https://orcid.org/0000-0001-7213-273X
Figures
Abstract
Chili peppers (Capsicum spp.) are among the most widely cultivated horticultural crops worldwide due to the high demand for their pungent fruits. Despite Colombia’s high diversity of Capsicum species and varieties, its genetic resources remain underrepresented in international markets and scientific studies. This study aims to characterize the genetic diversity and population structure of Capsicum accessions from southwestern Colombia. Accessions were collected through field surveys in local markets and protected natural areas and genotyped using DArTseq platform. A total of 69 accessions representing seven species were genotyped using 3681 high quality DArT-SNP markers. Standard genetic diversity metrics and population structure analyses were performed. The analysis revealed low observed heterozygosity (mean 1%) and high inbreeding coefficients (FIS: 0.24). However, expected heterozygosity values indicate that these accessions still retain substantial genetic variability, highlighting their potential for breeding and genetic improvement programs. Population structure analysis revealed clear genetic differentiation between Andean and domesticated Capsicum species. Moreover, Silico-DArT markers could discriminate between wild and domesticated accessions within C. annuum and C. frutescens. This study represents the first genome wide assessments of Andean Capsicum species using DArTseq genotyping. These findings contribute to the understanding and conservation of Capsicum genetic resources of Southwestern Colombian and provide valuable information for future breeding programs.
Citation: Viáfara-Vega RA, Cárdenas-Henao H (2026) Genome-wide assessment of genetic diversity and population structure of Capsicum in Southwestern Colombia using DArTseq markers. PLoS One 21(9): e0359207. https://doi.org/10.1371/journal.pone.0359207
Editor: Rajesh Mehrotra, Birla Institute of Technology and Science, INDIA
Received: March 12, 2026; Accepted: September 10, 2026; Published: September 25, 2026
Copyright: © 2026 Viáfara-Vega, Cárdenas-Henao. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the paper and its Supporting Information files and in the following repository: https://doi.org/10.5281/zenodo.17429447.
Funding: This study was funded by the internal call 2023 for the creation of a bank of eligible projects for research and artistic creation in the sciences, arts, humanities, technologies and innovation of the Universidad del Valle, Colombia (CI 71368). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Introduction
The chili pepper belonging to the genus Capsicum of the Solanaceae family is among the eight most widely cultivated crops worldwide. In 2023, approximately 18.25 million hectares were cultivated, and a total production of 41.13 million tons was produced [1]. The high demand for chili peppers is due to their pungency, a characteristic unique to the genus caused by capsaicinoid compounds present in the placenta of the fruit [2]. Eleven species of Capsicum have been recorded in Colombia [3–5], five of which belong to the Andean clade. This group is distributed in the west-northwest of South America and Central America. The Andean clade is a distinct group from the other Capsicum species and differs from them in chemical, anatomical, and cytological characteristics [4,6,7]. For example, fruits of the Andean clade do not produce capsaicinoid compounds, lack giant mesocarp cells, and their karyotype number is 2n = 2x = 26. Despite their particularities, knowledge about their genetic diversity remains limited beyond the available systematic studies. In contrast, the domesticated species in Colombia belong to the annuum group. The most commonly cultivated species in Colombia are C. annuum L. (Cayenne variety), C. frutescens L. (Tabasco variety), and C. chinense Jacq. (Habanero variety). These varieties are cultivated in a wide range of climates throughout the country [8].
Despite its potential, hot pepper production in Colombia has not yet reached significant levels in the global context with an estimated annual production of approximately 100610 tons, the country ranks 32nd worldwide [1]. This limited participation could be explained by the narrow focus of studies conducted in the country. Although they have addressed the crop for agricultural and scientific purposes [9–12], they have focused on specific regions, and some do not include wild species. As a result, the diversity of chili peppers in Colombia is not well documented, representing a missed opportunity. This is especially relevant considering that Colombia includes two key centers of speciation of the Capsicum genus: the Andes and the Amazon [6]. Consequently, there is a valuable genetic resource that has not yet been comprehensively characterized, which limits its use in both agricultural research and development.
