Keywords:

Chiltepín

RAPD

Diversidad genética

Descriptores morfológicos

Morphological and genetic variability of chili pepper (Capsicum annuum L.) populations

from northern of Mexico

Variabilidad morfológica y genética de poblaciones de chile (Capsicum annuum L.) del norte de

México

Variabilidade morfológica e genética de populações de pimenta (Capsicum annuum L.) do norte do

México

Karina C. Ibarra-Legarda

1,2

Rocío Infante-Ramirez

Loreto Robles-Hernández

Ana C. Gonzalez-Franco

Zilia Y. Muñoz-Ramirez

Ma. Carmen E. Delgado-Gardea

Rev. Fac. Agron. (LUZ). 2025, 42(2): e254218

ISSN 2477-9407

DOI: https://doi.org/10.47280/RevFacAgron(LUZ).v42.n2.II

Crop production

Associate editor: Dr. Jorge Vilchez-Perozo

University of Zulia, Faculty of Agronomy

Bolivarian Republic of Venezuela

Universidad Autónoma de Chihuahua, Facultad de Ciencias

Agrotecnológicas, Ciudad Universitaria S/N Campus 1,

Chihuahua, Chih. 31310, México.

Universidad Autónoma de Chihuahua, Facultad de Ciencias

Químicas, Campus 1I, Chihuahua, Chih. 31310, México.

Received: 06-02-2025

Accepted: 12-03-2025

Published: 14-04-2025

Abstract

This study investigated the genetic and morphological variability

of ve domesticated chili varieties (Árbol, Güerito, Mirasol, Negro

and Alcalá) and one wild variety (chiltepín) from Chihuahua,

Mexico. Morphological evaluation was carried out according to

the International Plant Genetic Resources Institute, combining

correspondence analyses and Chi-square tests. Genetic variability

was determined using the RAPD technique; a dendrogram

was constructed, and genetic diversity among populations was

estimated using principal coordinate methods, Shannon index, and

permutational multivariate analysis. The morphological analysis

revealed signicant variations, while the genetic analysis, using

the RAPD technique, showed 79.5 % polymorphism, indicating

considerable diversity among the varieties. The dendrogram

revealed the presence of three groups, highlighting chiltepín

as potential ancestor of the domesticated varieties. The study

emphasizes the importance of conserving and improving these plant

genetic resources.

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Rev. Fac. Agron. (LUZ). 2025, 42(2): e254218 April-June. ISSN 2477-9409.

2-6 |

Resumen

Este estudio investigó la variabilidad morfológica y genética de

cinco variedades de chile domesticadas (Árbol, Güerito, Mirasol,

Negro y Alcalá) y una silvestre (chiltepín) de Chihuahua, México.

La evaluación morfológica se realizó de acuerdo con el Instituto

Internacional de Recursos Fitogenéticos, combinando análisis de

correspondencias y pruebas de Chi cuadrada. La variabilidad genética

se determinó con la técnica RAPD, construyéndose un dendrograma

y estimándose la diversidad entre poblaciones mediante coordenadas

principales, índice de Shannon y análisis multivariado permutacional.

El análisis morfológico mostró variaciones signicativas, mientras

que el análisis genético, reveló un 79,5 % de polimorsmo, indicando

una gran diversidad entre las variedades. El dendrograma reveló la

presencia de tres grupos, destacando al chiltepín como un posible

ancestro de las variedades domesticadas. El estudio resalta la

importancia de conservar y mejorar estos recursos togenéticos.

