Fruit quality has long been well known as an important prerequisite for evaluating pepper resources. In the study, 75 cultivars belonging to four Capsicum species were investigated on the bases of fruit morphology and concentrations of fruit secondary metabolites. The results showed that C. annuum had a greater variation than C. chinense and C. frutescens in terms of fruit weight, size and contents of carotenoids, anthocyanidins, and capsaicinoids. Moreover, there were significant differences in the concentrations of total phenol, total soluble sugar, total soluble solids, titratable acid, and total soluble protein of all samples. Capsaicin and dihydrocapsaicin were the most important capsaicinoids components in pepper fruits, of which C. chinense both had the highest levels, whereas some accessions of C. annuum were not detected. Eighteen fatty acids were detected in pepper fruits, and the dominant member was linoleic acid (a polyunsaturated fatty acid) therein. We integrated a set of methods for metabolites, and the results indicated that there was a positive correlation between concentrations of capsaicinoids and fatty acids. Four accessions had the highest contents of quality-related compounds, two of which belonged to C. chinense (S23 and S24) and possessed high levels of capsaicin. However, S67 had a high level of β-carotene and S68 contained higher contents of total fatty acid and ascorbic acid, and both of them belonged to C. annuum. This work could provide a valid experimental basis for the potential application value of the four accessions mentioned above.

Carotenoids are important pigments in pepper fruits. The colors of each pepper are mainly determined by the composition and content of carotenoid. The ‘ZY’ variety, which has yellow fruit, is a natural mutant derived from a branch mutant of ‘ZR’ with different colors. ZY and ZR exhibit obvious differences in fruit color, but no other obvious differences in other traits. To investigate the main reasons for the formation of different colored pepper fruits, transcriptome and metabolome analyses were performed in three developmental stages (S1–S3) in two cultivars. The results revealed that these structural genes (PSY1, CRTISO, CCD1, CYP97C1, VDE1, CCS, NCED1 and NCED2) related to carotenoid biosynthesis were expressed differentially in the two cultivars. Capsanthin and capsorubin mainly accumulated in ZR and were almost non-existent in ZY. S2 is the fruit color-changing stage; this may be a critical period for the development of different color formation of ZY and ZR. A combination of transcriptome and metabolome analyses indicated that CCS, NCED2, AAO4, VDE1 and CYP97C1 genes were key to the differences in the total carotenoid content. These new insights into pepper fruit coloration may help to improve fruit breeding strategies.

Pepper is an important vegetable and economic crop, and the MYB family is one of the most numerous transcription factor families in plants, extensively participating in various biological processes such as plant growth, development, and stress resistance. In this study, CcMYB330 is identified as a differentially expressed gene in the pepper fruit, and CcMYB330 is expressed with higher expression levels in the placenta and pericarp at different development stages of pepper fruit. Analysis of the promoter cis-elements revealed that this gene contains not only core elements but also environmental factor response elements and plant hormone response elements. The silencing of CcMYB330 could reduce the capsaicinoid accumulation in pepper fruit, while the overexpression of CcMYB330 could increase capsaicinoid accumulation. Additionally, silencing or overexpressing CcMYB330 could regulate the expression of structural genes involved in capsaicinoid biosynthesis. In addition, through yeast one-hybrid experiments, we identified an interaction between CcMYB330 and the capsaicinoid biosynthesis structural gene CcPAL. Further evidence from EMSA experiments and dual luciferase assays confirmed that CcMYB330 can bind to the cis-element ACCAACAACCAAA in the CcPAL promoter. These results indicate that CcMYB330 may regulate the synthesis of capsaicinoids by modulating structural genes in the capsaicinoid biosynthesis pathway, providing new insights into the regulatory mechanisms of capsaicinoid synthesis.