DNA markers have been widely used to analyze genetic diversity in groups of interest because they are not influenced by environmental factors and can be measured at any stage of an organism’s development [13]. Advances in sequencing technologies have enabled the use of a growing number of DNA markers, especially SNPs (single nucleotide polymorphisms), to cover a more extensive portion of the genome. This increased coverage provides more comprehensive information and enhanced utility [14,15].
Diversity Arrays Technology sequencing (DArTseq) platform [16] has established itself as an effective tool for analyzing plant genetic diversity. Its usefulness lies in the generation of a high density of markers, the absence of the need for prior sequence information, its broad genome coverage, and its ability to be transferred between species [17,18]. This technology produces two types of markers, dominant SilicoDArT markers, which indicate presence or absence, and codominant SNPs. Both have been successfully used to characterize genetic diversity in various plant species, such as rice [18,19], macadamia [20], bean [21], fava bean [22].
Worldwide, there are few studies evaluating the genetic diversity of chili pepper using Capsicum accessions from Colombia. In fact, many of these studies include limited or no representation of Colombian material [6,23–26]. When Colombian material is included, it typically comes from international germplasm banks that primarily conserve domesticated varieties, while wild or semi-domesticated accessions are rarely used. Given this situation, the need to conduct molecular evaluations that covers a representative part of the Capsicum genome becomes evident, as a basis for developing genetic improvement programs in Colombia aimed at strengthening production and increasing exports. This study is the first to apply the DArTseq platform to analyze Capsicum accessions from southwestern Colombia. It is also pioneering in the characterization of the genetic diversity of accessions belonging to the species of the Andean clade.
Materials and methods
Accessions sampling
Field trips were carried out in rural and urban areas of Valle del Cauca and Nariño departments to collect the studied species. Public markets, family gardens, and plant nurseries were visited to collect ripe fruits for seed extraction. To sample wild species, natural reserves and rural areas were visited. The people in charge of these places were asked about the origin of the material and, if it is known, the level of artificial selections to which the accessions were submitted. This verification process aimed to ensure that all collected samples were native and not introduced from other countries.
Planting material and crop maintenance
A minimum of three individuals per accession were sown and cultivated under controlled conditions in a greenhouse at the biological station of the Universidad del Valle with geographic coordinates: 3º 22’22.23” N y 76º 31’47.82”O. Once the seedlings developed five leaves, foliar tissue was harvested and stored in silica gel bags to prevent DNA degradation, following the protocol described by Chase & Hills [27]. One individual per accession was used for genotyping.
Samples identification
Capsicum accessions were identified through a combination of morphological traits including seed and flower color, annular constriction of calix, number of flowers per node [4] as well as DNA-HRM barcoding. The latter employed primers developed by Jeong et al. [28] to Capsicum species and subsequently validated for southwestern Colombian species [29].
DNA extraction and genotyping
Genomic DNA was extracted from leaf tissue using the CTAB protocol described by Doyle & Doyle [30], with modifications according to Stewart [31]. DNA concentration and purity were assessed using Nanodrop 2000 spectrophotometer (Thermo Scientific, USA). Once quality parameters were confirmed, samples were submitted to the Genetic Analysis Service for Agriculture (SAGA) at CIMMYT (México) where genotyping process was performed using DArTseq™ technology [16,32]. Five accessions corresponding to commercial cultivars were included as control.
Databases and data cleaning
This study examined seven species of Capsicum, including three wild Andean species (C. lycianthoides Bitter, C. rhomboideum (Dunal) Kuntze and C. dimorphum (Miers) Kuntze) and four domesticated (C. annuum, C. frutescens, C. baccatum var. pendulum (Willd.) Eshbaugh and C. pubescens Ruiz & Pav.). Due to significant morphological differences between Andean species and domesticated ones, there is a potential for bias in the molecular analysis. To address this, the molecular marker database was divided into two separate datasets, according to Capsicum species particularities.
The first dataset, referred to as the Total Database (BT), comprises all species collected in this study, both wild and domesticated. The second dataset, known as the Domesticated Database (BD), includes only domesticated species except C. pubescens, which was excluded due to its distinct morphological and molecular characteristics that make it easily identifiable [4]. Each dataset underwent independent data cleaning and genetic analysis.
