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ARTICLE • Crop Breed. Appl. Biotechnol. 26 (1) • 2026 • https://doi.org/10.1590/1984-70332026v26n1a14 linkcopy

Open-access Cytogenetics of selected Solanum L. species within a phylogenetic framework

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Abstract

We characterized 12 Solanum species using CMA/DAPI banding and/or genome size estimation (1C value) within a phylogenetic perspective. Here, we reported new Constitutive Heterochromatic (CH) data for S. andreanum, S. peruvianum and S. paludosum and new 1C value for S. corneliomulleri and S. andreanum. CH ranged from two (S. viarum) to 42 bands (S. paludosum). Potato species exhibited a higher number of CH blocks, whereas Leptostemonum species generally had fewer blocks, except for S. paludosum. However, no relationship between heterochromatin and evolutive diversification within the genus could be inferred. Mean 1C value varied from 1.0 pg in S. melongena (diploid) to 1.80 pg in S. laciniatum (octaploid), with moderate correlation (r = 0.69) with the ploidy level of the species. Our data contribute to understanding genetic and cytogenetic diversification within Solanum in a phylogenetic context and are relevant to species characterization, supporting future genetic breeding programs of the genus.

Keywords:
CMA/DAPI banding; flow cytometry; cytogenetic diversity; tomato; karyotype evolution

INTRODUCTION

Solanum L. (Solanaceae Juss.), one of the largest and most diverse genera of flowering plant, comprises over 1,500 species distributed worldwide, with its center of origin and greatest genetic diversity located in South America (https://solanaceaesource.myspecies.info/). The genus includes 24 economically important crops, such as potato (S. tuberosum L.) and tomato (S. lycopersicum L.), which are among the most worldwide cultivated vegetables (Kawicha et al. 2023, Hilgenhof et al. 2023). Furthermore, the remarkable diversity in morphophysiological and reproductive traits, as well as ecological adaptations, makes Solanum an important genetic resource and an attractive model for scientific research.

These species, rich in vitamins, minerals, proteins and carbohydrates, are well known for their nutritional, medicinal and ecological importance, which makes them valuable resources for global food security and social stability (Balkrishna et al. 2022). Additionally, these species represent potential sources of alleles conferring tolerance to abiotic and biotics stresses. For instance, S. pimpinellifolium L. carries favorable alleles associated with adaptation to water and salt stress (Martínez-Cuenca et al. 2020). In S. tuberosum breeding programs, wild relatives have been employed, such as S. demissum Lindl. to improve pest resistance (Díaz-García et al. 2024), S. acaule Bitter to enhance tolerance to cold stress (Achakkagari et al. 2025), and S. bulbocastanum Dunal to improve resistance to drought stress and late blight disease (Dénes et al. 2024).

From a phylogenetic and evolutive perspective, Solanum is classified into three strongly supported main groups, which are denominated Thelopodium, Grade I and Clade II, with most species belonging to the Clade II (Hilgenhof et al. 2023). These groups are further divided into 12 major and 49 minor clades. The most economically important species, S. lycopersicum and S. tuberosum, are placed within Grade I, in the major Potato clade, but in two different minor clades: Tomato and Petota, respectively. Despite their high agricultural and socioeconomic relevance, several species from different groups and clades remain poorly investigated across various fields, including cytogenetics.

Solanum belongs to the x = 12 clade, a group characterized by a putative cytological synapomorphy of having chromosome numbers based on 12 pairs. This clade was first recognized by Olmstead and Palmer (1992), and the informal name “x = 12 clade” was later proposed by Olmstead and Sweere (1994). Tetraploid (2n = 4x = 48), hexaploid (2n = 6x = 72) and octaploid (2n = 8x = 96) species have also been reported (Chiarini et al. 2018). Cytogenetic analyses provide karyotypic characterization that contributes to understanding the diversity, structure and organization of plant genomes, with significant implications for taxonomy, phylogeny, evolution and germplasm conservation programs (Martins et al. 2018, Almeida et al. 2022, Mesquita et al. 2025). Cytogenetic techniques, such as fluorochrome banding with Chromomycin A3 (CMA) and 4´-6-diamidino-2-phenylindole (DAPI), are approaches for karyotyping, enabling chromosome number identification, morphology characterization, asymmetry assessment, and the evaluation of constitutive heterochromatin (CH) at inter- and intraspecific levels (Deanna et al. 2022, Mesquita et al. 2025).