Palabras clave: chiltepín, RAPD, diversidad genética, descriptores

morfológicos

Resumo

Este estudo investigou a variabilidade genética e morfológica de

cinco variedades de pimenta domesticadas (Árbol, Güerito, Mirasol,

Negro e Alcalá) e uma variedade selvagem (chiltepín) de Chihuahua,

México. A avaliação morfológica foi realizada de acordo com o

Instituto Internacional de Recursos Genéticos Vegetais, combinando

análises de correspondência e testes de Qui-quadrado. A variabilidade

genética foi determinada pela técnica RAPD; foi construído um

dendrograma e a diversidade genética entre populações foi estimada

através dos métodos de coordenadas principais, índice de Shannon

e análise multivariada permutacional. A análise morfológica revelou

variações signicativas, enquanto a análise genética, utilizando

a técnica RAPD, mostrou 79,5 % de polimorsmo, indicando

considerável diversidade entre as variedades. O dendrograma revelou

a presença de três grupos, destacando o chiltepín como um possível

ancestral das variedades domesticadas. O estudo destaca a importância

de conservar e melhorar esses recursos genéticos vegetais.

Palavras chave: chiltepin, RAPD, diversidade genética, descritores

morfológicos

Introduction

Chili pepper (Capsicum annuum L.) is a crop of great economic

and cultural importance, with Mexico recognized as its center of

domestication and diversication (Aguilar-Meléndez et al., 2018).

The extensive genetic diversity of C. annuum has resulted in numerous

landraces and cultivated varieties adapted to diverse agroecological

conditions, particularly in northern Mexico, where environmental

factors such as temperature uctuations, soil composition, and

precipitation patterns have inuenced their evolution (Aragón-

Cuevas & de la Torre, 2015).

The Capsicum genus is widely cultivated globally, with C.

annuum being one of the most extensively grown species (Aguilar-

Meléndez et al., 2018). In Mexico, chili peppers are a key component

of both traditional cuisine and the agricultural economy Aguirre y

Muñoz, 2015), ranking second in global production with an annual

output exceeding 3.6 million tons and a production value of over

4.5 billion pesos (FAOSTAT, 2019; SADER, 2023). Furthermore,

Mexico has the highest genetic diversity of chili peppers, making it

a crucial phylogenetic resource for conservation (Contreras-Toledo

et al., 2018). However, the introduction of commercial crop varieties

and shifts in agricultural practices threaten local cultivars. The

expansion of monocultures and habitat alterations are driving genetic

erosion, putting these traditionally selected varieties at risk (Hayano-

Kanashiro et al., 2016, Rodríguez, 2019).

Understanding the morphological and genetic variability of

C. annuum populations is essential for multiple reasons. From an

agricultural perspective, identifying traits associated with resistance

to abiotic and biotic stresses can contribute to breeding programs

aimed at improving resilience and productivity (Pérez-Castañeda

et al., 2015); Constantino et al., 2020). Additionally, preserving

genetic resources is vital to maintaining biodiversity and ensuring

the sustainability of chili cultivation in the face of climate change

and pest pressures (Votava et al., 2005). Therefore, this study aims to

assess the morphological and genetic diversity between domesticated

and wild varieties of C. annuum populations from northern Mexico

by analyzing key traits, and genetic markers.

Materials and methods

Collection of plant material

In 2023, fruits from domesticated and wild chili varieties were

collected from municipalities in Chihuahua (Table 1). Three samples

of fresh red fruits were gathered from each municipality, transported

to the MAFFP laboratory at the Autonomous University of Chihuahua,

and left to dry at room temperature (24±2°C). Healthy, uniformly

sized seeds were selected and stored at 4°C for future use.

Table 1. Geographical and climatic characteristics of chili pepper

varieties.

Samples Municipalities GL MASL CT

MAP

(mm)

MAT

(°C)

Chiltepin

(CHCH)

Chínipas

27°24′0″N,

108°32′0″W

555

Dry semi-hu-

mid

781.7 23.8

Alcala (Alc) &

Arbol (A)

Aldama

28°35′40.92″N,

105°34′15.6″W

1,119 Desert 318 19.5

Negro (N) Julimes

28°32′0″N,

105°3′0″W

1,700 Hyper-arid 60 18.3

Mirasol (M) &

Güerito (G)

Delicias

28°11′36″N,

105°28′16″W

1,170 Semi-arid 334 18.8

GL= geographic location, MASL = meters above sea level, CT = climate type, MAP = man

annual precipitation, MAT = mean annual temperature.

