Integrative Metabolome and Transcriptome Analyses Provide Insights into Carotenoid Variation in Different-Colored Peppers

Abstract

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.

Transcript Analysis Reveals Positive Regulation of CA12g04950 on Carotenoids of Pigment Pepper Fruit under Nitrogen Reduction

“…Except for GGPSS, other key genes of carotenoid content exhibited an increase in expression levels with the reduction in nitrogen application. GGPP, a precursor for the synthesis of numerous plant olefins and belonging to the upstream carotenoid metabolic pathway [12], did not show a significant effect of nitrogen. This further confirms that plants respond positively to environmental changes by regulating transcript levels to adapt to varying nutrient levels [60].…”

“…The 2 −∆∆CT method was used to calculate the relative expressions of target genes [44]. To standardize the relative expression, the actin gene (Actin Actin-depolymerizing factor 7 [T. aestivum]) was employed as the housekeeping gene [12]. The qRT-PCR primers were designed using Primer 5.0 software [45], and all primer sequences are provided in Table 2.…”

“…Therefore, it is believed that the color variation in this mutant fruit is related to the regulatory mechanism of the CCS gene. Through the integration of transcriptomics and metabolomics approaches, it was discerned that the genes CCS, NCED2, AAO4, VDE1, and CYP97C1 serve as pivotal regulators in the synthesis of carotenoids [12].…”