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Article

A Comparative Analysis of Fruit Quality and Flavor in Capsicum chinense and Capsicum annuum from Myanmar, Peru, and Japan

by
Claudia F. Ortega Morales
1,*,
Kenji Irie
2 and
Makoto Kawase
3,†
1
Graduate School of International Food and Agricultural Studies, Tokyo University of Agriculture, Tokyo 156-8502, Japan
2
Faculty of International Food and Agricultural Studies, Tokyo University of Agriculture, Tokyo 156-8502, Japan
3
Faculty of Agriculture, Tokyo University of Agriculture, Atsugi 243-0034, Japan
*
Author to whom correspondence should be addressed.
Retired.
Int. J. Plant Biol. 2025, 16(3), 90; https://doi.org/10.3390/ijpb16030090 (registering DOI)
Submission received: 29 July 2025 / Revised: 11 August 2025 / Accepted: 12 August 2025 / Published: 14 August 2025
(This article belongs to the Section Plant Biochemistry and Genetics)

Abstract

Chili peppers, a staple spice in global cuisine, hold substantial economic value due to their diverse pungency levels and distinctive aromatic profiles. In addition to their sensory attributes, Capsicum fruits exhibit notable morphological diversity and potential health benefits. While contemporary Capsicum breeding efforts have focused on the yield, shelf life, and resistance to biotic and abiotic stresses, comparatively less emphasis has been placed on the fruit quality and flavor traits increasingly valued by consumers seeking novel flavors and functional foods. We evaluated seven underutilized Capsicum landraces collected from Peru, Myanmar, and Japan and conducted an integrative analysis of their morphological traits, nutritional composition, pungency, and volatile compounds. Our findings highlight C. chinense from Myanmar and Peru as a particularly diverse species, encompassing accessions with mild to very highly pungent, elevated antioxidant content, and significant contributions to fruity aromatic notes. These findings support the development of flavor-driven chili-pepper-based food products with enhanced nutritional value and tailored pungency. Our identification of beneficial alleles also offers opportunities for interspecific breeding to produce novel cultivars aligned with evolving consumer preferences, thereby supporting the commercialization of traditional varieties, conserving genetic resources, and expanding the market potential of new cultivars.

1. Introduction

Chili peppers, classified under the genus Capsicum in the Solanaceae family, are among the oldest domesticated crops [1]. The genus comprises five cultivated species: C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens [2]. These species are valued for their culinary flavor importance, exhibiting variation in pungency, fruit morphology, and bioactive components [3,4]. The primary economic value of Capsicum lies in its pungency, which is conferred by capsaicinoids that are synthesized in the placental tissues and internal tissues of the fruit [4,5,6]. Although these capsaicinoid compounds cause a characteristic burning sensation upon consumption, they are also associated with health-promoting properties, including anti-obesity effects, cancer prevention, and stress reduction via endorphin release [5,6,7].
Pungency, together with aroma, plays a critical role in shaping the sensory perception of Capsicum fruits. This has led to the expansion of research focusing on the flavor and volatile profiles of chili peppers [4]. Fruity and aromatic tones, commonly attributed to esters, are frequently reported in Capsicum accessions [8]. However, comprehensive analyses of aroma composition remain challenging due to the complexity of the flavor-compound quantification and qualification. Unlike other crops such as tomato and strawberry, which possess a detailed aroma profile [8], Capsicum data remain limited, thus constraining the breeding efforts aimed at flavor improvement.
In parallel, evaluations of the nutritional composition are essential for breeding programs to enhance fruits’ quality and consumption. The antioxidant capacity of Capsicum is attributed mainly to polyphenols, vitamin C, and carotenoids [1]. These compounds not only contribute to health benefits such as cancer prevention and mitigation of chronic diseases [3]; they also influence visual attributes through pigmentation in red, orange, and yellow fruits [9]. Chili peppers are particularly rich in vitamin C, providing approx. 60 mg per half-cup serving, equivalent to 67% of the recommended daily intake [10]. Given that humans cannot synthesize polyphenols, vitamin C, and carotenoids, dietary sources are vital [11]. It is thus important to identify Capsicum genotypes with high level of antioxidant to be able to realize its functional benefits for human consumption.
Although recent Capsicum breeding efforts have focused on traits such as the yield, quality, shelf life, and disease resistance [12], limited attention has been given to the integration of flavor and nutritional-quality traits. The lack of focus on integrative traits constrains the development of new cultivars that could meet the growing modern consumer demands for sensory-appealing and health-related attributes [13]. This gap highlights the need to explore underutilized landraces, which may contain alleles that will help improve fruit quality and expand the genetic base of cultivated varieties.
In this study, we analyzed C. annuum and C. chinense accessions collected from Myanmar, Peru, and Japan, excluding widely cultivated commercial varieties. The accessions’ aroma and pungency (key contributors to fruit flavor) and morphological and nutritional traits were investigated. We sought to identify accessions with desirable combinations of fruit quality characteristics that can inform the development of novel cultivars aligned with consumer preferences. The characterization of these landraces will support the conservation and valorization of local Capsicum genetic resources through the landraces’ integration into high-quality chili pepper products.

