Keywords:

Pearl millet

SSR marker

Genetic diversity

Regional diversity

Algerian landraces

Geographical dierentiation and genetic diversity of Algerian pearl millet assessed with

microsatellites

Diferenciación geográca y diversidad genética del mijo perla argelino evaluadas mediante

microsatélites

Diferenciação geográca e diversidade genética do milheto pérola argelino avaliada por microsatélites

Abderrezzak Kirouani

1,2*

Elyes Babay

3,4

Redha Ouldkiar

1,2

Badreddine Belhadi

2,5

Rachid Souilah

2,6

Leila Boukhalfoun

Djaafar Djabali

Boubekeur Nadjemi

Rev. Fac. Agron. (LUZ). 2025, 42(4): e254256

ISSN 2477-9407

DOI: https://doi.org/10.47280/RevFacAgron(LUZ).v42.n4.XIII

Crop production

Associate editor: Dra. Evelyn Pérez Pérez

University of Zulia, Faculty of Agronomy

Bolivarian Republic of Venezuela

Laboratory of Nutrition, Biodiversity and Environment,

Agronomy Department, Faculty of Sciences, University of

Médéa, Algeria.

Laboratoire d’Etude et de Développement des Techniques

d’Epuration et de Traitement des Eaux et Gestion

Environnementale, Ecole Normale Supérieure de Kouba,

Alger, Algeria. 16000.

National Gene Bank of Tunisia (BNG), Tunis, Tunisia.

Agricultural Applied Biotechnology Laboratory

(LR16INRAT06), Institut National de la Recherche

Agronomique de Tunisie (INRAT), University of Carthage,

Tunis, Tunisia.

Département des sciences et techniques, Faculté de

technologie, Université Amar Télidji, Laghouat, Algeria.

Département de physique, Ecole Normale Supérieure Taleb

Abderrahmane, ENSL, B.P 4033. Laghouat, Algeria.

Received: 27-08-2025

Accepted: 15-11-2025

Published: 08-12-2025

Abstract

Pearl millet, a drought-tolerant cereal, is a crucial role in

food security, in arid and semi-arid regions. Despite its global

signicance, genetic diversity of Algerian pearl millet populations

remains underexplored. This study assessed the genetic diversity of

22 pearl millet genotypes from four distinct Saharan agroclimatic

zones in Algeria using 24 SSR markers. A total of 87 alleles were

detected, with an average of 3.62 alleles per locus and polymorphic

information content (PIC) values ranging from 0.043 to 0.815,

indicating substantial genetic variability. Analysis of Molecular

Variance (AMOVA) revealed greater genetic variance within

individuals than among them. Genotypes from Tamanrasset and In

Salah exhibited higher diversity than those from Oued Souf and

Adrar, with private and rare alleles underscoring the impact of

geographic isolation. Cluster analysis and principal coordinates

analysis (PCoA) grouped genotypes by geographic origin,

identifying ve major genetic groups, conrming patterns of

gene ow and local adaptation. Populations from Niger and India

were highly genetic distant from Algerian landraces making them

promising candidates for heterotic hybrid development. These

ndings provide insights for broadening the genetic base of breeding

strategies targeting yield and stress resilience in pearl millet.

This scientic publication in digital format is a continuation of the Printed Review: Legal Deposit pp 196802ZU42, ISSN 0378-7818.

Rev. Fac. Agron. (LUZ). 2025, 42(4): e254256 October-December. ISSN 2477-9409.

2-8 |

Resumen

El mijo perla, cereal tolerante a la sequía, es esencial para la

seguridad alimentaria en regiones áridas y semiáridas. A pesar de su

importancia global, la diversidad genética del mijo perla en Argelia

sigue poco estudiada. Este trabajo evaluó 22 genotipos de cuatro

zonas agroclimáticas saharianas mediante 24 marcadores SSR. Se

detectaron 87 alelos (media= 3,62 por locus), con valores de contenido

de información polimórca (PIC) entre 0,043 y 0,815, lo que evidencia

una variabilidad considerable. El Análisis de Varianza Molecular

(AMOVA) mostró mayor varianza dentro de los individuos que entre

ellos. Los genotipos de Tamanrasset e In Salah presentaron mayor

diversidad que los de Oued Souf y Adrar, destacando la presencia

de alelos privados y raros por efecto del aislamiento geográco. Los

análisis de conglomerados y de coordenadas principales (PCoA)

agruparon los genotipos por origen geográco, identicando cinco

grupos genéticos principales. Las poblaciones de Níger e India

mostraron gran distancia genética respecto a las argelinas, lo que las

convierte en candidatas prometedoras para el desarrollo de híbridos

heteróticos. Estos resultados aportan información útil para ampliar

la base genética en programas de mejoramiento orientados a la

productividad y la resiliencia al estrés del mijo perla.

Palabras clave: Mijo perla, marcador SSR, diversidad genética,

diversidad regional, razas locales argelinas.

