Pepper (Capsicum spp.) is one of the most important crops worldwide. The fruits of Capsicum species are known to contain high amounts of vitamins and carotenoids, and they have health-promoting properties. In this study, a total of 513 pepper accessions belonging to two Capsicum species, C. annuum and C. frutescens, were investigated for their morphological characteristics and contents of phytochemicals including carotenoids, β-carotene, vitamin C, capsaicinoids, and total soluble solids. The results revealed wide variations in morphological traits and phytochemical contents between the accessions and across species. In addition, the association of fruit color and orientation with phytochemical contents was evaluated; the results indicated that germplasm with yellow-colored and pendant-oriented fruits could be important due to their high vitamin C levels. Multivariate analysis of the agro-morphological and phytochemical parameters revealed that Capsicum germplasm were clearly distinguished according to species. Furthermore, cluster analysis showed that germplasms belonged to three groups, and six genotypes were determined as being good genetic resources with high health-promoting phytochemical contents. Especially, vitamin C content was positively correlated with fruit diameter, weight, and wall thickness. Our findings revealed morphological and phytochemical characteristics potentially useful for breeding programs.

Pepper is a highly important vegetable globally, both economically and nutritionally. However, to efficiently select and identify genetic resources for pepper breeding programs, it is crucial to understand the association between important traits and genetic factors. In this study, we investigated the genetic basis of carotenoid and capsaicinoid content in 160 Capsicum chinense germplasms. The study observed significant variability in carotenoid and capsaicinoid content among the germplasms. Correlation analysis revealed a strong positive correlation between violaxanthin and antheraxanthin. In contrast, capsaicin and dihydrocapsaicin displayed negative correlations with individual carotenoids but exhibited a strong positive correlation between the two compounds (r = 0.90 ***). Genotyping-by-sequencing (GBS) was performed on 160 genotypes of pepper germplasm, which identified 47,810 high-quality SNPs. A comprehensive genome-wide association analysis was performed using these SNPs to identify SNPs associated with carotenoids and capsaicinoids, revealing 193 SNPs that exhibited significant associations. Specifically, 4 SNPs were associated with violaxanthin, 2 with antheraxanthin, 86 with capsorubin, 5 with capsanthin, 63 with zeaxanthin, 3 with β-cryptoxanthin, and 2 with α-carotene. With further studies, the significantly associated SNPs identified in this study have the potential to be utilized for selecting pepper accessions with high carotenoid and capsaicinoid contents. Additionally, the genes associated with these significant SNPs will be used to understand their roles and involvement in the biosynthesis pathway of carotenoids and capsaicinoids. Understanding the function of these genes can provide insights into the molecular mechanisms underlying the production of these bioactive compounds in pepper. The findings of this study hold valuable implications for selecting pepper varieties with desirable traits and developing breeding programs aimed at enhancing the nutritional and medicinal properties of pepper.

This study investigated carotenoid content and fruit color variation in 306 pepper accessions from diverse Capsicum species. Red-fruited accessions were predominant (245 accessions), followed by orange (35) and yellow (20). Carotenoid profiles varied significantly across accessions, with capsanthin showing the highest mean concentration (239.12 μg/g), followed by β-cryptoxanthin (63.70 μg/g) and zeaxanthin (63.25 μg/g). Total carotenoid content ranged from 7.09 to 2566.67 μg/g, emphasizing the diversity within the dataset. Correlation analysis revealed complex relationships between carotenoids, with strong positive correlations observed between total carotenoids and capsanthin (r = 0.94 ***), β-cryptoxanthin (r = 0.87 ***), and zeaxanthin (r = 0.84 ***). Principal component analysis (PCA) identified two distinct carotenoid groups, accounting for 67.6% of the total variance. A genome-wide association study (GWAS) identified 91 significant single nucleotide polymorphisms (SNPs) associated with fruit color (15 SNPs) and carotenoid content (76 SNPs). These SNPs were distributed across all chromosomes, with varying numbers on each. Among individual carotenoids, α-carotene was associated with 28 SNPs, while other carotenoids showed different numbers of associated SNPs. Candidate genes encoding diverse proteins were identified near significant SNPs, potentially contributing to fruit color variation and carotenoid accumulation. These included pentatricopeptide repeat-containing proteins, mitochondrial proton/calcium exchangers, E3 ubiquitin-protein ligase SINAT2, histone–lysine N-methyltransferase, sucrose synthase, and various enzymes involved in metabolic processes. Seven SNPs exhibited pleiotropic effects on multiple carotenoids, particularly β-cryptoxanthin and capsanthin. The findings of this study provide insights into the genetic architecture of carotenoid biosynthesis and fruit color in peppers, offering valuable resources for targeted breeding programs aimed at enhancing the nutritional and sensory attributes of pepper varieties.