2. Materials and Methods

2.1. Plant Material

The seven Capsicum accessions listed in Table 1 were selected for detailed characterization. The sampling included one C. annuum accession collected from Minamiashigara, Japan, and two C. chinense accessions obtained from the Sagaing Region, Myanmar. Four C. chinense accessions originating from Peru were provided by Japan’s National Agriculture and Food Research Organization (NARO) Genebank, Yokohama City University, and Kyoto University. All accessions were grown in 10L pots containing a prepared soil mix. Pots were installed in controlled greenhouse conditions at the Setagaya Campus of Tokyo University of Agriculture, maintained at 22 °C, with a 12 h light and 12 h dark photoperiod, and without humidity control. Irrigation was programmed once a day, and fertilization was carried out every three months with granular Akadama soil. The experimental design included four replications per accession, each consisting of one plant. Fruits were harvested at the stage of full botanical maturity.
Table 1. Comprehensive list of Capsicum spp. accessions used in the analysis of chili pepper fruit quality.
Table 1. Comprehensive list of Capsicum spp. accessions used in the analysis of chili pepper fruit quality.
AccessionSupplierOriginSpecies
C34NARO GenebankPeruC. chinense
C37Yokohama City UniversityPeruC. chinense
C39Yokohama City UniversityPeruC. chinense
SP4Kyoto UniversityPeruC. chinense
C44Collected material [14]Sagaing Region, MyanmarC. chinense
C47Collected materialSagaing Region, MyanmarC. chinense
A7Collected materialMinamiashigara, JapanC. annuum

2.2. Morphological Characterization

The morphological analysis was conducted using five fresh fruits per each accession and evaluated using six characters from the Capsicum species descriptors outlined by Bioversity International [15]. This assessment focused on the following fruit characteristics: the fruit pedicel diameter (mm), the number of seeds per fruit, the pericarp thickness (mm), fruit weight (g), fruit length (cm), and fruit width (cm).

2.3. Capsaicinoid Quantification

Capsaicinoids were extracted separately from five freeze-dried fruits per accession and pulverized with a Mixer Mill MM400 (Retsch, Haan, Germany). A 100 mg sample was dissolved in 10 mL of methanol, vortexed, and sonicated for 30 min. The mixture was filtered through Toyo No. 2 filter paper (Advantec Toyo Kaisha, Tokyo, Japan), and the concentrated mixture was placed in a Centrifugal Evaporator (Eyela CVE-3110 and UT-2000, Tokyo Rikakikai Co., Tokyo, Japan) for 12 h, followed by 24 h of freeze-drying (Eyela FDU-1100, Tokyo Rikakikai). The sample was then diluted with 1 mL of methanol, vortexed, sonicated, and filtered through a 13 mm PTFE membrane filter, yielding a final solution in a 2 mL vial.
The crude extract was diluted in methanol to fit in the calibration curve and quantified by liquid chromatography–mass spectrometry (LC-MS) (LC-2060C 3D and LCMS-2050, Shimadzu, Kyoto, Japan) with a C18 column (particle size 2 μm, 2.1 × 150 mm). Acetonitrile was used for the mobile phase at a flow rate of 0.3 mL/min, with oven conditions at 40 °C and detection at 280 nm over a 20 min run time. The quantification and retention times were validated with the use of commercial standards for capsaicin (93%) (Wako Pure Chemical Industries, Osaka, Japan), dihydrocapsaicin (99%) (Wako), nordihydrocapsaicin (95%) (PhytoLab, Vestenbergsgreuth, Germany), and a capsaicinoid mixture of the mentioned components.