In addition to cytogenetic analyses, the nuclear genome size (1C value), which is estimated by flow cytometry, represents another genomic parameter relevant to understanding plant diversity and evolution. It is also used to assess inter- and intraspecific variation among populations and species (Macková et al. 2017, Braz et al. 2024). The 1C value enables the inference of ploidy levels and facilitates the detection of natural or induced polyploids (Walter et al. 2025) and hybrids (Macková et al. 2017). Furthermore, genome size data provides essential qualitative and quantitative insights into the genetic diversity, organization, and cytogenetic stability of species (Urfus et al. 2025, Zhang et al. 2025). Consequently, this information serves as a basis for developing more efficient strategies for plant breeding as well as for the preservation, management, and restoration of native flora (Urfus et al. 2025, Zhang et al. 2025).

In Solanum, data on the diversity of CMA banding patterns and 1C value are currently available for less than 10% of the species, mostly belonging to the Potato and Leptostemonum clades (Brasileiro-Vidal et al. 2009, Melo et al. 2011, Acosta et al. 2012, Moyetta et al. 2016, Mesquita et al. 2025, https://cvalues.science.kew.org/). Consequently, the full extent of the karyotype variability of Solanum remains largely unknown. To expand this knowledge, we performed a detailed karyotype characterization of 12 wild and domesticated species with different ploidy levels, representing different phylogenetic groups, along with 1C values for three of them, complementing our findings with literature data. Here, we discuss the heterochromatin banding pattern and 1C value among Solanum species in a phylogenetic framework. Our results contribute to species characterization and delimitation, providing valuable insights for breeding programs aimed at unlocking unexplored genetic diversity in Solanum.

MATERIAL AND METHODS

Plant materials

Twelve Solanum species belonging to different phylogenetic groups (Grade I and Clade II), major clades (Potato, VANAns, Leptostemonum and Geminata) and minor clades (Tomato, Petota, Acanthophora, Erythrotrichum, Eastern Hemisphere Spiny and Geminata) were analyzed. Seeds were obtained from the Germplasm Resource Information Network (GRIN Global), from the National Germplasm Resources Laboratory (United States) and from Empresa Brasileira de Pesquisa Agropecuária (Embrapa) Hortaliças (Brasília, Distrito Federal, Brazil). Seeds of S. andreanum and S. macrocarpon were multiplied at the Instituto Agronômico de Pernambuco (IPA, Pernambuco, Recife, Brazil), and S. lycopersicum seeds were obtained from commercial sources. A list of the species studied, including their phylogenetic groups, voucher numbers and provenance, is provided in Table 1.

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Table 1
Chromosome number, morphometric parameters, CMA+ bands, and mean 1C value (pg) in twelve Solanum species, distributed across two main groups, four major clades and seven minor clades, following the phylogeny of Hilgenhof et al. (2023)

Chromosome preparation

Solanum seeds were placed in Petri dishes lined with filter paper and moistened with distilled water. After over five days, root tips (~1cm in length) from germinated seeds were collected and pretreated with 0.002 M 8-hydroxyquinoline for 4.5 h at 18 °C, fixed in Carnoy’s solution (methanol: acetic acid, 3:1 v/v), and stored at -20 °C until use. Root tips were macerated in an enzymatic mixture containing 2% Cellulase ‘Ozonuka R-10’ (Serva) and 20% Pectinase (v/v) (Sigma Aldrich) for 4.5 h at 37 °C. Slides were prepared following de Carvalho and Saraiva (1993) protocol, with minor modifications: slides were immersed in 45% acetic acid for 15 s and then air-dried at room temperature. The best slides were selected in 2 µg mL-1 DAPI: glycerol (1:3, v/v), de-stained in ethanol: acetic acid (3:1, v/v) for 30 min followed by ethanol immersion for 30 min, air dried at room temperature and aged for three days.

CMA/DAPI fluorochrome staining and microscopy

Fluorochrome staining was performed following Schweizer and Ambros (1994), with minor modifications. Slides were stained with 10 µL of 0.5 mg mL-1 CMA for 1.5 h, counterstained with 10 μl of 2 mg mL-1 DAPI for 1 h, mounted in glycerol/McIlvaine buffer (pH 7.0, 1:1, v/v), and stored at 4 °C for three days. The best metaphases were photographed using a DF7000GT digital camera coupled to a Leica DM4B microscope (Universidade Federal do Piauí). Images were optimized for brightness and contrast using Adobe Photoshop CS3 and Adobe Photoshop 2022.