Genotypic data were curated through five filters; all filters were made using DArTRverse package from R software. First, all monomorphic loci were filtered in the database. Then, loci with a reproducibility lower to 0.99 were filtered. For call rate filter, Due to the distinct genetic profile of Andean species compared to other Capsicum species analyzed in this study, some individuals from the Andean group exhibited missing data rate exceeding 10% when call rate filter of 0.89 was applied. These individuals were retained in the BT dataset, as understanding the relationship between Andean and domesticated groups were central objective of this study. However, for BD dataset a stricter call rate threshold of 95% was applied. The fourth filter eliminated secondaries loci, this consists in keeping only one locus in each DArT-seq fragment to reduce dependence between markers. For fifth filter, loci with MAF < 0.05 were filtered. Finally, an LD pruning was made for loci with a R2 > 0.2. Missing genotypes were imputed using the nearest-neighbor algorithm through gl.impute function of DArTRverse. The image in Supporting information 1 in S1 File summarizes the pipeline use in this study including the functions of DArTRverse.
Genetic diversity and population structure analysis
SNP marker matrices and silico DArT were analyzed using DartRverse library [33,34] in the R environment, version 4.4.2 [35].. Using the functions of this library, diversity indices like Ho, He, and population structure statistics like Wrights’s F were estimated. For diversity indices, Andean species were excluded because of their low sample size. To visualize genetic relationships among Capsicum accessions, UPGMA dendrograms based on Euclidean distances (SNP-DArT) and Jaccard distances (Silico-DArT) were constructed, in both cases a bootstrap node support with 1000 replicates was made. In addition, the SNP markers were used population structure analysis using STRUCTURE v.2.3.4 [36], with the aim of estimating the number of subpopulations (K) present in the data. Ten individual Markov Chain Monte Carlo (MCMC) simulations were used for each K-value from 3 to 8 for BD and from 2 to 10 for BT. In both simulations, there was a burn-in phase of 100000 iterations, followed by 100000 iterations. The optimal number of subpopulations (k) was determined following the methodology proposed by [37] and the estimated log probability of the data, LnP(D), as implemented by [36]. Kindship matrix (k-matrix) and its heatmap were made using DArtRverse.
Results
Number of accessions collected
A total of 69 accessions corresponding to seven Capsicum species were collected, as shown in Table 1 and Fig 1. The most represented species was C. annuum, with 38 accessions, followed by C. frutescens with 15. In the department of Valle del Cauca three wild Capsicum species belonging to the Andean clade were identified: C. dimorphum (one accession), C. rhomboideum (two accessions), and C. lycianthoides (three accessions). Of the total accessions, fifty-three were collected in the Valle del Cauca, and the remaining 16 in the department of Nariño. The species C. pubescens and C. baccatum were found exclusively in Nariño. The five commercial cultivars representing three species were included as controls: three samples of C. annuum var. annuum, one of C. pubescens, and one of C. baccatum.
Data filtering
A total of 129810 SNP-DArT markers and 330763 Silico-DArT markers were genotyped using DArT-seq technology in 69 accessions. After the filtering process, the number of SNP markers was reduced to 3681 for BT and 2821 for BD, while the Silico-DArT markers were reduced to 140207 for BT and 2501 for BD. Furthermore, a total of 3258 SNP-DArT markers could be mapped on the twelve Capsicum chromosomes (Supporting information 2 in S1 File), demonstrating that the genomic reduction of the DArTseq library resulted in a nearly equal number of markers for each chromosome. The proportion of missing data prior to imputation was 7.72% in BT dataset and 1.66% in BD dataset. The slightly higher proportion of missing data in BT is likely attributable to the greater evolutionary divergence among the included species, which may reduce the recovery of homologous DArT-seq loci across taxa.
Genetic diversity
SNP-DArT markers revealed a low level of observed heterozygosity in Capsicum accessions (Table 2). The heterozygosity ranges between 0.003 to 0.036, reaching a maximum of 0.187 in B6 (C. annuum accession). Similarly, expected heterozygosity was low, range between 0.003 to 0.040. There is a difference between two varieties of C. annuum, while C. annuum var. annuum showed the highest values as Ho as He, the wild variety C. annuum var. glabriusculum showed a low value. FIS indexes were variable, ranging from 0.007 to 0.330, suggesting an excess of homozygotes in Capsicum species. In the case of Andean accessions, the low sample size avoids inferring genetic diversity to species, but individuals showed a low Ho and He like other Capsicum species.