2.4. Ascorbic Acid Analysis

Ascorbic acid in chili peppers was quantified with a RQflex plus10 reflectometer (Merck, Darmstadt, Germany) and Reflectoquant® ascorbic strips (Merck). Powdered tissue from five freeze-dried fruits per accession (0.05 g) were homogenized individually by mixing with 1.5 mL of 5% metaphosphoric acid in a 2 mL Eppendorf tube. The mixture was centrifuged at 5000 rpm and 25 °C for 5 min (MX-307 centrifuge, Tomy Seiko, Tokyo, Japan). Each ascorbic strip was immersed in the solution and analyzed with the reflectometer.

2.5. Carotenoid Content

Carotenoids were extracted from the powder of five freeze-dried chili pepper fruits per accession by mixing 0.02 g of each repetition with 10 mL of methanol in a Falcon tube. The mixture was vortexed for 15 s, sonicated for 15 min (Branson M1800 ultrasonic cleaner, Yamato Scientific Co., Tokyo, Japan), then centrifuged at 12,000 rpm, 4 °C for 5 min (MX-307 centrifuge (Tomy Seiko Co., Ltd., Tokyo, Japan), and stored at 4 °C for 24 h. The supernatant was collected, and carotenoid content was measured at absorbance wavelengths of 470 nm, 665.4 nm, and 652.4 nm (UV-VIS Spectrophotometer UV-1900i, Shimadzu, Japan).

2.6. Total Polyphenols

A modified Folin–Ciocalteu method [16] was used. Powder (0.02 g) from five freeze-dried fruits per accession were independently mixed with a 100-fold dilution of 80% ethanol, vortexed, and centrifuged at 8000 rpm for 5 min (MX-307 centrifuge). The supernatant was transferred, and only 0.1 mL was diluted with 6.9 mL of distilled water in a Falcon tube. Then, 0.5 mL of 10% Folin–Ciocalteu reagent was added and incubated for 3 min, followed by the addition of 1 mL of 7.5% sodium carbonate. After the mixture was heated for 60 min at 25 °C, absorbance was measured at 750 nm with the above-mentioned spectrophotometer. A calibration curve was created using gallic acid standards at 500, 400, 300, 200, and 100 ppm concentrations.

2.7. Aromatic Composition

Freeze-dried chili pepper powder (0.5 g) from 5 fruits per accession were placed individually in a headspace vial with a solid phase microextraction (SPME) holder and fibers, and incubated at 40 °C for 20 min. The fibers were exposed to a gas chromatography–mass spectrometry (GC-MS) injection port (QP2020NX, Shimadzu, Japan) at 250 °C under splitless conditions. Volatile compounds were separated using an RTX-5MS capillary column (Restek, Bellefonte, PA, USA) (30 m length × 0.25 mm i.d., 0.25 m film) with helium as the carrier gas (1 mL/min). The oven temperature was set to rise from 100° to 250 °C at a rate of 5 °C/min, then held at 250 °C for 10 min. The mass spectrometry detection used 70 eV ionizing energy, a 200 °C ion source temperature, and a 35–450 m/z scanning range. Volatile compounds were identified using the NIST Special 20 Database [17], with quantification based on peak areas (%) and retention times.

2.8. Statistical Analysis

The morphological traits (n = 6), pungency level (n = 1), and bioactive compounds (n = 3) were expressed as mean  ±  standard error, excluding the aroma profile evaluation. Statistical significance among groups was assessed by an analysis of variance (ANOVA), followed by Tukey’s post hoc test, with the significance threshold set at p < 0.05. Pearson’s correlation coefficients were estimated based on the mean values of each trait. All assessed fruit quality parameters were subjected to principal component analysis (PCA) for a multivariate analysis to explore data relationships and patterns. All statistical analysis were performed using Rstudio (version 1.1.383) [18].