This study utilized a diverse Capsicum accessions (5658) sourced from various species and geographical regions, deposited at the National Agrobiodiversity Center, Genebank. We employed 19 SNP markers through a Fluidigm genotyping system and screened these accessions against eight prevalent diseases of pepper. This study revealed accessions resistant to individual diseases as well as those exhibiting resistance to multiple diseases, including bacterial spot, anthracnose, powdery mildew, phytophthora root rot, and potyvirus. The C. chacoense accessions were identified as resistant materials against bacterial spot, anthracnose, powdery mildew, and phytophthora root rot, underscoring the robust natural defense mechanisms inherent in the wild Capsicum species and its potential uses as sources of resistance for breeding. C. baccatum species also demonstrated to be a promising source of resistance to major pepper diseases. Generally, disease-resistant germplasm has been identified from various Capsicum species. Originating from diverse locations such as Argentina, Bolivia, and the United Kingdom, these accessions consistently demonstrated resistance, indicating the widespread prevalence of disease-resistant traits across varied environments. Additionally, we selected ten pepper accessions based on their resistance to multiple diseases, including CMV, Phytophthora root rot, potyviruses, and TSWV, sourced from diverse geographical regions like Hungary, Peru, the United States, and the Netherlands. This comprehensive analysis provides valuable insights into disease resistance in Capsicum, crucial for fostering sustainable agricultural practices and advancing crop improvement through breeding strategies.

Due to the vulnerability of pepper (Capsicum spp.) and the virulence of tomato spotted wilt virus (TSWV), seasonal shortages and surges of prices are a challenge and thus threaten household income. Traditional bioassays for detecting TSWV, such as observation for symptoms and reverse transcription-PCR, are time-consuming, labor-intensive, and sometimes lack precision, highlighting the need for a faster and more reliable approach to plant disease assessment. Here, two imaging techniques—Red–Green–Blue (RGB) and hyperspectral imaging (using NDVI and wavelength intensities)—were compared with a bioassay method to study the incidence and severity of TSWV in different pepper accessions. The bioassay results gave TSWV an incidence from 0 to 100% among the accessions, while severity ranged from 0 to 5.68% based on RGB analysis. The normalized difference vegetative index (NDVI) scored from 0.21 to 0.23 for healthy spots on the leaf but from 0.14 to 0.19 for disease spots, depending on the severity of the damage. The peak reflectance of the disease spots on the leaves was identified in the visible light spectrum (430–470 nm) when spectral bands were studied in the broad spectrum (400.93–1004.5 nm). For the selected wavelength in the visible light spectrum, a high reflectance intensity of 340 to 430 was identified for disease areas, but between 270 and 290 for healthy leaves. RGB and hyperspectral imaging techniques can be recommended for precise and accurate detection and quantification of TSWV infection.

This study utilized 303 pepper accessions from diverse Capsicum species to explore fruit traits, including length, width, wall thickness, and weight. Descriptive statistics revealed a mean fruit length of 66.19 mm, width of 23.48 mm, wall thickness of 1.89 mm, and weight of 15.29 g, with significant variability, particularly in fruit weight. Correlation analysis demonstrated strong positive relationships between fruit width, weight, and fruit wall thickness (r = 0.89 and r = 0.86, respectively), while fruit length showed weaker correlations with these traits. Analysis of fruit positions revealed that the majority of accessions had a pendent fruit position (156), followed by erect (85) and intermediate (8). In terms of fruit shape, triangular and narrow triangular shapes were the most common, observed in 102 and 98 accessions, respectively. Genome-wide association studies (GWAS) identified significant single nucleotide polymorphisms (SNPs) associated with fruit traits across four models (Blink, FarmCPU, MLM, MLMM). The number of significantly associated SNPs were as follows: fruit length (89), fruit width (55), fruit weight (63), fruit wall thickness (48), fruit shape (151), and fruit position (51). Several genes were also identified where the SNPs are located or adjacent to, providing candidate genes for further exploration of the genetic basis of fruit morphology. Notably, genes such as E3 ubiquitin-protein ligase RGLG1 (associated with fruit width), Homeobox-leucine zipper protein HDG11 (involved in fruit width), Auxin response factor 23 (linked to fruit shape), and ATP-dependent zinc metalloprotease FtsH (related to fruit weight) were identified. These findings enhance our understanding of the genetic basis of fruit morphology in Capsicum, offering valuable insights for breeding and agricultural practices.