Population structure
The BT-based PCoA plots show a clear differentiation between Andean and domesticated accessions, both in the SNP analysis (Fig 2A) and in the Silico-DArT analysis (Fig 3A). The Andean group clustered separately of the rest of the accessions. Within the domesticated species, C. pubescens is the most separate group, while C. annuum and C. frutescens appear to be the closest species in this assessment. On the other hand, the BD-based PCoA plots (Fig 2B and 3B) show that excluding the Andean and C. pubescens species allows for a better understanding of the relationships between the accessions in the white-flower group. In this context, C. baccatum is positioned as the most distant species while, C. annuum and C. frutescens accessions were grouped as closest species but with no distinction among the varieties inside each species. FST pairwise index (Supporting information 3 in S1 File) reflects a similar structure for the Capsicum accessions with Andean accessions have the highest values of genetic differentiation against domesticated species, while C. annuum has the lowest value against C. frutescens.
Can: C. annuum, Cbp: C. baccatum var. pendulum, Cdi: C. dimorphum, Cly: C. lycianthoides, Crh: C. rhomboideum, Cfr: C. frutescens and Cpu: C. pubescens.
Caa: C. annuum var. annuum, Cag: C. annuum var. glabriusculum, Cbp: C. baccatum var. pendulum, Cdi: C. dimorphum, Cly: C. lycianthoides, Crh: C. rhomboideum, Cft: C. frutescens (tabasco variety), Cfw: C. frutescens (Wild variety), Cfo: C. frutescens (other varieties) and Cpu: C. pubescens. Bootstrap values greater than 70 are visible in each node.
STRUCTURE analysis suggested that the number of populations in the BT database is K = 3 (Supporting information 4 in S1 File). These three groups are Andean group and C. pubescens, C. baccatum and finally, C. annuum and C. frutescens. The assignment of accessions to the groups is 100% for all the cases. The relationship between Andean accessions, C. pubescens and the rest of the Capsicum species representing in this plot, agrees with the genetic divergence registered in PCoA plot. In fact, C. pubescens is so different to the rest of domesticated species that are clustered together with the Andean group. On the other hand, both the ΔK statistic and the plateau of the log-likelihood suggested K = 5 for BD as the optimal number of clusters, the STRUCTURE barplot revealed only three biologically meaningful genetic groups corresponding to C. annuum, C. frutescens, and C. baccatum. The remaining inferred clusters contributed negligibly to individual membership coefficients, indicating that additional clusters did not represent distinct genetic entities. This interpretation is further supported by the PCoA, UPGMA dendrogram, and kinship matrix, all of which consistently recovered the same three major genetic groups.
The UPGMA dendrograms constructed using Euclidean’s distance (Fig 3A) and Jaccard’s distance (Fig 4A) for BT show a high degree of concordance the PCoA plots. In both graphs, the Andean Capsicum accessions are grouped together and exhibit considerable distances from the domesticated species. Furthermore, accessions of C. lycianthoides and C. rhomboideum appear more closely related to each other than to C. dimorphum accession, a relationship also reflected in the PCoA results as SNP for Silico-DArT markers. Similarly, C. pubescens stands apart from the other domesticated species. Its clusters with the Andean group in the SNP-based dendrogram, while in the Silico-DArT dendrogram, its groups with the domesticated varieties. Regarding the white-flower group, both dendrograms display a consistent structure: C. baccatum forms the outer group, and C. annuum is separated from C. frutescens.
Caa: C. annuum var. annuum, Cag: C. annuum var. glabriusculum, Cbp: C. baccatum var. pendulum, Cdi: C. dimorphum, Cly: C. lycianthoides, Crh: C. rhomboideum, Cft: C. frutescens (tabasco variety), Cfw: C. frutescens (Wild variety), Cfo: C. frutescens (other varieties) and Cpu: C. pubescens. Bootstrap values greater than 70 are visible in each node.