Chromosome measurements and idiogram construction

Three to five best metaphases from each species were used for chromosome measurements, performed using Drawid v0.26 (Kirov et al. 2017). The following morphometric parameters were determined: range of chromosome size (RCS), karyotypic formula (KF), chromosome medium length (CML), and haploid karyotype length (HKL), according to Guerra (1988). Centromere position was classified according to Levan et al. 1964 (Table 1). Idiograms were constructed using Adobe Photoshop CS3 and were plotted onto the phylogenetic tree proposed by Hilgenhof et al. (2023).

Nuclear 1C value measurement by flow cytometry

The nuclear 1C values of S. andreanum, S. peruvianum and S. corneliomulleri were determined by flow cytometry using leaf nuclei suspensions prepared according to Praça-Fontes et al. (2011) (Figure S1). Solanum lycopersicum ‘Stupické’ (2C = 2.00 pg) was used as an internal reference. This species has a well-established and stable genome size, with highly reproducible 1C values reported across independent studies, which facilitates inter-study comparability. Moreover, S. lycopersicum presents low interference from secondary metabolites under the extraction protocol used, resulting in well-defined G₀/G₁ peaks and low coefficients of variation. Each species was represented by at least four plants, with three replicates per plant, and suspensions containing more than 10,000 nuclei.

The relationship between ploidy level (x) and mean nuclear DNA content (1C value) in nine Solanum species (Table 1) was evaluated using simple linear regression, with the 1C value as the dependent variable and ploidy level as the independent variable. Genome size data (1C values) obtained by flow cytometry for S. laciniatum, S. pennellii, S. pimpinellifolium, S. viarum, S. paludosum, S. melongena, S. macrocarpon and S. pseudocapsicum were retrieved from the Plant C-Values Database (https://cvalues.science.kew.org/). The strength and direction of the association were quantified using Pearson’s correlation coefficient (r), and the proportion of explained variance was estimated by the coefficient of determination (R²). The statistical significance of the relationship was assessed using the associated p-value, adopting a significance level of 5%. Model assumptions were evaluated prior to interpretation. Homoscedasticity was assessed by visual inspection of residuals versus fitted values and formally tested using the Breusch-Pagan test, which indicated no significant deviation from constant variance (p ≤ 0.05). Normality of residuals was evaluated using Q-Q plots, showing no strong departures from normality. A scatterplot was generated to visualize the relationship between ploidy level and genome size, including the fitted regression line and 95% confidence intervals. All statistical analyses were performed in R version 4.2 (R Core Team 2022).

RESULTS AND DISCUSSION

The Solanum species examined exhibited chromosome numbers of 2n = 24, 48, and the dysploid 92 (Table 1, Figure 1a). Most species predominantly have metacentric and submetacentric chromosomes, with the most common karyotype formula being 12M (metacentric). Solanum pseudocapsicum, S. paludosum and S. pimpinellifolium possessed at least one pair of subtelocentric chromosomes (11SM + 1ST). Solanum species generally exhibited small to medium-sized chromosomes (Chiarini et al. 2018), ranging from 1.14 μm in S. laciniatum (octaploid) to 6.81 μm in S. paludosum (diploid), with haploid karyotype lengths varying from 25.04 μm in S. macrocarpon to 49.58 μm in S. paludosum. Detailed chromosome morphometric data for the analyzed species are presented in Table 1.

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Figure 1
CMA/DAPI banding in metaphase chromosomes of different Solanum species belonging to Grade I. The chromosomes are pseudocolored in grey (DAPI, a-f), while blocks of constitutive heterochromatin are stained yellow (CMA, a’-f’). The merged images are presented in the third column (a’’-f’’). (a-a’’) S. laciniatum, (b-b’’) S. pennellii, (c-c’’) S. peruvianum, (d-d’’) S. lycopersicum, (e-e’’) S. pimpinellifolium, (f-f’’) S. andreanum. Bar = 10 μm.

Due to recent advances in genomics over the last decades, karyotyping and genome size have become increasingly fundamental steps in biological research, particularly within the field of cytogenomics. However, few studies have addressed the distribution patterns of CH within Solanum (Brasileiro-Vidal et al. 2009, Rego et al. 2009, Melo et al. 2011, Acosta et al. 2012, Moyetta et al. 2016, Mesquita et al. 2025). Here, we describe the CH distribution patterns of 12 Solanum species, providing new data for S. andreanum, S. peruvianum and S. paludosum (Table 1, Figures 1 and 2). Each species exhibited a unique heterochromatic banding profile, enabling specific cytogenetic characterization of these wild and cultivated genetic resources. To facilitate the comparative interpretation of heterochromatin distribution across Solanum, idiograms were constructed for each species and plotted onto a recent phylogenetic tree of the genus (Figure 3).