3. Results and Discussion

3.1. Morphology

Detailed morphological data are presented in Table 2. Significant morphological variation was observed among the C. chinense accessions from Peru, particularly in fruit length, pericarp thickness, and weight, reinforcing Peru’s status as a center of Capsicum domestication [3]. In contrast, the C. chinense accessions from Myanmar exhibited greater uniformity in fruit morphology, with trait values closely aligned with the average measurements observed for the Peruvian accessions. The C. annuum accession was distinguished by its large fruit size (91  ±  4.25 mm), thinner pericarp (1.04  ±  0.16 mm), and lower fruit weight (3.71  ±  0.55 g).
The correlation analysis revealed that most of the traits’ associations were positive, which is consistent with previous findings [13,19]. However, negative correlations were detected between the fruit length and pericarp thickness (r  =  −0.21) as well as between the fruit pedicel diameter and pericarp thickness (r  =  −0.15). These findings suggest that larger fruits do not necessarily exhibit thicker pericarps, underscoring the high morphological diversity within C. chinense accessions. This divergence challenges the alignment of morphotypes with a strict species classification, a pattern that was also observed in earlier studies [20].
Despite the morphological diversity, specific fruit traits remain crucial for market-oriented breeding, particularly for chili pepper powder and flake production, which favor larger fruit size and weight [13]. In the present study, the accessions from Myanmar and Peru (specifically C34, C44, C47, and C39) demonstrated desirable characteristics, including substantial fruit and pedicel dimensions, thick pericarps, and significant weight. Although these morphological attributes are essential for product quality, they must be considered alongside flavor and nutritional traits. Current consumer trends, particularly among younger consumers, indicate a strong preference for products offering exotic flavors and health benefits [13]. Breeding strategies should therefore integrate morphological selection with evaluations of aroma and nutritional composition in order to ensure the development of high-quality chili pepper cultivars.

3.2. Spiciness in chili pepper

Pungency, a vital determinant of chili pepper quality, is influenced primarily by the capsaicinoid concentration [13]. The total capsaicinoid content across the evaluated accessions exhibited substantial variation, ranging from 106.83  ±  0 to 961.71  ±  5.33 mg/100 g dry weight (DW), as shown in Table 3. The C. chinense accessions exhibited both the highest and lowest capsaicinoid concentrations, whereas the C. annuum accessions showed moderate levels, consistent with previous reports [4].
Capsaicin was the predominant capsaicinoid in all accessions, followed by dihydrocapsaicin, and nordihydrocapsaicin. The accessions classified as ‘very highly pungent’ contained >70% capsaicin, while those categorized as ‘moderately/highly pungent’ exhibited a >60% combined content of capsaicin and dihydrocapsaicin. The capsaicin-to-dihydrocapsaicin ratio ranged from 1:1 to 4:1, exceeding the reported range 1:1 to 2:1 [22]. Although capsaicin consistently emerged as the most abundant capsaicinoid across the present population [23], the accession C39 (C. chinense) was an exception, exhibiting the lowest total of capsaicinoid content.
Although Scoville heat units (SHUs) are commonly used to estimate pungency based on the capsaicinoid concentration, the SHU scale provides only a generalized measure. The SHU values in this study ranged from 14,346.38  ±  0 to 15,0319.36  ±  845.97, which is in line with reported data [22]. Notably, C. annuum demonstrated a high SHU value at 76,501.27  ±  339.39, which categorizes this accession as highly pungent and surpassing the levels typically reported for this species [4,12]. Although C. annuum is typically characterized as non-pungent [24], the accession evaluated herein displayed significant pungency. This finding highlights the lack of a consistent correlation between species identity and capsaicinoid content [25].
The observed variability in capsaicinoid levels can be attributed to multiple factors including the cultivar type, harvesting time, and enzymatic activity, particularly that of capsaicin synthase [4,26]. Given that there is no stable species-specific association with capsaicinoid content [1,25], genotype selection is essential in chili pepper varieties with mild-to-lower pungency.