For BD, Euclidean’s distance and Jaccard’s distance agree to separate each domesticated species into a different cluster, with C. baccatum as outer group and C. annuum closer to C. frutescens as BT dendrograms. However, SNP and Silico-DArT markers reflect different clustering respect to varieties in C. annuum and C. frutescens. While SNP markers were unable to discriminate against varieties of both species with low values of boostrap in dendrogram. Silico-DArT was able to separate C. annuum into three well supported clusters, one of them corresponding to wild variety C. annuum var. glabrisuculum (Fig 4B). In the same way, C. frutescens wild variety was separated from the other accessions of this species with Silico-DArT.
Finally, the genomic kinship matrices for the BT(A) and BD(B) datasets based on SNP markers (Fig 5) revealed the same patterns of genetic differentiation that PCoA, STRUCTURE and distances dendrogram, with all accessions assigned to their respective species, showing the genetic divergence between domesticated Capsicum and Andean. B6 accession, despite the morphological identification assigned to C. annuum, showed different relationships depending on the analysis. For PCoA (SNP and Silico-DArT), STRUCTURE and Jaccard’s distances, this accession is group together C. baccatum, while Euclidean’s distances and K-matrix clustering as an outer group of the C. annuum and C. frutescens group. In both scenarios B6 is not cluster inside C. annuum, additionally, B6 was the accessions with the highest Ho value. Therefore, more analyses are necessary to solve its relationship in Capsicum.
Hierarchical clustering was applied to group accessions according to their genomic relatedness. Colored side bars represent species assignment. Can: C. annuum, Cba: C. baccatum var. pendulum, Cdi: C. dimorphum, Cly: C. lycianthoides, Crh: C. rhomboideum, Cfr: C. frutescens and Cpu: C. pubescens.
Discussion
Patterns of genetic diversity and intraspecific differentiation
In this study, a low level of observed heterozygosity (HO) was observed, a recurring pattern in other Capsicum studies. For example, Ibiza et al. [38] reported a HO value of 0.10 for C. baccatum and 0.05 for annuum complex and C. pubescens using AFLP markers. This pattern was also observed in studies using a large number of markers, for example, studies using GBS, such us [24,39,40] reported mean HO of 0.023, 0.031 and 0.1, respectively. Notably, the last two studies reported a higher Ho in C. baccatum than in annuum complex species. Colonna et al. [26] is one of the few studies that found Ho higher than 0.3, which reported a Ho of 0.49 for a wild Capsicum species, C. chacoense, and found a lower value for domesticated species (C. annuum and C. chinense). For Colombian studies the pattern is similar, Pardey-Rodríguez and Dávila [11] and Viáfara et al. [41] reported a Ho of 0.1 and 0 for Capsicum accessions of annuum complex. The low Ho may be explained by the high level of autogamy and low level of autoincompatibility of the species of Capsicum genus [42–45], that tends to increase the homozygosity in the populations [46]. The high FIS values found in this study show an excess of homozygotes in the accessions.
In this study, interspecific variation represented the dominant genetic signal and was therefore primarily recovered by the PCoA, STRUCTURE, and K-matrix analyses. Differences among varieties (intraspecific) represent a subtle signal, and it was recovered only by UPGMA/Jaccard analysis in this case. C. annuum and C. frutescens wild varieties are clearly distinguished from their domesticated counterparts using morphological characters (data not shown). The concordance between morphological differentiation and clustering of the UPGMA/Jaccard analysis suggests that these morphotypes probably reflect a real genetic structure though at a lower magnitude than the species differentiation. This intraspecific structure was also observed in other domesticated Capsicum species [47,48].
Geographical structure and the role of public markets in maintaining Capsicum genetic diversity
This study shows an absence of geographical structure among accessions beyond that expected from species ecological preferences. C. baccatum and C. pubescens were found only in the Nariño department but this is explained by the fact that in this department the Capsicum cultivation occurs in the highlands (over 2000 m.a.s.l.) with low temperatures, these two species grow well in these conditions but C. annuum and C. frutescens are species more commonly cultivated in the lowlands with warmer temperatures, like those found in Valle del Cauca. Therefore, this geographical division is explained by the availability of suitable cultivation areas instead of an underlying genetic structure associated with geography.
