Dependence of Pepper Fruit Colour on Basic Pigments Ratio and Expression Pattern of Carotenoid and Anthocyanin Biosynthesis Genes


Fruit biochemical analysis of four pepper (Capsicum annuum L.) cultivars, contrasting in immature and ripe fruit colour, was performed, and chlorophylls, carotenoids and anthocyanins were profiled in the peel and pulp during fruit ripening. It was found that pericarp parts (peel and pulp) differ in pigment composition and accumulation mode. In the same fruit tissues, the expression pattern of structural genes of the carotenoid (PSY1, PSY2, LCYb, and CCS) and anthocyanin (CHS, F3 '5 'H, DFR, ANS, and UFGT) pathways was evaluated. It was shown that carotenoid content positively correlates with the PSY1, LCYb and CCS expression level in the fruit pulp and with CCS expression level in the fruit peel. In pepper cultivars with purple-coloured immature fruits (Sirenevyj cub, Otello), a positive correlation was shown between the CHS, F3 '5 'H, DFR, ANS, and UFGT expression levels and the anthocyanin content in the peel. Thus, it was shown that in the pepper fruit, peel and pulp colours are regulated independently and determined by the main pigment ratio and the activity of carotenoid and anthocyanin biosynthesis genes.


Many plants form coloured flowers and fleshy fruit to attract insects, birds, and other animals as pollinators or seed distributors. In addition, in crops, the fruit colour affects their commercial value. Pepper (Capsicum annuum L.) is one of the main vegetable crops of Solanaceae [1]. Wild C. annuum accessions form small bright red fruit that attract birds, while in the process of domestication and breeding, new genotypes with large red, yellow, orange, brown, and even white fruits appeared [2].

In modern C. annuum cultivars, the fruit colour at the stage of biological ripeness, with rare exceptions, can be red, yellow, or orange, while pigmentation of an unripe fruit (technical ripeness) varyes significantly: from light green to purple, chocolate brown, and almost black. Such diversity of peel colour (exocarp) is due to a combination of three main groups of pigments: chlorophylls, carotenoids, and anthocyanins [1, 3]. Chlorophylls give the fruit a green color, while carotenoids capsanthin and capsorubin—red [1, 4, 5]. The yellow and orange color of the fruit is mainly due to carotenoids violoxanthin, lutein, and β-carotene [6]. The purple color of unripe fruit is determined by the accumulation of anthocyanidins (delphinidin derivatives) in the exocarp [7, 8]. The simultaneous presence of large amounts of anthocyanins, chlorophyll, and some carotenoids in the exocarp leads to visually black-coloured fruit [9]. Such diversity of the fruit colour, as well as its changes in the ripening process, made pepper C. annuum a model for studying the molecular genetic underlying fruit pigmentation [2]. The dynamics of changes in the pigment content and composition in pepper fruit has been actively studied over the past 30 years; however, as a rule, these studies have analyzed either the whole fruit (pericarp) or its pulp (mesocarp and endocarp) [1, 2, 10, 11].

The biosynthesis of carotenoids in fruits of higher plants is characterized in detail; all pathway enzymes and genes encoding them have been identified (Fig. 1a) [3, 11, 12]. The initial substrate is phytoene, from which lycopene is synthesized as a result of several desaturation reactions, which is a precursor of α- and β-carotenes. During further enzymatic reactions, β‑carotene is saturated with oxygen atoms and xanthophylls β-cryptoxanthin, zeaxanthin, anthraxanthin, and violoxanthin are formed. Capsicum species-specific enzyme capsanthin-capsorubin synthase (CCS) catalyzes the synthesis from xanthophylls of two red pigments—capsanthin and capsorubin, which give the red colour to the pepper fruit [4]. Mutations in the CCS gene knock out or reduce the amount and activity of the encoded protein, and as a result, the pepper fruit turns yellow or orange colour [1, 2, 11, 13]. Moreover, the different shades of yellow and orange are the result of mutations in other structural genes of carotenoid biosynthesis [3].

