stress remain unknown. Transcriptomic and metabolomic analyses were used to investigate the responses of two pepper cultivars, XS (cold-sensitive) and GZ (cold-resistant), to cold stress; these were screened from 45 pepper materials. In this study, compared with the control group (0 h), we identified 10,931 differentially expressed genes (DEGs) in XS and GZ, 657 differentially expressed metabolites (DEMs) in the positive ion mode, and 390 DEMs in the negative ion mode. Most DEGs were involved in amino acid biosynthesis, plant hormone signal transduction, and the mitogen-activated protein kinase (MAPK) signaling pathway. Furthermore, metabolomic analysis revealed that the content of free polyamines (PAs), plant hormones, and osmolytes, mainly contained increased putrescine, spermine, spermidine, abscisic acid (ABA), jasmonic acid (JA), raffinose, and proline, in response to cold stress. Importantly, the regulation of the ICE (inducer of CBF expression)-CBF (C repeat binding factors)-COR (cold regulated) pathway by Ca2+ signaling, MAPK signaling, and reactive oxygen species (ROS) signaling plays a key role in regulating responses of peppers to cold stress. Above all, the results of the present study provide important insights into the response of peppers to cold stress, which will reveal the potential molecular mechanisms and contribute to pepper screening and breeding in the future.

Genome-Wide Identification of Polyamine Oxidase (PAO) Family Genes: Roles of CaPAO2 and CaPAO4 in the Cold Tolerance of Pepper (Capsicum annuum L.)

“…In addition, we analyzed the transcription level of CaPAO genes in response to cold stress using previous transcriptome data [ 30 ]. Compared with the control, CaPAO2 and CaPAO4 gene expression levels first increased and then decreased throughout the treatment period, but they were significantly higher than control levels, except for the expression level of CaPAO4 at 24 h. There were no significant differences between the remaining genes and the control group ( Figure 3 B).…”

“…All primer sequences are shown in Tables S2 and S3 . Preliminary RNA-seq data [ 30 ] were used to determine the expression of the CaPAO genes in response to cold stress.…”

“…Free PA (Put, Spd, Spm) content was determined as previously described [ 30 ]. MDA content was determined using a plant MDA assay kit (Nanjing Jiancheng, Nanjing, China).…”

“…R-Dev1: root (six-leaf stage); S-Dev1: stem (six-leaf stage); L-Dev1: leaf (six-leaf stage); F-Dev2: fruit (Immature stage, green, fruits length between 1–2 cm); F-Dev3: fruit (mature stage, yellow, fruits length between 2–4 cm); R-Dev3: root (Fruit maturity); S-Dev3: stem (fruit maturity); L-Dev3: leaf (fruit maturity). ( B ) Transcriptome analysis of CaPAO genes in response to cold stress [ 30 ]. ‘**’ indicates a significant difference between the treatment and the control at p < 0.01.…”

“…Pepper seedlings are specifically vulnerable to cold stress in early spring. Previously, a multiomics analysis demonstrated that the expression levels of two genes encoding polyamine oxidase (LOC107859655 and LOC107878076) in pepper increased significantly under cold stress, indicating that these genes may regulate cold stress response [ 30 ]. Here, we identified six CaPAO genes in pepper and analyzed the evolutionary tree, gene structure, and cis-elements in the promoter.…”