Plant homeodomain (PHD) transcription factor genes are involved in plant development and in a plant’s response to stress. However, there are few reports about this gene family in peppers (Capsicum annuum L.). In this study, the pepper inbred line “Zunla-1” was used as the reference genome, and a total of 43 PHD genes were identified, and systematic analysis was performed to study the chromosomal location, evolutionary relationship, gene structure, domains, and upstream cis-regulatory elements of the CaPHD genes. The fewest CaPHD genes were located on chromosome 4, while the most were on chromosome 3. Genes with similar gene structures and domains were clustered together. Expression analysis showed that the expression of CaPHD genes was quite different in different tissues and in response to various stress treatments. The expression of CaPHD17 was different in the early stage of flower bud development in the near-isogenic cytoplasmic male-sterile inbred and the maintainer inbred lines. It is speculated that this gene is involved in the development of male sterility in pepper. CaPHD37 was significantly upregulated in leaves and roots after heat stress, and it is speculated that CaPHD37 plays an important role in tolerating heat stress in pepper; in addition, CaPHD9, CaPHD10, CaPHD11, CaPHD17, CaPHD19, CaPHD20, and CaPHD43 were not sensitive to abiotic stress or hormonal factors. This study will provide the basis for further research into the function of CaPHD genes in plant development and responses to abiotic stresses and hormones.

Pepper is an economically important vegetable worldwide, containing various specialized metabolites crucial for its development and flavor. Capsaicinoids, especially, are genus-specialized metabolites that confer a spicy flavor to Capsicum fruits. In this work, two pepper cultivars, YB (Capsicum frutescens L.) and JC (Capsicum baccatum L.) pepper, showed distinct differences in the accumulation of capsaicin and flavonoid. However, the molecular mechanism underlying them was still unclear. Metabolome analysis showed that the JC pepper induced a more abundant accumulation of metabolites associated with alkaloids, flavonoids, and capsaicinoids in the red ripening stages, leading to a spicier flavor in the JC pepper. Transcriptome analysis confirmed that the increased expression of transcripts associated with phenylpropanoid and flavonoid metabolic pathways occurred in the JC pepper. Integrative analysis of metabolome and transcriptome suggested that four structural genes, 4CL7, 4CL6, CHS, and COMT, were responsible for the higher accumulation of metabolites relevant to capsaicin and flavonoids. Through weighted gene co-expression network analyses, modules related to flavonoid biosynthesis and potential regulators for candidate genes were identified. The promoter analysis of four candidate genes showed they contained several cis-elements that were bonded to MYB, bZIP, and WRKY transcription factors. Further RT-qPCR examination verified three transcription factors, MYB, bZIP53, and WRKY25, that exhibited increased expression in the red ripening stage of the JC pepper compared to YB, which potentially regulated their expression. Altogether, our findings provide comprehensive understanding and valuable information for pepper breeding programs in the future.

Fruit color serves as a crucial visual indicator in chili peppers and is closely linked to the bioactive components that determine their economic and nutritional value. However, the specific components and potential molecular mechanisms that impact fruits’ development and color changes are less thoroughly understood. Here, we utilized three chili pepper varieties (CS03, CS29, and L816) at different developmental stages (young fruit stage, turning color stage, and mature stage) as research materials and integrated transcriptome and non-targeted metabolome analyses to explore the variation in bioactive components and color to explain the molecular regulatory mechanisms underlying different colors of chili peppers during the young fruit stage. Our results showed that flavonoids were the most enriched differential metabolites; aromadendrin 4′-glucoside, diospyrin, precarthamin, kaempferol-3-O-rutinoside, and kaempferol-3-O-Glucoside were significantly enriched in the young fruit stage of pepper CS03; and cyanidin, delphinidin, and cyanidin 3-glucoside were major contributors to the color formation. The upregulation of anthocyanin was related to the structural genes CaC4H, Ca4CL, CaCHS, CaF3H, CaANS, and CaUFGT, and key transcription factors such as CaMYBs and CabHLHs may have contributed to the differential accumulation of anthocyanins in CS03; in addition, RT-qPCR validation was correlated with anthocyanins, but also with flavonoids. This article mainly focuses on the changes in chili pigments, particularly anthocyanins, and explores the molecular mechanisms involved. This provides a reference for research on color in solanaceae vegetables and lays a theoretical foundation for further research on the bioactive components of chili peppers, as well as for optimizing harvesting practices and dietary recommendations.