Fig. 1.

Scheme of biosynthesis of carotenoids (a) and anthocyanins (b) in Capsicum fruit [11, 12, 14, 15]. Enzymes catalyzing these reactions are indicated next to the arrows: (a) phytoene synthase (PSY), phytoene desaturase (PDS), ζ-carotene desaturase (ZDS), β-lycopene cyclase (β-LCY), ɛ-lycopene cyclase (ɛ-LCY), β-carotene hydroxylase (β-CH), ɛ-carotene hydroxylase (ɛ-CH), zeaxanthin epoxidase (ZE), violaxanthin de-epoxidase (VDE), capsanthin-capsorubin synthase (CCS); (b) phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), 4-coumarate coenzyme A-ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavonoid-3'-hydroxylase (F3'H), flavonoid-3',5'-hydroxylase (F3'5'H), dihydroflavonol-4-reductase (DFR), anthocyanidin synthase (ANS), UDP-glucose-flavonoid-3-O-glucosyl transferase (UFGT).

Anthocyanin biosynthesis pathway (flavonoid pathway) in Capsicum species is also well studied; all enzymes and their encoding genes have been identified [14, 15] (Fig. 1b). As a result of six enzymatic reactions, dihydrocampferol and then dihydromyreticin are formed from the initial phenylalanine substrate. Then, as a result of three consecutive enzymatic reactions, the pigment delphinidin-3-O-glucoside is formed, which determines the violet colour [14, 16]. These reactions are mediated by dihydroflavonol-4-reductase (DFR), anthocyanidin synthase (ANS), and UDP-glucose-flavonoid-3-O-glucosyl transferase (UFGT).

This work is focused on the study of the molecular genetic basis of the fruit peel and pulp colour changes during fruit ripening in pepper (C. annuum) by comparing biochemical data on the main pigment content and composition with expression patterns of structural genes for carotenoid and anthocyanin biosynthesis in cultivars with a different model of fruit pigmentation.


Fruits of four cultivars of pepper (Capsicum annuum L.) at three stages of development were used for biochemical and expression analysis (Figs. 2a–2d). The plants were grown in a greenhouse at the Federal Scientific Vegetable Center (FSVC, Moscow region), and the fruit of each cultivar at three stages of development were collected on the same day. Stage 1 corresponds to unripe fruits, stage 2—to the transition from unripe to ripe fruits (blange fruit), and stage 3—to biological ripeness of the fruit. The selected cultivars differed in the colour dynamics of the fruit peel and pulp during ripening (Figs. 2a–2d). For biochemical and expression analysis, for each fruit, separate parts of the pericarp were used: the peel (exocarp) and longitudinal (from the stem to the tip of the fruit) pulp segments (mesocarp and endocarp) from different parts of the fruit. The resulting material was grinded in liquid nitrogen and stored at –80°C.

Fig. 2.

Fruits of pepper C. annuum cultivars at different stages of ripening, where stages 1 and 2 correspond to the unripe fruit, and stage 3 to the fruit of biological ripeness. Cultivars: (a) Zheltyj buket, (b) Sibiryak, (c) Sirenevyj cub, (d) Otello.

The contents of chlorophylls (a and b), carotenoids (total), and anthocyanins (total) in the fruit peel and pulp were determined spectrophotometrically in chloroform-methanol extracts, and the pigment content was calculated by the formulas [17, 18] in two biological and three technical repeats. Total RNA from the fruit peel and pulp was isolated and purified from DNA impurities using the RNeasy Plant Mini Kit and RNase free DNasy set (Qiagen, Germany). cDNA preparations were synthesized using “GoScripttm Reverse Transcription System” (Promega, United States).