3.3. Antioxidant Activity

Previous data confirmed that Capsicum fruits are rich sources of ascorbic acid (vitamin C) [1]. As shown in Table 4, the accessions evaluated in this study exhibited ascorbic acid concentrations ranging from 269  ±  5 to 777  ±  15.40 mg/100 g DW, exceeding the values reported for Capsicum species [12,27,28]. These levels are considerably higher than the recommended daily intake of 75–90 mg [29], indicating that the consumption of approx. 10 g of dried fruit from most of the chili pepper accessions examined in the present study is sufficient to meet the daily vitamin C requirement. Ascorbic acid not only addresses micronutrient deficiencies; it also plays a protective role in maintaining the stability of other bioactive compounds such as carotenoids, which contribute to fruits’ coloration and antioxidative potential [30]. Accordingly, further assessments of polyphenols and carotenoids will be essential to understand the antioxidant activity of chili pepper genotypes.
Chili pepper fruits also represent an important dietary source of carotenoids, which are the compounds responsible for the red, orange, and yellow pigmentation of fruits [13,31]. Carotenoid concentrations in the evaluated accessions ranged from 28.97  ±  0.71 to 89.97  ±  0.44 mg/100 g DW (Table 4), which is consistent with earlier studies [28,32]. These levels surpass those found in commonly consumed fruits and vegetables such as apples (30 μg/100 g), tomatoes (112 μg/100 g), and carrots (15,000 μg/100 g) [28], reinforcing the role of Capsicum as a substantial source of carotenoids. Carotenoids also contribute to the content of provitamin A, which is associated with reduced risks of certain cancers and cardiovascular diseases [12,33]. From a commercial perspective, these compounds also enhance the visual appeal and health functionality of chili pepper powder products, making carotenoid-rich accessions particularly valuable for value-added food applications.
The total antioxidant capacity, measured by the Folin–Ciocalteu method in this study, further supports the high nutraceutical potential of the evaluated accessions [34]. The polyphenol concentrations ranged from 967.38  ±  19.57 to 2435.09  ±  733.88 mg/100 g DW, aligning with previous studies [1]. Notably, the C. chinense accessions categorized as ‘very highly pungent’ exhibited the highest polyphenol levels. Conversely, accessions C39 and C34, both ‘moderately pungent,’ showed the lowest concentrations, although still exceeding the 759.12 mg/100 g reported for commercial ‘Habanero’ peppers [35]. The C. annuum accession also demonstrated elevated polyphenol levels, surpassing 1000 mg/100 g DW, which exceeds the reported values [36]. Overall, the polyphenol concentrations varied considerably across the accessions examined herein, but they remained higher than those found in commonly consumed fruits, such as strawberries (235 mg/100 g), apples (136 mg/100 g), and peaches (59 mg/100 g) [37]. These findings highlight the exceptional capacity of the evaluated Capsicum accessions and underscore their potential as functional foods with significant health-promoting properties.