The absence of geographical clustering suggests that in domesticated Capsicum species factors such as seed exchange, farmer’s selection and fruit trade could promote the dispersal of genetic material among multiple localities. For example, local farmers from different localities may select the same desirable traits of their plants, also, they could share seeds with their neighbors, these activities obscure detecting geographical structure, but may work to avoid local extinctions. This phenomenon has also been reported in other studies like in C. annuum var. glabriusculum in Mexico [49] or in domesticated Capsicum species [50].
The genetic diversity of Capsicum accessions is not only reflected in the results shown in this study but also in the number of collected accessions, the two departments sampled in this study represent less than 5% of the Colombian territory and it was found 69 Capsicum accessions. Many of these were collected from public markets instead of germplasm banks. Materials from different municipalities converge in these markets and they work as meeting point of Capsicum genetic resource. Interviews with farmers in public markets revealed that the fruits sold came from their own home gardens or farms located in the same or nearby veredas (rural administrative divisions), where they maintain a few Capsicum plants. Consequently, a public market acts as a meeting point for the genetic diversity of a microregion. Additionally, the presence of Capsicum accessions in public markets suggests that this resource is being used by the community and Capsicum fruits have economic value in a local context. Studies in Latin America, like Guatemala [51], Ecuador and Peru [52] and México [53,54] corroborate the importance of public markets in Capsicum genetic resources. Though they do not substitute germplasm banks could complement the strategies of prospection and conservation in situ of Capsicum.
Genomic differentiation of the Andean Capsicum group
Andean group represents the ancestral group from the other Capsicum species; they have marked morphological and cytogenetic differences within which capsaicinoid absent and chromosomal number 2n = 2x = 26 are the most notorious [4]. Hence, it is coherent that genomic analysis reflects these differences, for example, PCoA, STRUCTURE analysis and Kinship matrix identified Andean accessions as a marked different cluster. Since this study is the first to includes Andean accessions in a genomic analysis of Capsicum, there is no studies to compare with, but, the genomic relationship within Andean group found in this study are same as the reported by phylogenetic analysis, with Andean accessions separated from the rest of Capsicum species and with C. rhomboideum more related with C. lycianthoides than with C. dimorphum [7]. Ho values for these six accessions didn’t surpass 1%, suggesting a high homozygotes level in these individuals, however further genetic studies into wild species of Capsicum are necessary to confirm the hypothesis of low level of heterozygosity in Capsicum Andean species.
In the STRUCTURE analysis and the UPGMA dendrogram with both types of markers, B6 was an accession that did not have a membership probability of 100%, indicating a relationship with C. annuum and C. baccatum. Morphologically, B6 has a white corolla without yellow spots and a calyx without conspicuous teeth, which are the main differences between C. annuum and C. baccatum, so a misidentification is unlikely. Furthermore, this accession exhibited the highest level of HO in this study (0.187), a value forty-four times higher than the median and rare in other Colombian Capsicum studies, as previously mentioned. This suggests that B6 may represent a putative hybrid individual. However, additional analyses are required to confirm this hypothesis. This event could be favored by the traditional cultivation system, in which plants are kept by local farmers without physical isolation or pollination control [45]. To determine its agronomic potential, further studies on this accession are necessary.
SNP-DArT vs Silico-DArT markers
In this study both types of markers used in genomic characterization showed similar results, as PCoA and as dendrograms could discriminate Capsicum accessions for species. Additionally, both types of markers recognized that Andean accessions have a big genetic divergence respect the other Capsicum accessions and C. pubescens is genetically different from the rest of domesticated species. Even B6 accession, was identified as problematic sample with both types of markers. This consistency in results obtained of these two markers have been reported by other studies that use DArT-seq platform [20,55].
The Silico-DArT UPGMA dendrogram resolved genetic subdivisions within C. annuum and C. frutescens that were not recovered by the SNP-based analyses. Because different marker systems and genetic distance measures were used, it is not possible to attribute this increased resolution exclusively to the marker type [56,57]. Nevertheless, the results suggest that fine-scale genetic structure within domesticated species exists but is likely masked by the much stronger interspecific differentiation in multivariate and model-based analyses.
