Comparative Transcriptome Analysis Reveals Differential Gene Expression Pattern Associated with Heat Tolerance in Pepper (Capsicum annuum L.)

Abstract

Pepper (Capsicum annuum L.) represents a highly significant agricultural commodity worldwide. Heat stress (HS) poses a severe threat to pepper productivity and quality. However, our understanding of the molecular alterations triggered by HS remains insufficient. This study focused on characterizing P19055 and P17087 as heat-tolerant and heat-sensitive pepper lines, respectively. Through RNA sequencing, we quantified transcript abundance in pepper fruit to investigate the impact of HS on gene expression. A total of 41,793 differentially expressed genes (DEGs) was identified, encompassing 33,703 known genes and 8090 novel genes. Additionally, we obtained 89,821 expressed transcripts, including 52,726 known transcripts and 37,095 new transcripts. By comparing gene expression levels between P17087 and P19055 fruit, we pinpointed 2324 genes exhibiting differential expression across three time points (0.5 h, 2 h, 6 h). Leveraging the weighted correlation network analysis (WGCNA) approach, we constructed a co-expression network of DEGs in P19055 and P17087 based on transcriptomic data acquired at these time points. Notably, nineteen modules displayed significant correlations with the time points following HS during the fruiting stage in both genotypes. Functional enrichment analysis revealed that the DEGs were primarily associated with metabolic and cellular processes in response to stress, particularly photosynthesis at the 2 h and 6 h time points. Moreover, we identified and categorized 26 families of transcription factors, including ERF (19), WRKY (12), MYB (15), NAC (7), bHLH (7), MIKC (7), GRAS (6), and 40 others, which may potentially regulate the expression of key genes in response to HS. Our findings contribute to a comprehensive understanding of the molecular mechanisms governing HS during the fruiting stage of pepper cultivation.