In our fluorochrome-based banding analysis, we observed notable variation in the number, location, size and intensity of heterochromatic bands among analyzed species (Table 1, Figures 1 and 2). Two patterns of CH distribution were identified: i) strongly labeled CMA++/DAPI- terminal bands, related to the nucleolar organizer region (NOR); and ii) small terminal and proximal CMA+/ DAPI- or CMA+/ DAPI0 bands not associated with the NOR. All species exhibited at least one pair of CMA++/DAPI- bands (NOR) located in the terminal region of a chromosome pair, as previously reported by Chiarini et al. (2018). In S. viarum (Clade II, Leptostemonum, Acanthophora), only one CMA++/DAPI- pair was detected, which was heteromorphic in size, with one chromosome having distended NOR and their corresponding block not distended (Figure 2a-a”). Additional CMA+ bands were mainly located in terminal and proximal regions of Solanum chromosomes. For example, the wild potato S. andreanum (Grade I, Potato, Petota) presented 12 large CH pairs preferentially distributed in proximal chromosomal regions, including six bands located in terminal/subterminal regions. One chromosome pair exhibited two CH bands, being one terminal (NOR-related) and one proximal band on the same chromosome (Figure 1f-f’’, Figure 3).

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Figure 2
CMA/DAPI banding in metaphase chromosomes of Solanum species belonging to Clade II. The chromosomes are pseudocolored in grey (DAPI, a-e), while blocks of constitutive heterochromatin are stained in yellow (CMA, a’-e’). The merged images are presented in the third column (a’’-e’’). (a-a’’) Solanum viarum, (b-b’’) S. paludosum, (c-c’’) S. melongena, (d-d’’) S. macrocarpon, and (e-e’’) S. pseudocapsicum. Bar = 10 μm.

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Figure 3
Idiograms showing the number, size and position of heterochromatic CMA+ bands (yellow blocks) and/or mean 1C value (pg) of twelve Solanum species plotted in a phylogenetic tree based on Hilgenhof (2023). Chromosomes are traditionally ordered from the longest to the shortest. In S. viarum, the heteromorphic chromosome pair is underlined. EHS = Eastern Hemisphere Spiny.

Solanum laciniatum (Grade I, Archaesolanum), despite having the highest chromosome number among the analyzed species, exhibited one of the lowest chromosome numbers of CMA+ bands (two band pairs, Figure 1 a-a”), corroborating the findings of Melo et al. (2011). In contrast, S. peruvianum (Grade I, Potato, Tomato) displayed the highest number of bands (19 pairs), distributed across all chromosomes, mainly in the terminal regions (Figure 1c-c’’).

In general, we observed a similar number of CMA+ bands among species within the same clade. For example, in the Potato (minor clade Tomato) the mean number of CH blocks was 13-14 CMA+ pairs (Figures 1 and 3). Similar data were previously reported for eight of the 17 Tomato clade species, which also exhibited a high number of CMA+ bands, with a mean of 19 CH pairs among the analyzed species (Brasileiro-Vidal et al. 2009). Conversely, species belonging to the Leptostemonum clade displayed fewer CH blocks, averaging between one and four CMA+ block pairs (present work, Rego et al. 2009, Melo et al. 2011, Mesquita et al. 2025). An exception was observed in the minor clade Erythrotrichum, where S. paludosum displayed a discrepant CH pattern, with 21 terminal CMA+ band pairs (Figure 2 b-b’’). Cytogenetically, this species shares a more similar pattern with S. pseudocapsicum (Geminata, 18 pairs, Figure 2 e-e”) than its closely related species (Melo et al. 2011).

In Solanum, heterochromatin (a repeatome fraction) is highly dynamic, independent, and not homogeneous across the genus (Chiarini et al. 2018). Despite this heterochromatin heterogeneity, no clear evolutive trends associated with clade diversification could be inferred, probably due to the limited number of samples analyzed in this work. Broader cytogenetic sampling, including other species from additional major and minor clades, will be essential to confirm or refine these patterns.