The expression profile of the structural genes of carotenoid (PSY1, PSY2, LCYb, and CCS) and anthocyanin (CHS, F3'5'H, DFR, ANS, and UFGT) pathways were determined by real-time quantitative PCR (qRT-PCR). Primer pairs for RT-PCR were designed based on the sequences available in the NCBI database: PSY1 (X68017), PSY2 (XM_016704726.1), LCYb (X86221), CCS (X77289), CHS (NM_001325005.1), F3'5'H (XM_016693437.1), DFR (JN885196), UFGT (NM_001324611.1) (Table 1). For the ANS gene, primers from [15] were used. The relative genes expression level was estimated using the reference gene Actin7 [19]. For qRT-PCR, “Reaction mixture for RT-PCR in the presence of SYBR GreenI and ROX” kit (Syntol, Russia) and CFX96 Real-Time PCR Detection System (Bio-Rad Laboratories, United States) were applied. The reactions were performed in three technical replicates under the following conditions: 95°C for 5 min; 40 cycles (95°C for 15 s, 62°C for 50 s). Statistical analysis was performed using GraphPad Prism v. 7.02 (

Table 1.   Sequences of primers for qRT-PCR


Dynamics of the Pigment Content in Pepper Fruits During Ripening

In the fruit peel and pulp of four pepper cultivars, contrasting in unripe and ripe fruit colour, the content of three main groups of pigments was determined. The highest content of chlorophylls (a + b) was found in the peel and pulp of unripe fruit of the cv. Zheltyj buket (312.6 and 72.5 μg/g, respectively) and cv. Sibiryak (147.8 and 43.5 μg/g, respectively), which determined their dark green colour; however, the chlorophyll content in the peel decreased significantly as the fruit ripened (Figs. 3a, 3b). Despite the yellow and red colour of the ripe fruits, a small amount of chlorophyll was also detected in their peel, which, apparently, caused the green shade of some parts of the fruit. In the pulp of cv. Zheltyj buket and Sibiryak, the presence of chlorophylls was detected only at stage 1.

Fig. 3.

Content (μg/g of fresh weight) of chlorophyll a (a), chlorophyll b (b), sum of carotenoids (c), and sum of anthocyanins (d) in the peel (S) and pulp (P) of pepper fruits during ripening (1 and 2 are unripe fruit, 3 is fruit of biological maturity).

In cv. Sirenevyj cub, the pulp of unripe fruits with a greenish shade contained a relatively small amount of chlorophylls: 20.5 (stage 1) and 3.2 (stage 2) μg/g. Ripe fruits (stage 3) were characterized by traces of chlorophyll b present only in the peel. In cv. Otello unripe fruit, minimal amounts of chlorophylls (a + b) were observed both in the peel (16.7 μg/g) and in the pulp (5.8 μg/g). Furthermore, in contrast the other analyzed cultivars, the total chlorophyll content in the peel increased significantly (by 3.1 times) with ripening (Figs. 3a, 3b).

All accessions showed a positive dynamics of carotenoid accumulation in fruit peel and pulp during ripening (Fig. 3c). The maximum of carotenoids was detected in the ripe fruit pulp (stage 3) of cv, Sibiryak (685 μg/g) and Otello (723 μg/g). The peel of ripe fruits of the Zheltyj buket and Sibiryak cultivars was characterized by approximately the same carotenoid content (Fig. 3c). In the ripe fruit pulp of cv. Zheltyj buket, the carotenoid content was minimal in comparison with the other three pepper cultivars (Fig. 3c). It was previously shown that the content of carotenoids in yellow and orange pepper fruits is generally lower than in red fruits [3, 11].

Anthocyanins were detected only in the fruit peel of cv. Sirenevyj cub and Otello (Fig. 3d). The maximum content was found in the unripe fruit peel (stage 1) of cv. Sirenevyj cub (462 μg/g). At the same time, the content of anthocyanins in the exocarp of the Sirenevyj kub and Otello fruits decreased significantly with ripening (Fig. 3d). The dynamic pattern of pigment accumulation visually corresponded to the colour change of the fruit peel during development. The highest pigment content corresponded to the violet colour of the unripe fruit, and a decrease in the anthocyanin content with a simultaneous increase in the carotenoid content as the fruit ripened correlated with a change in the peel colou from violet to red (Fig. 3).