3.4. Aroma Profile

We detected >400 volatile compounds, of which 93 were selected for analysis across the evaluated accessions. C. chinense exhibited higher concentrations of esters and terpenoids, in line with reported findings [38], while C. annuum was predominantly characterized by aldehydes, alkanes, and alcohols. As summarized in Table S1, C. chinense displayed a more complex aroma profile than C. annuum.
Regarding the ester content, C. annuum demonstrated the lowest levels, with an average peak area of 0.13  ±  0.10. The C. chinense accessions contained substantial quantitates of esters such as 4-methylpentyl 3-methylbutanoate, 4-methylpentyl 4-methylpetanoate, hexyl isovalerate, and hexyl 2-methylbutyrate, which are compounds that have been linked to fruity and sweet aromatic notes [5,39]. These esters were either absent or detected in minimal amounts in C. annuum and in the moderately pungent C. chinense accession C39. The presence of high ester concentrations in C. chinense is largely responsible for its exotic and complex fruity aroma.
Terpenoids, including germacrene D, cubebenes, and himachalenes, were prevalent in the highly pungent C. chinense genotypes, consistent with earlier reports [38,40]. Conversely, C. annuum and the moderately pungent C. chinense accessions C34 and C39 exhibited significantly lower terpenoid concentrations. Interestingly, the C. annuum accession, despite its high pungency, contained minimal terpene levels, diverging from reports of elevated terpenoid content in pungent C. chinense and C. annuum accessions [5,41]. In sensory terms, terpenoids contributed to the citrus and woody notes that were especially pronounced in C. chinense.
We also identified minor volatile compounds (including alcohols, furans, ketones, and hydrocarbons), particularly in the very highly pungent C. chinense accessions. Notably, the moderately pungent C. chinense accession C39 exhibited elevated alcohol levels but reduced ester concentrations. This pattern is in contrast to previous reports, suggesting a positive correlation between the alcohol content and ester biosynthesis, as alcohols serve as precursors in ester formation [38,41].
Alkanes and alkenes were abundant in the very highly pungent C. chinense cultivars but less prevalent in C. annuum and the moderately pungent C. chinense accession C39. This may be linked to the involvement of methyl-branched and aliphatic hydrocarbons in capsaicin biosynthesis pathways [38]. Aldehydes such nonanal, hexanal, and 3-methyl-benzaldehyde were detected at low concentrations in most of the accessions, though C. annuum exhibited relatively higher levels, contributing to earthy and green notes. This is consistent with prior findings in fresh green bell pepper, where aldehydes play a prominent role in aroma perception [40,41].
Overall, based on the data presented in Figure 1, the C. annuum accession was characterized by weak green-vegetable and citrus notes, which can be attributed to its aldehyde, alkane, alcohol, and limited ester content. In contrast, the C. chinense accessions displayed intense fruity, sweet, and peachy-like aromas due to high concentrations of esters and terpenoids. However, exceptions were observed in accessions C39 and C34, which, despite their moderate pungency, presented low levels of these volatiles. These accessions yielded sweet and earthy aroma profiles that, while less complex than those of highly pungent C. chinense, were still more aromatic than C. annuum. The identification of such genotypes is valuable, as they offer desirable aroma profiles with reduced pungency — a rare trait in C. chinense, which is typically associated with high pungency and intense fruity notes [22,42]. The overlap in biosynthetic pathways for capsaicinoids and esters, particularly 6-methy- (E)-4-heptenyl [24,42,43], presents challenges in distinguishing ester-derived aromas from pungency. This underscores the importance of identifying genotypes that combine complex fruity aromas with mild pungency, which are particularly attractive for breeding programs targeting both sensory factors and consumer acceptability. Although non-pungent cultivars often exhibit reduced aromatic complexity, the highly aromatic yet pungent C. chinense remains prevalent in current germplasm collections [24].
The selection of Capsicum genotypes remains challenging due to the complex relationships among metabolic pathways and volatile flavor compounds [8]. Our present analyses revealed significant variation in fruit quality traits across the chili pepper accessions (Figure 2). Fruit pedicel length showed the most significant contribution overall trait variance (17.79%), followed by fruit weight (14.99%), total capsaicinoid content (12.80%), and seed number per fruit (12.65%), consistent with previous findings [44]. Most accessions exhibited large, heavy fruits with thick pericarps, traits desirable for powder and flake production. However, when selecting genotypes for improving fruit quality, fruit morphology is as important as flavor profile, which emerges from the interaction between pungency and aroma [33]. The first two principal components (PC) explained 67.2% of total variability, effectively capturing trait associations. C. annuum accessions generally exhibited a citrus-like aroma with weaker intensity in comparison to C. chinense, particularly C34, C44, and C47, which had strong fruity aromas. Notably, C34 combined mild pungency with high aroma intensity, which is highly suitable for interspecific hybridization. As recommended by a previous study [44], traits contributing most to PC1 should be prioritized in the selection of genotypes. Our results depict the importance of incorporating both fruit morphology and bioactive compounds in breeding programs.
Antioxidant activity contributed less than 10% to either PC, although all accessions showed high levels of polyphenols, vitamin C, and carotenoids. The lyophilization applied in the current study preserved the bioactive components integrity, enhancing the accuracy of dry-weight assessments compared to fresh fruit analysis [45]. While antioxidant composition, aroma intensity, and pungency contributed positively to PC2, excessive pungency may limit its culinary use [42]. Although placental and seed removal is traditionally employed to reduce pungency [11], this practice can diminish both flavor and health-promoting constituents, potentially compromising the full sensory profile of the fruit.
In Capsicum, it is important to analyze aroma along with pungency [33], which significantly influences consumers’ acceptance of spicy foods [42]. Therefore, our findings support the utility of these agronomic traits and biochemical traits in interspecific hybridization strategies aimed at accelerating Capsicum breeding efforts [46]. C. chinense accessions from Peru (C34 and C39) exhibited a rare combination of large fruit size, mild pungency, and intense fruity notes, traits suitable for developing less spicy yet flavorful cultivars. In contrast, Myanmar C. chinense accessions (C44 and C47), characterized by high pungency and strong fruity notes, may be suited for markets with a preference for very spicy products. These accessions present valuable alleles that can be used for diversifying current breeding programs, which are still dominated by crossings between genotypes from North America, Europe [47], Japan [48], and India [49].

4. Conclusions

The agronomic and biochemical traits identified in this study support the development of interspecific hybridization. Peruvian and Myanmar landraces exhibited varying morphological types and pungency levels, with distinct volatile profiles. This contributes to the expansion of the literature for breeding programs that integrate flavor diversity. Traits such as high antioxidant content, large fruit size, and specific volatile compounds (e.g., 4-methylpentyl esters and hexyl derivates) are important considerations when selecting genotypes for chili pepper-based products. While pungency remains important, selection should align with market preferences. These underutilized landraces represent a rich genetic resource capable of enhancing flavor, nutritional value, and consumer appeal. Their incorporation into breeding efforts may support the identification of novel alleles and strengthen germplasm conserved by small-scale farmers. Further studies are recommended to explore their hybridization potential, particularly with pollen-compatible species within the C. annuum complex.