In vitro germination and seedling production

Viable seeds were disinfected with a 10 % sodium hypochlorite

solution for 30 minutes and then rinsed with sterile water. After

disinfection, the seeds were incubated in an acidic solution at 24

± 1 °C for 48 hours, then dried on sterile paper. Twenty-ve seeds

were placed in each of the ten Petri dishes with sterile lter paper,

moistened with sterile water, and sealed. The dishes were placed in

a germination chamber with a 16-hour light/8-hour dark photoperiod

at 25 ± 1 °C for germination, and the seedlings were ready for

transplantation after 20 days. For seedling production, all in vitro

germinated seeds were placed in germination trays with peat moss

and compost substrate, then kept in a chamber at 24 ± 1 °C with a

16-hour light/8-hour dark photoperiod. Watering occurred every

3 days until the plants developed eight true leaves. Domesticated

chili seeds undergo the same disinfection process as wild varieties.

After sterilization, seeds were sown in trays, each cavity containing

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3-6 |

two seeds, and watered until they developed eight true leaves. The

seedlings were then transferred to small pots with a soil and peat moss

mix, placed in a greenhouse, and watered and fertilized every 3 days

for 12 weeks using a nutrient solution (1.5 g.L

-1

of 12-61-00 (N-P-K),

1.5 mL.L

-1

of Ca, and 1.5 g.L

-1

of 18-18-18 (N-P-K). Additionally,

3 mL.L

-1

of Nutrisorb®, 2 mL.L

-1

of Radigrow®, and 3 mL.L

-1

ATPUP®).

Morphological characterization

Morphological characterization was done using the International

Plant Genetic Resources Institute (IPGRI, 1995), focusing on

qualitative traits at the seedling, plant, inorescence, and seed stages.

The traits examined included hypocotyl and stem pubescence,

cotyledon leaf color and shape, stem and seed color, anthocyanin

presence, growth habit, branching and leaf density, leaf color and

shape, ower position, fruit shape at bloosom end.

Sample preparation and DNA extraction

Leaf samples were collected from 12-week-old chili plants.

For DNA extraction, 200 mg of leaf tissue was macerated and

extracted by CTAB (cetyltrimethylammonium bromide) technique

as suggested by Michiels et al. (2003) with some modications.

Genetic material was puried using the Zymo Research DNA Clean

& Concentrator™-5 kit following the manufacturer’s instructions.

DNA purity and concentration were evaluated using a Nanodrop

2000 spectrophotometer (Thermo Scientic, Massachusetts, USA).

DNA concentration was adjusted to 50 ng.µL

-1

for use in the RAPD

technique. Only extractions with a 260/280 ratio between 1.8 and 2.0

were used to ensure genomic DNA integrity, veried through 2 %

agarose gel electrophoresis.

RAPD analysis

For RAPD analysis, primers OPF 05 (Lanteri et al., 2003), MFG

17 (Hermosillo-Cereceres et al., 2008), OPA 02 (Bobadilla et al.,

2017), OPA 07 and OPB 11 (Bhadragoudar & Patil, 2011), OPA 20

(González-Jara et al., 2011) and AF 20 (Adetula, 2006) were selected

based on their ability to generate a higher number of polymorphic

bands. The RAPD amplication was performed according to the

methodology proposed by Khan et al. (2010), with modications. A

lettuce sample was included as an out-group. Amplied DNA was

visualized on a 2 % agarose gel using a photo-documenter (KODAK

1D 3.6). Electrophoresis was carried out at 70 V for 120 min.

Statistical analysis

Statistical correspondence analysis was performed on

morphological descriptors using RStudio (version 1.2.5033), and

Chi-square tests were conducted to assess statistical dierences

(p < 0.05). For RAPD analysis, a binary matrix was created based

on the presence or absence of amplied bands. A dendrogram was

constructed using.

