Light is vital for plant growth and development, and the germination of many plant seeds and the development of seedlings are very sensitive to the light environment. Under no or low light conditions, pepper seedlings will accelerate the elongation of the hypocotyl to obtain light. To elucidate the molecular mechanism by which light regulates hypocotyl elongation in pepper, RNA sequencing was performed to analyze the hypocotyls and cotyledons of the yellowing mutant R24 under three different light intensity treatments. A total of 35,341 gene were identified; moreover, during the treatment, 9695 new genes and 13,123 differentially expressed genes (DEGs) were observed, respectively. Some genes related to brassino-lide receptor protein kinase BRI1, light capture proteins LHCA and LHCB, and auxin response factor may regulate the response of hot pepper cotyledons and hypocotyls to different light intensity. KEGG functional enrichment analysis revealed that the most abundant pathways were phenylpropane biosynthesis, plant hormone signal transduction, and carbon metabolism. This study provides a valuable reference for understanding the molecular mechanism of pepper’s response to different light intensities at the seedling stage and for improving the local light environment to overcome the hypocotyl elongation of pepper crop under low light conditions.

Light is a crucial environmental component for plant growth, and light intensity plays a crucial function in controlling pigment anabolism in plants. We performed physiological characterisation, transcriptome, and metabolome investigations on purple leaf peppers treated with different light intensities to evaluate the effect on plant leaf colour. The results showed that the leaves of the peppers became significantly purplish under high light, with significantly higher anthocyanin, chlorophyll a, and carotenoid contents. A total of 44,263 genes were quantified using RNA-Seq, with the photoprotein-related genes LRP and LIP maintaining high expression levels under high and medium light. The anthocyanin synthesis pathway was variously enriched among the comparison groups, according to KEGG. The expression of the genes involved in the anthocyanin synthesis pathway, such as CHI, F3H, DFR, and BZ1, was significantly higher under high light. In addition, MYB and bHLH gene families were the most abundant, and MYB1R1, MYB113-like, and bHLH90-like were significantly expressed under high light and highly positively correlated with the above anthocyanin synthesis genes. According to our metabolomic analysis, delphinidin-3-O-rutinoside and delphinidin-3-O-glucoside accumulated in significant concentrations in purple leaves under high light. This study is useful for understanding the process of anthocyanin synthesis and metabolism in pepper leaves that is generated and regulated by varied light intensity.

Pepper is one of the most important vegetable crops in China and has high economic value. However, the pepper fruit is easily softened and spoiled after harvest, which seriously affects its flavor, transportation, and economic value. In this study, we used pepper lines with different levels of storage resistance, A144 and A361, and performed physiological examination, transcriptomics, and metabolomics on them at 0 and 3 days after harvest in order to analyze their gene expression patterns and molecular regulatory mechanisms for storage tolerance. A total of 23,477 genes and 985 metabolites were identified. After comparing and analyzing each sample, we identified 7829 differentially expressed genes and 296 differential metabolites. We found that the genes such as ethylene-responsive transcriptional factor (ERFs), polygalacturonase (PG), cellulose synthase (CESA), abscisic acid insensitive (ABI), protein kinase 2 (SnRK2), and protein phosphatase 2C (PP2C) and metabolites such as phenylalanine and glycyl-tyrosine were differentially expressed between different storage times in the two materials. Through GO and KEGG enrichment analysis, we found that the differential genes were mainly enriched in carbohydrate metabolism, small molecule metabolism, and plant hormone signal transduction, and the differential metabolites were mainly enriched in flavonoid biosynthesis, glutathione metabolism, and cysteine and methionine metabolism pathways. This study provides a scientific basis for investigating the molecular mechanisms of storage tolerance and developing new pepper varieties with improved storage resistance.

Trichomes are specialized organs located in the plant epidermis that play important defense roles against biotic and abiotic stresses. However, the mechanisms regulating the development of pepper epidermal trichomes and the related regulatory genes at the molecular level are not clear. Therefore, we performed transcriptome analyses of A114 (less trichome) and A115 (more trichome) to dig deeper into the genes involved in the regulatory mechanisms of epidermal trichome development in peppers. In this study, the epidermal trichome density of A115 was found to be higher by phenotypic observation and was highest in the leaves at the flowering stage. A total of 39,261 genes were quantified by RNA-Seq, including 11,939 genes not annotated in the previous genome analysis and 18,833 differentially expressed genes. Based on KEGG functional enrichment, it was found that DEGs were mainly concentrated in three pathways: plant–pathogen interaction, MAPK signaling pathway-plant, and plant hormone signal transduction. We further screened the DEGs associated with the development of epidermal trichomes in peppers, and the expression of the plant signaling genes GID1B-like (Capana03g003488) and PR-6 (Capana09g001847), the transcription factors MYB108 (Capana05g002225) and ABR1-like (Capana04g001261), and the plant resistance genes PGIP-like (Capana09g002077) and At5g49770 (Capana08g001721) in the DEGs were higher at A115 compared to A114, and were highly expressed in leaves at the flowering stage. In addition, based on the WGCNA results and the establishment of co-expression networks showed that the above genes were highly positively correlated with each other. The transcriptomic data and analysis of this study provide a basis for the study of the regulatory mechanisms of pepper epidermal trichomes.

Pepper (Capsicum annuum L.) is one of the most widely grown vegetable crops in China, with widespread cultivation worldwide. Fruit weight (size) is a complex trait controlled by multiple factors and is an essential determinant of pepper yield. In this study, we analyzed the transcriptome of two pepper recombinant lines with different fruit weights, ‘B302’ and ‘B400’, at five developmental stages to reveal some of the differentially expressed genes and mechanisms controlling fruit weight. The results showed that 21,878 differential genes were identified between the two specimens. Further analysis of the differentially expressed genes revealed that Boron transporter 4 was significantly highly expressed in the large-fruited pepper and almost not expressed at all in the small-fruited pepper. CaAUX1, CaAUX/IAA, CaGH3, CaSAUR, and other related genes in the Auxin signal transduction pathway were highly expressed in the large-fruited pepper but significantly reduced in the small-fruited pepper. In addition, a comparison of differentially expressed transcription factors at different times revealed that transcription factors such as CaMADS3, CaAGL8, CaATHB13, and CaATHB-40 were highly differentially expressed in the large-fruited pepper, and these transcription factors may be related to pepper fruit expansion. Through weighted gene co-expression network analysis (WGCNA), the MEorangered4 module was shown to have a highly significant correlation with fruit weight, and the key modules were analyzed by constructing the hub core gene network interactions map and core genes regulating fruit weight such as APETALA 2 were found. In conclusion, we find that the expression of relevant genes at different developmental stages was different in ‘B302’ and ‘B400’, and it was hypothesized that these genes play essential roles in the development of fruit size and that the interactions occurring between transcription factors and phytohormones may regulate the development of fruit size.

The yield of pepper with purple leaves (PF) is low, while the pepper with green leaves (GM) is not resistant to strong light and high temperature. In this study, we analyzed the photosynthesis characteristics and genetic stability of their hybrid progenies using PF(CS3) and GM(SJ11-3) as controls. Based on the decreased purple color and increased green color, the hybrid pepper was divided into five groups: Z1, Z2, Z3, Z4 and Z5. Results showed that as the purple color increased, the anthocyanin content in leaves increased. Simultaneously, we found that PF exhibited higher resistance to strong light and high temperature. Thus, the purple hybrid progenies with higher photosynthetic rate were recommended, as they showed higher yield and better resistance to strong light and high temperature.