Supplementary Materials

The following supporting information can be downloaded at https://www.mdpi.com/article/10.3390/ijpb16030090/s1, Table S1: Profile of aroma composition in C. annuum and C. chinense [50,51,52].

Author Contributions

Conceptualization, C.F.O.M.; methodology, C.F.O.M.; formal analysis, C.F.O.M.; investigation, C.F.O.M.; resources, M.K.; data curation, C.F.O.M.; writing—original draft preparation, C.F.O.M.; writing—review and editing, K.I. and M.K.; visualization, C.F.O.M.; supervision, K.I. and M.K.; project administration, C.F.O.M., K.I. and M.K.; funding acquisition, C.F.O.M. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Japan Science and Technology (JST) Challenging Research Program for Next-Generation Researchers, grant number JPMJSP2122.

Data Availability Statement

All data contained within this study is included in the manuscript.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Main volatile groups in the aroma profile of the evaluated accessions.
Figure 1. Main volatile groups in the aroma profile of the evaluated accessions.
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Figure 2. PCA plot showing (a) the contribution of each of the evaluated characters and (b) the distribution of the seven Capsicum accessions and its interaction with the evaluated parameters, fruit pedicel diameter (FPD) (mm), number of seeds per fruit (NSF), fruit pedicel length (FPL) (mm), fruit weight (FW) (g), fruit width (FWD) (mm), pericarp thickness (PT) (mm).
Figure 2. PCA plot showing (a) the contribution of each of the evaluated characters and (b) the distribution of the seven Capsicum accessions and its interaction with the evaluated parameters, fruit pedicel diameter (FPD) (mm), number of seeds per fruit (NSF), fruit pedicel length (FPL) (mm), fruit weight (FW) (g), fruit width (FWD) (mm), pericarp thickness (PT) (mm).
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Table 2. Morphological evaluation of fresh fruits from C. chinense and C. annuum.
Table 2. Morphological evaluation of fresh fruits from C. chinense and C. annuum.
AccessionFPLFPDNSFPTFWFLFWD
C344.04 ± 0.16 b2.12 ± 0.19 a,b79.4 ± 14.16 a1.9 ± 0.24 b13.98 ± 4.10 b62.82 ± 17.03 b21.06 ± 5.53 b
C371.78 ± 0.10 b,c0.9 ± 0.06 b,c6.2 ± 1.02 b1.06 ± 0.10 b0.69 ± 0.06 c15.02 ± 0.61 b,c10.64 ± 0.57 b,c
C393.28 ± 0.24 b,c1.54 ± 0.09 c,d28.2 ± 5.85 b2.64 ± 0.15 c19.28 ± 1.09 c38.54 ± 4.69 b,c39.52 ± 2.41 cd
SP41.5 ± 0.03 d1.02 ± 0.14 e15.2 ± 1.99 b1.62 ± 0.09 c0.6 ± 0.05 c10.46 ± 0.29 d9.22 ± 0.37 e
C442.92 ± 0.26 c2.22 ± 0.20 d22.8 ± 9.85 b1.16 ± 0.09 c5.46 ± 0.58 c54.5 ± 3.32 c25.72 ± 0.74 d,e
A73.42 ± 0.06 a2.54 ± 0.09 a58.6 ± 5.11 a1.04 ± 0.16 a3.71 ± 0.55 a91 ± 4.25 a8 ± 0.57 a
C472.86 ± 0.19 d1.78 ± 0.08 e11.8 ± 2.94 b0.94 ± 0.05 c3.64 ± 0.36 c56.26 ± 1.50 d17.34 ± 0.92 e
p-value<0.01<0.01<0.01<0.01<0.01<0.01<0.01
Data are mean  ±  standard error. Different letters in the same category denote significant differences as analyzed by Tukey test at p < 0.05. FPL = fruit pedicel length (mm), FPD = fruit pedicel diameter (mm), NSF = number of seeds per fruit, PT = pericarp thickness (mm), FW = fruit weight (g), FL = fruit length (mm), FWD = fruit width (mm).