Nei genetic distance and the Unweighted Pair Group Method with

Arithmetic Mean (UPGMA) algorithm were used to visualize genetic

relationships (Oksanen et al., 2020). Principal Coordinate Analysis

(PCoA) and the Shannon index were used to analyze genetic diversity.

Diversity dierences were evaluated using the Kruskal-Wallis test

(p < 0.05), followed by a PERMANOVA with 999 permutations to

assess RAPD prole dierences.

Results and discussion

Qualitative morphology

Morphological characterization is considered a crucial step in

dening and classifying germplasm (Ratna et al., 2024). Our results

conrm that the multiple qualitative descriptors presented statistically

signicant dierences among C. annuum varieties evaluated in

this study (Figures 1a & 1b). These dierences, detected through

correspondence analysis and Chi-square tests, reect the intrinsic

genetic variability of the analyzed varieties. Phenotypic diversity,

showed highly signicant dierences, with p-values below 0.001 in

descriptors such as cotyledonous leaf shape (p = 0.00119), stem color

(p < 0.001), anthocyanin at the node (p = 0.00022), stem pubescence

(p < 0.001), growth habit (p < 0.001), branching density (p < 0.001),

leaf color (p = 0.00020), leaf shape (p < 0.001), ower position (p

< 0.001), fruit shape (p < 0.001), fruit shape at the blossom end (p

< 0.001), and seed color (p < 0.001). These results demonstrate the

heterogeneity among the domesticated chili varieties and the wild

chiltepin variety, as each analyzed descriptor is key to understanding

how these chili species have adapted to dierent environmental

and cultivation conditions. Previous studies have highlighted that

morphological traits such as pubescence are important adaptations

to specic cultivation conditions, although their variability might

be limited in certain genetic groups. This trait is associated with

resistance to pests and diseases and reduced water loss, which is

particularly relevant in dry climates (Bobadilla-Larios et al., 2017).

Figure 1a. Morphological treats (cotyledonous leaf shape, stem

pubescence, leaf density, branching and plant growth

habit, nodal anthocyanin, and branching habit) of

domesticated and wild chili varieties.

Figure 1b. Morphological treats (fruit shape at blossom end, fruit

and leaf shape, seed and leaf color) of domesticated

and wild chili varieties.

Variations in leaf shape are linked to adaptive strategies and

productivity under diverse environmental conditions (Carrillo-

Montoya y Vargas-Rojas, 2023). These results reinforce leaf

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4-6 |

morphology as a key indicator in taxonomy and crop genetic

improvement.

Stem color has been associated with anthocyanins, which

possess antioxidant properties and are inuenced by genetic and

environmental factors focused on abiotic stress resistance (Bobadilla-

Larios et al., 2017). Additionally, highly dierences in branching

density reect ecological adaptations as well as leaf density, although

marginal dierences was detected in the last trait (p = 0.02498).

These traits are important for optimizing agronomic management,

such as planting density, phytosanitary management, photosynthesis

potential, and fruit production to maximize yield in various cultivation

systems (Bobadilla-Larios et al., 2017; Carrillo-Montoya y Vargas-

Rojas, 2023). These adaptations may be associated with specic light

and temperature conditions. Leaf color has implications for selecting

varieties suited to dierent climatic zones, as do other described traits.

Fruit shape diversity reects both natural and articial selective

pressures. In the commercial context, preference for specic fruit

shapes can signicantly inuence product acceptance in local and

global markets, making this trait indispensable for dierentiating chili

species (Figure 2) (Bobadilla-Larios et al., 2017; Carrillo-Montoya y

Vargas-Rojas, 2023).

Figure 2. Morphology of chili fruits varieties. Domesticated

varieties: a = Alcalá, b = Árbol, c = Negro, d = Güerito, e

= Mirasol, and wild variety: f = Chiltepin.

Characterization of RAPD markers

The molecular characterization of six chili varieties generated

181 amplied bands, of which 144 were polymorphic (79.5 %).