Thus, the dynamics of pigment accumulation in the fruit peel and pulp was determined in four pepper cultivars, contrasting in the ripe fruit colour and the mode of colour formation. The data obtained correlated with the visual fruit pigmentation. Thus, in the Zheltyj buket and Sibiryak cultivars, the chlorophyll content decreased in the fruit exocarp during ripening, and the carotenoid content increased, which was accompanied by a change in the peel colour from green to yellow and red, respectively.

The exocarp violet colour in the unripe fruit of cv. Sirenevyj cub was due to the high content of anthocyanins and traces of chlorophylls and carotenoids. The unripe fruit peel of cv. Otello also contained anthocyanins, but the fruit had a purple-brown colour due to the presence of a notable amounts of chlorophylls and carotenoids. These results correspond to the previously shown dependence of the violet colour and its shades on the ratio of the content of anthocyanins (delphinidin derivatives), chlorophylls, and carotenoids [9]. In both cultivars, the anthocyanin contents in the peel fell sharply as the fruit ripened, and carotenoids increased to comparable values. In this case, the fruit peel of cv. Sirenevyj cub contained only chlorophylls traces, unlike cv. Otello, is which fruit peel chlorophyll level increased significantly. This led to the brown-colored areas in cv. Otello fruit at stage 2; however, it was not visually reflected on the peel of a ripe fruit.

Our data (on the pulp of fruit) are generally consistent with the previously proposed model of the pepper fruit’s pigmentation as it ripens [1, 10]. When the fruit ripen, chloroplasts are gradually replaced by chromoplasts, which can also formed de novo from proplastids [5, 20]. This is accompanied by the replacement of chlorophylls with carotenoids capsanthin and capsorubin, which give the pepper fruit a red colour [1, 10, 11]. The dynamics of changes in the pigment content and composition in pepper fruit were previously studied exclusively on the whole fruit without dividing it into the peel and pulp [1, 2, 11]. However, our results show that different parts of the pericarp (peel and pulp) have different pigment composition and pattern of their accumulation.

Changes in the composition and dynamics of accumulation of the pigments in pepper fruits was compared with the expression profile of key genes for the carotenoid and anthocyanin biosynthesis during fruit ripening in the four analyzed cultivars, contrasting in fruit pigmentation pattern.

Expression Pattern of Carotenoid Pathway Genes in Pepper Fruit During Ripening

Expression patterns of four structural genes of the carotenoid pathway, PSY1, PSY2, LCYb, and CCS, were determined in the fruit peel and pulp of the studied pepper cultivars (Fig. 4). Phytoene synthase catalyzing the synthesis of a precursor of carotenoids (phytoene) is encoded by two genes, PSY1 and PSY2, characterized by tissue-specific activity [21]. The transcripts of the PSY1 phytoene synthase gene found in the fruit peel and pulp all cultivars (Fig. 4). PSY1 expression level increased during fruit ripening: from trace amounts in unripe fruit (0–0.004) to a relatively high level in the fruit peel and pulp at stages 2 and 3 (Fig. 4); however, a significant correlation with an increase in carotenoid content was found only in the fruit pulp (R2 = 0.484; p-value = 0.01) (Fig. 5, Table 2). Previous studies have also revealed a positive correlation between carotenoid content in whole pepper fruit and PSY1 expression level [20, 22]. The same dependence was shown for tomato fruit [21]. The maximum PSY1 expression level was detected in the ripe fruit pulp of cv. Otello (Fig. 4).

Fig. 4.