The amplification or deletion of different classes of repetitive DNA that constitute heterochromatin likely represents one of the main mechanisms underlying speciation and genomic differentiation within Solanum. For example, Gaiero et al. (2019) reported that the most abundant repeats in the genomes of 12 wild and cultivated species belonging to the Tomato and Petota minor clades are long terminal repeat (LRT) retrotransposons, particularly the Ty3/ Gypsy elements, which are preferentially located in the heterochromatin, being more abundant in tomatoes. Conversely, the satellite DNA CL14 was found to be exclusive to the Tomato species and absent in wild potatoes. Further investigation into the specific repetitive DNA families that make up heterochromatin in Solanum species, such as transposable elements and satellite DNAs, will be essential for elucidating the structural genomic divergence and evolutive dynamics of the genus. Such analyses will clarify how these repetitive sequences contribute to the organization and evolution of Solanum.

A moderate and statistically significant positive linear relationship was detected between ploidy level (x) and mean nuclear DNA content (1C value), as evidenced by both Pearson’s correlation (r = 0.69, p = 0.040) and simple linear regression (R² = 0.48; Figure 4). These results indicate that increases in ploidy level tend to be associated with increases in genome size among Solanum species, although this pattern should be interpreted with caution given the limited number of species analyzed. This pattern is consistent with reports for other plant taxa, such as Psidium guajava L. (1C = 0.47 ± 0.01 pg; 2n = 2x = 22) and P. cattleyanum Sabine (1C = 1.78 ± 0.08 pg; 2n = 6x = 66) (Tuler et al. 2019), as well as Allium dentiferum Webb & Berthel. (1C = 47.80 ± 0.60 pg; 2n = 4x = 32) and A. dentiferum (1C = 57.30 ± 1.10 pg; 2n = 5x = 40) (Kobrlová et al. 2024).

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Figure 4
Relationship between ploidy level (x) and mean nuclear DNA content (1C value) in Solanum species. Points represent species mean values. The solid line indicates the fitted linear regression, and the shaded area corresponds to the 95% confidence interval.

Although a moderate and significant positive correlation between ploidy level and mean 1C value was detected, the relationship is not strictly proportional across Solanum species. Notably, S. andreanum (4x) exhibits 1C values comparable to or even lower than those of some diploid species, and S. laciniatum (8x) does not show a genome size proportional to its high ploidy level (Table 1). These patterns are consistent with genome downsizing and diploidization processes commonly observed after polyploidization, involving DNA sequence loss, particularly of repetitive elements, chromosomal rearrangements, and differential retention of duplicated genomic regions. Such processes can decouple genome size from chromosome set number, especially in older or stabilized polyploids (Wang et al. 2021, Heslop-Harrison et al. 2023). Therefore, while polyploidy contributes to an overall increase in genome size at a broader evolutionary scale, post-polyploid genomic restructuring plays a key role in shaping the observed variation in nuclear DNA content among Solanum species.

Despite its importance and broad applications, most cytogenetic and genetic studies remain restricted to economically important Solanum species and their close relatives, even when employing classical approaches, such as CMA/DAPI banding and 1C value estimation. Recent advances in next generation cytomolecular techniques, such as Fluorescent in situ Hybridization (FISH) using single-copy oligonucleotide probes, have been applied, but still in a limited number of species (Braz et al. 2018). Similarly, genome sequencing and synteny comparisons are restricted to a few representatives, mainly within the Potato clade (Tang et al. 2022, Benoit et al. 2025, https://www.plabipd.de/timeline_view.ep). This limitation coverage constrains our understanding of the cytogenetic and genomic diversity of the genus, hindering the identification of evolutionary patterns and the exploration of under-investigated genetic resources.

Understanding the diversity of heterochromatin and genome size is essential for elucidating genome structure and organization in plants. Here, we provide unpublished and reviewed genomic Solanum data, expanding the current cytogenetic and genome size knowledge of the genus, as well as a detailed characterization of CH distribution across species’ karyotypes. These findings open new perspectives for future cytomolecular studies and offer new insights into the cytogenetic diversity of wild and cultivated Solanum within a phylogenetic context. Additional cytomolecular and genomic investigations are needed to further elucidate karyotype organization and evolutionary trends within the genus.

ACKNOWLEDGEMENTS

We thank Embrapa Hortaliças and Grin Global for supplying seeds. We are also grateful to the Brazilian agencies CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico), and FAPEPI (Fundação de Amparo à Pesquisa do Estado do Piauí) for providing scholarships. This work was supported by FAPEMA (Fundação de Amparo à Pesquisa do Estado do Maranhão) under process number APP-12290/22.

Data Availability

The datasets generated and/or analyzed during the current research are available from the corresponding author upon reasonable request.

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Publication Dates

  • Publication in this collection
    23 Mar 2026
  • Date of issue
    2026

History

  • Received
    11 Nov 2025
  • Accepted
    02 Feb 2026
  • Published
    12 Feb 2026
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