Additionally, the number of amplied fragments ranged from 21

(OPB11) to 37 (MFG17), and the polymorphism range varied from

64 % for OPF05 to 96 % for AF20 (Table 3). In contrast, a study using

10 primers obtained only 45 polymorphic bands, ranging from 3 to 7

bands per primer (Votava et al., 2005). Achieving a high percentage

of polymorphisms could reveal greater signicant genetic variability

within the studied population (Figure 3).

Table 3. Random primers used, number of PCR amplied bands

and polimorphism.

Primers

Number of Amplied

Bands

Polymorphic

Bands

Polymorphism

(%)

MFG17 37 33 89

OPA07 24 20 83

OPF05 25 16 64

OPA20 24 18 75

OPA02 23 16 70

OPB11 21 15 71

AF20 27 26 96

Figure 3. PCR-RAPD amplication of six chili pepper varieties

using primers OPB11 (a) and OPF05 (b). (a) Lanes: 1)

MPM, 2-13) duplicate samples of domesticated chili (A,

G, M, N, Alc) and wild chili (CHCH), 14-15) duplicate

lettuce samples (L, outgroup), 16) negative control. (b)

Lanes: 17-28) duplicate samples of domesticated chili (A,

G, M, N, Alc) and wild chili (CHCH), 29-30) duplicate

lettuce samples (L, outgroup), 31) negative control, 32)

MPM.

Bobadilla-Larios et al. (2017) reported 45.45 % polymorphism

for the OPA02 marker, whereas González-Jara et al. (2011) reported

40 % for the same marker and 81.25 % for OPA20. In contrast, the

results obtained in this study showed 70 % polymorphism for OPA02

and 75 % for OPA20 (Table 3). In a similar study on C. annuum L.

genotypes, Bhadragoudar & Patil (2011) reported 88 % polymorphism

for the OPA07 molecular marker, comparable to our results (83 %

polymorphism). Meanwhile, polymorphism with the OPB11 marker

was reported to be 66.6 %, compared to polymorphism with 71 %

in our study. The distance matrix oers a clear view of the genetic

diversity, with values ranging from 0.2588 to 0.9429. The closest

genetic distance was between Güerito and Arbol samples, while the

most distant relationship was between Arbol and lettuce samples.,

where Lettuce was used as an out-group sample.

In 2017, Bobadilla-Larios et al. reported low genetic variability

(0.74 and 0.96) in their study, with the most signicant variability

among the Ancho, Calera, and Mirasol Don Luis SLP chili varieties.

Another study reported a range of genetic variability from 0.20

to 0.94 (Bhadragoudar & Patil, 2011). A study of chili samples in

Nigeria found a genetic distance (Jaccard coecient) ranging from

0.21 to 0.88, with an average of 0.61 (Adeyemo & Lawal, 2020).

These ndings align with our results.

A dendrogram was constructed, resulting in three groups

(Figure 4a). This dendrogram was generated based on the genetic

relationships among the analyzed varieties, including domesticated

chili cultivars and the wild Chiltepin chili variety. Group A includes

the lettuce population, with an average genetic similarity value of

0.70 compared to the Chili pepper varieties. Since this species does

not belong to the Capsicum genus, it was considered an out-group

sample, indicating that this result is consistent. Meanwhile, Group B

consists solely of the Chiltepin chili variety, with an average genetic

distance of 0.61. This result conrms that Chiltepin is the potencial

ancestor of other chili varieties, as mentioned by Votava et al. (2005),

González-Jara et al. (2011) and Hayano-Kanashiro et al. (2016). The

remaining domesticated chili populations were grouped into Group

C, forming two subgroups. Alcala and Negro chilies represented

the rst subgroup (C.1). In contrast, the second subgroup (C.2) was

represented by the Arbol, Güerito, and Mirasol chili samples, similar

to groups F and G reported in another study (Votava et al., 2005).