Table 3. Total capsaicinoid composition (mg/100 DW) and SHU values in C. chinense and C. annuum.
Table 3. Total capsaicinoid composition (mg/100 DW) and SHU values in C. chinense and C. annuum.
AccessionCAPDIHNDHTotalSHUsClassification 1
C3453.75 ± 0.09 a50.99 ± 0.06 a41.97 ± 0 b146.7 ± 0.14 b20,765.56 ± 22.78 aModerately pungent
C37728.91 ± 4.00 b158.8 ± 0.94 b60.18 ± 0.16 c947.89 ± 5.10 c148,518.3 ± 810.71 bVery highly pungent
C3923.9 ± 0 c40.97 ± 0 c41.97 ± 0 d106.83 ± 0 d14,346.38 ± 0 cModerately pungent
SP4404.05 ± 3.97 f119.52 ± 0.59 f111.72 ± 0.36 f635.3 ± 4.88 g94,685.2 ± 761.45 fVery highly pungent
C44659.97 ± 3.28 d169.01 ± 0.72 d63.56 ± 0.20 e892.54 ± 4.19 e139,376.75 ± 661.24 dVery highly pungent
A7306.71 ± 1.43 a138.37 ± 0.61 a52.08 ± 0.13 a497.16 ± 2.16 a76,501.27 ± 339.39 aHighly pungent
C47726.87 ± 4.18 e168.42 ± 1.10 e66.42 ± 0.18 f961.71 ± 5.33 f150,319.36 ± 845.97 eVery highly pungent
p-value<0.01<0.01<0.01<0.01<0.01<0.01
Data are mean  ±  standard error. Different letters in the same category denote significant differ-ences as analyzed by Tukey test at p < 0.05. CAP = capsaicin (mg/100 g), DIH = dihydrocapsaicin (mg/100 g), NDH = nordihydrocapsaicin (mg/100 g), SHUs = Scoville heat units. 1 Classification based on [21].
Table 4. Polyphenol, vitamin C, and carotenoid content (mg/100 g DW) in C. annuum and C. chinense.
Table 4. Polyphenol, vitamin C, and carotenoid content (mg/100 g DW) in C. annuum and C. chinense.
AccessionCarotenoidPolyphenolsVitamin C
C3489.97 ± 0.44 b1254.4 ± 424.16 a768 ± 23.30 a
C3732.05 ± 0.25 c1071.75 ± 6.52 a777 ± 15.40 b
C3935.6 ± 0.96 d967.38 ± 19.57 a645 ± 17.059 b,c
SP444.88 ± 0.32 g2258.97 ± 733.88 a269 ± 5 e
C4464.61 ± 0.85 e2435.09 ± 733.88 a680 ± 13.45 c
A766.56 ± 0.19 a1534.9 ± 403.12 a506 ± 6.08 a
C4728.97 ± 0.71 f1554.47 ± 0 a715 ± 10.58 d
p-valuep < 0.05n.s.p < 0.05
Data are mean ± standard error. Different letters in the same category denote significant differences as analyzed by Tukey test at p < 0.05. n.s. = nonsignificant.
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Ortega Morales, C.F.; Irie, K.; Kawase, M. A Comparative Analysis of Fruit Quality and Flavor in Capsicum chinense and Capsicum annuum from Myanmar, Peru, and Japan. Int. J. Plant Biol. 2025, 16, 90. https://doi.org/10.3390/ijpb16030090

AMA Style

Ortega Morales CF, Irie K, Kawase M. A Comparative Analysis of Fruit Quality and Flavor in Capsicum chinense and Capsicum annuum from Myanmar, Peru, and Japan. International Journal of Plant Biology. 2025; 16(3):90. https://doi.org/10.3390/ijpb16030090

Chicago/Turabian Style

Ortega Morales, Claudia F., Kenji Irie, and Makoto Kawase. 2025. "A Comparative Analysis of Fruit Quality and Flavor in Capsicum chinense and Capsicum annuum from Myanmar, Peru, and Japan" International Journal of Plant Biology 16, no. 3: 90. https://doi.org/10.3390/ijpb16030090

APA Style

Ortega Morales, C. F., Irie, K., & Kawase, M. (2025). A Comparative Analysis of Fruit Quality and Flavor in Capsicum chinense and Capsicum annuum from Myanmar, Peru, and Japan. International Journal of Plant Biology, 16(3), 90. https://doi.org/10.3390/ijpb16030090

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