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.

Cytoplasmic male-sterility (CMS) is important for the utilization of crop heterosis and study of the molecular mechanisms involved in CMS could improve breeding programs. In the present study, anthers of the pepper CMS line HZ1A and its maintainer line HZ1B were collected from stages S1, S2, and S3 for transcriptome sequencing. A total of 47.95 million clean reads were obtained, and the reads were assembled into 31,603 unigenes. We obtained 42 (27 up-regulated and 15 down-regulated), 691 (346 up-regulated and 345 down-regulated), and 709 (281 up-regulated and 428 down-regulated) differentially expressed genes (DEGs) in stages S1, S2, and S3, respectively. Through Gene Ontology (GO) analysis, the DEGs were found to be composed of 46 functional groups. Two GO terms involved in photosynthesis, photosynthesis (GO:0015986) and photosystem I (GO:0009522), may be related to CMS. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, oxidative phosphorylation (ko00190) and phenylpropanoid biosynthesis (ko00940) were significantly enriched in the S1 and S2 stages, respectively. Through the analysis of 104 lipid metabolism-related DEGs, four significantly enriched KEGG pathways may help to regulate male sterility during anther development. The mitochondrial genes orf470 and atp6 were identified as candidate genes of male sterility for the CMS line HZ1A. Overall, the results will provide insights into the molecular mechanisms of pepper CMS.