Other studies have grouped between 14 and 18 groups (Votava et

al., 2005; Bhadragoudar & Patil, 2011). Meanwhile, other authors

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5-6 |

have reported between 2 and 4 groups (Bobadilla-Larios et al., 2017;

Mbasani-Mansi et al., 2019; Constantino et al., 2020).

Figure 4. Dendrogram (a) and Principal Coordinates Analysis

[PCoA] (b). Where: Alc = Alcala, N = Negro, A = Arbol,

G = Güerito, M = Mirasol, CHCH = Chiltepin, L =

Lettuce (out-group).

A principal Coordinates Analysis (PCoA) was conducted using

distances calculated by Nei’s algorithm (Figure 4b). In this analysis,

the rst three principal components explained 89 % of the variation

in the dispersion of Capsicum annuum L. varieties. Specically,

Principal Component 1 (PCo1) accounted for 50 %, Component 2

(PCo2) explained 20 %, and Component 3 (PCo3) explained 19 %

of the variance.

In Figure 4b, clear discrimination can be observed among the

Capsicum annuum L. chili species, including Alcala, Negro, Güerito,

Mirasol, Arbol, and the wild Chiltepin chili. The results of this

experiment are consistent with those reported for Coordinate 1, with

45 % (Pacheco-Olvera et al., 2012). These ndings strongly support

the topology observed in the dendrogram Figure 4a.

The Permutational Multivariate Analysis (PERMANOVA) was

performed using a reduced model to evaluate dierences among the

samples based on the distance matrix. The analysis examined whether

signicant dierences existed in the multivariate structure among the

varieties, considering variability within groups and their similarity

or dissimilarity. The analysis revealed that the sample factor had 6

degrees of freedom, a sum of squares value of 1.98, and a coecient

of determination of 0.9445, explaining 94.45 % of the total variation.

The p-value (0.001) indicates signicant dierences among all the

samples analyzed. Identifying and correctly interpreting the genetic

relationships among the dierent genotypes studied is crucial to these

experiments.

Our study reveals that the genetic variation of chili pepper varieties

under investigation is directly related to their shared geographical

characteristics, particularly the domesticated varieties that exhibit

closer genetic proximity. This genetic proximity is supported by the

formation of group C and subgroups C.1 and C.2 in the dendrogram

(Figure 4a).

Genetic diversity of chili varieties

The Shannon index was used to calculate genetic diversity,

obtaining values higher than 4.3 for this index. A high index value

indicates greater diversity among the analyzed samples (Figure 5),

implying more alleles or genetic variability. The lowest value was

4.31 for the lettuce sample, while the highest value was attributed

to the Arbol chili, with a value of 4.58. The p-value was 0.05227

(slightly above the commonly used signicance level of p < 0.05).

This clear separation of populations can also be observed across

dierent axes in the Principal Component Analysis, accounting for

89 % of the variability. Therefore, this variety’s remarkable genetic

variability is attributed to its geographical location in the municipality

of Chínipas, Chihuahua, Mexico, at an altitude of 555 meters above

sea level. It has a warm-temperate climate and an average annual

precipitation of 781.7 mm, which signicantly diers from the

domesticated populations.

Figure 5. Diversity of analyzed chili varieties according to the

Shannon Index. Where: Alc = Alcala, A = Arbol, CHCH

= Chiltepin, G = Güerito, L = Lettuce, M = Mirasol, N =

Negro.

Conclusions

This study highlights the genetic variability between domesticated

and wild chili varieties, oering valuable insights for conservation and

breeding. Chiltepin, the potential ancestor of cultivated chilis, shows

signicant genetic diversity, supporting genetic improvement eorts

for higher yields. Morphological dierences demonstrate adaptability

and potential for yield, assisting breeding under dierent conditions.

The research emphasizes the importance of using multidisciplinary

approaches, including morphological, agronomic, and molecular

analyses, to understand species dynamics, population evolution, and

ecological interactions.

Acknowledgments

We thank to Fundación Produce, Chihuahua, A.C., for their

valuable approval and support in eld experiments, which were

essential for developing this work.

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