Expression pattern of PSY1 (a), PSY2 (b), LCYb (c), and CCS (d) in the peel (S) and pulp (P) of the fruits of four pepper cultivars at three stages of development (1 and 2 are unripe fruit, 3 is fruit of biological maturity).

Fig. 5.

Linear regression of PSY1, PSY2, LCYb, and CCS gene expression and carotenoid content in the fruit peel (a) and pulp (b) of the pepper cultivars.

Table 2.   Multiple correlation coefficients (R2) between PSY1, PSY2, LCYb, and CCS gene expression and the carotenoid content in the peel and pulp of pepper fruits

The PSY2 gene expression was also detected in the fruit peel and pulp of all analyzed cultivars; however, the level of PSY2 transcription was significantly lower than that of PSY1 (Fig. 4). The maximum transcription level was found in the fruit peel of cv. Zheltyj buket (stages 1–3) and Sibiryak (stage 1) (Fig. 4). No significant relationship was found between the PSY2 expression level and carotenoid content in the fruits of the analyzed pepper cultivars (p-value > 0.18) (Fig. 5, Table 2). The data obtained are consistent with the previously shown low expression of PSY2 in tomato fruit with its simultaneously high expression in petals and photosynthetic leaves [21]. Apparently, the presence of PSY2 transcription in the peel and pulp of unripe pepper fruit is associated not with the fruit colour, but with the synthesis of carotenoids in chloroplasts, which are necessary for photoprotection/photosynthesis [23].

β-lycopene cyclase gene LCYb, which catalyzes the transition from lycopene to carotenes, was expressed at approximately the same level in the fruit peel and pulp of all pepper cultivars at all three stages (Fig. 4). The exception was the cv. Zheltyj buket fruit, in the peel of which at the stage 2, LCYb transcription level increased by more than 12-fold compared with stages 1 and 3 (Fig. 4), which presumably leads to a bright yellow colour of the ripe fruit at stage 3 (Fig. 2). This may be due to the active conversion of lycopene into yellow-colored carotenoids (mainly α- and β-carotenes and lutein) [5]. Interestingly, the expression of both genes PSY also significantly increased in the stage 2 fruit peel of this cultivar. Low LCYb gene expression in the fruit peel and pulp was similar for the remaining cultivars at all stages of development, which can explain the absence of yellow/orange shades in the ripe fruit colour of these cultivars. Linear regressions constructed separately for the peel and pulp revealed a significant correlation between LCYb expression of and carotenoid content only in the pulp of pepper fruit (R2 = 0.787; p-value = 0.0001) (Fig. 5b, Table 2).

CCS gene encodes capsanthin-capsorubin synthase, which synthesizes Capsicum specific pigments capsanthin and capsorubin, giving the fruit a rich red color [1, 4, 5, 20]. In the analyzed pepper cultivars, CCS gene expression was detected only in the fruit of the cultivars Sibiryak, Sirenevyj cub, and Otello (Figs. 4a, 4b). The CCS transcription level was 0.0002–0.75 in the peel and pulp of unripe fruit (stage 1), and significantly higher (8.75–30.14) in red fruits (stages 2 and 3) (Figs. 4a, 4b). Change in the CCS expression level in the peel and pulp of pepper fruit during ripening was positively correlated (R2 = 0.525 and 0.551; p-value = 0.02) with accumulation of carotenoids (Table 2).

In general, the expression pattern of the studied carotenoid biosynthesis genes in pepper cultivars with a red color of the ripe fruit (Sibiryak, Sirenevyj cub, and Otello) was similar. The PSY1, PSY2, and LCYb expression pattern in the fruit peel and pulp of cv. Zheltyj buket differed from the other three analyzed cultivars, and CCS transcripts were not detected (Fig. 4). As shown earlier, the yellow and orange colour of pepper fruit is due to the lack of CCS gene expression and, therefore, the enzyme capsanthin-capsorubin synthase activity [1, 2, 11]. Some yellow-fruited pepper genotypes have CCS gene expression; however, mutations were identified in the coding part of the gene leading to a premature stop codon [2, 11].