Finally, DArT-seq technology allowed us to extract a good number of markers (SNP and Silico) in the Capsicum species evaluated in this study. Despite the great genetic differences between Andean group and domesticated species, 3681 SNP could be used to characterize the genetic diversity of these accessions. This suggested that DArT markers could be a good choice to execute genomic studies of various species within a genus. With respect to Silico-DArT, it is clear that the number of markers obtained is bigger than SNP and many of the analyses showed the same results than the SNP markers, however, do not allow the calculation of observed heterozygosity, hence its dominant characteristic and their great abundance make them more appropriate to genetic mapping, phenotypic association (GWAS) and plant identification.
Limitations and perspectives
The region sampled in this study represent approximately 5% of Colombia’s geographic area. Therefore, the results of this study only represent a part of Capsicum genetic resources in the country. Despite this, the accessions showed a broad genetic diversity and multiples genetic groups. Though morphological diversity was not evaluated in this study, the accessions studied also display a broad morphological diversity. Hence, it is reasonable to think that expanding the sampling areas to other regions of the country would probably increase the genetic diversity and the number of genetic groups. Since most studies in Colombia have been focused on Amazonian and southwestern regions, studies focused on the Caribbean and Central region are necessary to adequately represent national diversity. In the same way, the results of this study justify the importance of amply national collections of Capsicum to conserve not only the wild species but also the diversity inside C. annuum and C. frutescens.
This study is the first to include Andean Capsicum species in a genomic characterization. However, the low and unbalanced sample size limits the ability to make important inferences. Unlike domesticated species, wild species are not abundant and finding individuals with flowers and/or fruits for an accurate taxonomic identification could be difficult. Therefore, this study presents an exploratory analysis of these species, a larger sample size is needed to confirm whether these groups also present a low level of Ho as it was observed in the domesticated species. Nevertheless, the differences in morphological and cytogenetic features reported by other studies [4,58] were also observed in this study using genomic analyses, the Andean accessions evaluated had a marked genetic divergence from the other accessions, even affecting the number of markers retained in the BT and BD databases, since Andean accessions shared fewer markers with domesticated accessions than domesticated accessions shared among themselves.
Conclusions
This study reported the rich genetic diversity of Capsicum species distributed in Colombian southwest including some accessions that have been adapted to urban environments. Despite the unbalanced sample size, the dataset includes representatives of seven Capsicum species, including rarely studied Andean taxa. The use of DArT-seq markers reflects the genetic differentiation between Andean and domesticated Capsicum accessions. Moreover, they demonstrated that both groups have low levels of observed heterozygosity and a high level of inbreeding. However, there are groups genetically diverse and structured, suggesting a promising potential genetic resource for future breeding programs. Therefore, more studies with greater geographical coverage, bigger sample size and including other Andean Capsicum species are needed. In the same way, wild varieties inside C. annuum and C. frutescens could be discriminated. Overall, the DArT-seq platform proved to be a valuable tool to obtain a high number of markers in Capsicum species independently of its level of breeding and phylogenetic relationship.
Supporting information
S1 File.
S1 Figure: Pipeline used for Quality control and genomic analyses. S2 Table: Chromosomal location of DArT-SNP markers. S3 Figure: FST index for Capsicum species. S4 Figure: STRUCTURE model selection plots (BT) showing mean LnP(K) and ΔK values used to infer the most likely number of genetic clusters. S5 Figure: STRUCTURE model selection plots (BD) showing mean LnP(K) and ΔK values used to infer the most likely number of genetic clusters.
https://doi.org/10.1371/journal.pone.0359207.s001
(RAR)
Acknowledgments
We are very grateful to Jhon Jairo Calderón for his support in collecting samples in the department of Nariño. To Leidy Laura Arias, Jorge Mario Ruiz, Mary Belcy Bonilla, Héctor Cifuentes, Mauricio Peñuela and José Cándelo for their guidance and support in collecting samples in the department of Valle del Cauca.
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