Anthocyanin Gene Expression Pattern in Pepper Fruits during Ripening

The expression profile of five structural genes of anthocyanin biosynthesis pathway was analyzed in the fruit of the four analyzed pepper cultivars: CHS, F3'5'H, DFR, ANS, and UFGT (Fig. 1b). Transcripts of all analyzed genes were found only in cv. Sirenevyj cub and Otello, in which anthocyanins were detected by biochemical analysis (Fig. 3), and that only in the peel (Fig. 6). The maximum transcription levels were detected in the peel of unripe fruit (stage 1), while all five genes were expressed at an extremely low level (0.0001–0.006) in the peel of stage 2 and ripe stage 3 fruits (Fig. 6).

Fig. 6.

Expression profile of anthocyanin biosynthesis genes CHS (a), F3'5'H (b), DFR (c) , ANS (d), and UFGT (e) in the peel of pepper fruits of cv. Sirenevyj cub and Otello cultivars during ripening (1 and 2 are unripe fruit, 3 is fruit of biological maturity).

In comparison with cv. Otello, the transcription levels of the analyzed genes in the peel of an unripe fruit (stage 1) of cv. Sirenevyj cub were 2–3.3 times higher (Fig. 6), while the anthocyanin content was only 1.5 times higher (Fig. 3d). At subsequent stages of development, in the fruit peel, a strong downregulation of gene expression was accompanied by the sharp decrease of the anthocyanin content (Fig. 3d). It can be assumed that, as the fruit ripens, along with a decrease in the expression of anthocyanin biosynthesis genes, transcription of genes encoding anthocyanin- degrading enzymes is activated, as was shown earlier for other crops [8].

Expression levels of all analyzed anthocyanin biosynthesis genes highly correlated with the anthocyanin content (R2 = 0.95–0.99; p-value < 0.001). For F3'5'H, DFR, and UFGT gene expression, a positive correlation with the anthocyanin accumulation in the fruit has already been shown [24]. This study revealed also a relationship between CHS and ANS expression and the anthocyanin content the peel of pepper fruits.

Thus, the pattern of changes in the content of the main pigments (chlorophylls, carotenoids, and anthocyanins) in the fruit peel and pulp during ripening was determined in four pepper cultivars, contrasting in colour of the unripe and ripe fruit. The data obtained were compared with the expression patterns of carotenoid and anthocyanin biosynthesis structural genes. A positive correlation was found between the PSY1, LCYb, and CCS expression levels and the carotenoid content in the fruit pulp. In the fruit peel, the carotenoid content positively correlated only with the CCS gene expression. For pepper cultivars with a purple unripe fruit (cv. Sirenevyj cub, Otello), a positive correlation was shown between the expression level of anthocyanin biosynthesis structural genes (CHS, F3'5'H, DFR, ANS, and UFGT) and the anthocyanin content in the fruit peel. Thus, visually observed changes in the colour of pepper fruit during ripening are directly dependent on the ratio of the three main types of pigments and the activity of the genes of their biosynthesis pathways. It can be assumed that the dynamic patterns of pigmentation of the peel and pulp of pepper fruit are regulated independently.


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This work was supported by the grant of the Russian Science Foundation (no. 19-16-00016) and, in part, by the Ministry of Science and Higher Education (M.A. Filyushin, determination of the chlorophyll content in pepper fruits, statistical analysis).

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Filyushin, M.A., Dzhos, E.A., Shchennikova, A.V. et al. Dependence of Pepper Fruit Colour on Basic Pigments Ratio and Expression Pattern of Carotenoid and Anthocyanin Biosynthesis Genes. Russ J Plant Physiol 67, 1054–1062 (2020).

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  • Capsicum annuum cultivars
  • fruit pigmentation pattern
  • fruit colour changing dynamics
  • fruit ripening
  • fruit pericarp