Resumo

O milheto pérola, cereal tolerante à seca, é fundamental para a

segurança alimentar em regiões áridas e semiáridas. Apesar de sua

relevância global, a diversidade genética do milheto na Argélia

permanece pouco explorada. Este estudo avaliou 22 genótipos de

quatro zonas agroclimáticas saharianas utilizando 24 marcadores

SSR. Foram detectados 87 alelos (média= 3,62 por loco), com

valores de conteúdo de informação polimórca (PIC) entre 0,043

e 0,815, indicando elevada variabilidade. A análise de variância

molecular (AMOVA) mostrou maior variação dentro dos indivíduos

do que entre eles. Genótipos de Tamanrasset e In Salah apresentaram

maior diversidade que os de Oued Souf e Adrar, com alelos privados

e raros reetindo o impacto do isolamento geográco. As análises

de agrupamento e de coordenadas principais (PCoA) organizaram

os genótipos por origem geográca, identicando cinco grupos

principais. As populações do Níger e da Índia mostraram grande

distância genética em relação às argelinas, tornando-se candidatas

promissoras para o desenvolvimento de híbridos heteróticos. Esses

resultados fornecem subsídios para ampliar a base genética em

programas de melhoramento voltados à produtividade e à resiliência

ao estresse do milheto pérola.

Palavras-chave: Milheto pérola, marcador SSR, diversidade

genética, diversidade regional, raças locais argelinas.

Introduction

Pearl millet (Pennisetum glaucum (L.) R. Br.) is the sixth most

important cereal crop worldwide, after maize (Zea mays L.), rice

(Oryza sativa L.), wheat (Triticum aestivum L.), barley (Hordeum

vulgare L.), and sorghum (Sorghum bicolor (L.) Moench), and

it remains a key staple in arid and semi-arid regions due to its

resilience to drought, poor soils, and high temperatures (Shinde et

al., 2020; Deevi et al., 2024). India accounts for about 42 % of global

production, followed by Niger, China, and several African countries

(Yadav et al., 2021).

Pearl millet (Pennisetum glaucum [L.] R. Br.) was domesticated

in the western Sahel of Africa around 4000-5000 years ago and

subsequently spread across arid and semi-arid regions of Africa and

Asia (Oumar et al., 2008; Manning et al., 2011). It has become a vital

staple crop in environments where rainfall is scarce, temperatures

are high, and soils are poor-conditions under which other cereals

rarely succeed (Yadav et al., 2021). Its wide ecological distribution

has led to the accumulation of considerable phenotypic and genetic

variability, reected in diverse landraces adapted to contrasting

environments (Serba & Yadav, 2016). This diversity, shaped by both

natural selection and farmer seed exchange, forms a key resource

for breeding programs targeting drought tolerance, earliness, and

nutritional quality (Satyavathi et al., 2021; Govindaraj et al., 2020).

Morphologically, it exhibits wide variability in panicle size, tillering

capacity, and grain color, while physiologically, it displays deep

rooting and ecient water use typical of C₄ cereals (Satyavathi et

al., 2021). In addition, Lemgharbi et al. (2023) revealed signicant

morphological diversity among local, domesticated, and wild forms in

Tidikelt region, mainly in plant height, panicle traits, and seed color.

These landraces demonstrated strong adaptation to extreme Saharan

conditions and high phenotypic variability, suggesting valuable

genetic resources for future breeding and conservation programs.

Despite these phenotypic insights, molecular data on North African

germplasm remain scarce. Establishing the extent and structure

of their genetic variation is therefore essential for understanding

evolutionary relationships and guiding breeding strategies adapted to

local agroecological conditions.

Genetic diversity assessment of pearl millet is fundamental for

breeding programs aiming at yield improvement, stress tolerance, and

disease resistance. While morphological traits are inuenced by the

environment (Kirouani et al., 2023), molecular markers provide more

reliable evaluations of variability Kirouani et al., 2018; Triki et al.,

2023). SSRs are co-dominant, highly polymorphic, and reproducible,

making them valuable tools in plant breeding for assessing genetic

relationships and population structure (Choudhary et al., 2016). SSRs

have been widely used to characterize pearl millet genetic diversity

(Stich et al., 2010; Nepolean et al., 2012; Gupta et al., 2018).

Furthermore, assessing genetic diversity in pearl millet landraces

is particularly important for hybrid development, as diversity among

inbred line enables the identication of parental combinations

that contribute benecial alleles for yield improvement and stress

adaptation (Singh & Gupta 2019). However, most previous studies

have focused on West African populations (Rhoné et al., 2020),

whereas little information exists for North African germplasm,

especially in Algeria-the northernmost limit of pearl millet distribution

in Africa. Algerian landraces have evolved under contrasting Saharan

and sub-humid environments, from oasis systems to Mediterranean

foothills, potentially harboring unique allelic combinations associated

with drought resilience and local adaptation. This work therefore

constitutes the rst comprehensive molecular characterization

of Algerian pearl millet using SSR markers, lling a signicant

geographical and genetic gap in the species’ diversity analysis. The

ndings provide a national contribution to the understanding of pearl

millet diversity and oer a valuable resource for future regional

breeding, conservation, and germplasm exchange programs. The

objectives of this study were to: (i) assess the genetic diversity among

This scientic publication in digital format is a continuation of the Printed Review: Legal Deposit pp 196802ZU42, ISSN 0378-7818.

Kirouani et al. Rev. Fac. Agron. (LUZ). 2025, 42(4): e254256

3-8 |

sown in eld plots during April 2024, at a depth of about 2 cm in clay-

loam soil. The soil was irrigated before sowing to ensure uniform

germination, and manual watering was provided when needed until

seedling establishment. Leaf samples were collected 15 days after

sowing, when plants reached the three-leaf stage. Five fresh leaves

were placed in labeled glass tubes, kept in a portable icebox (Iceco

GO20, China), and transported to the laboratory of molecular biology

(University of Médéa) for DNA extraction using CTAB method

(Fulton et al., 1995). A set of 24 highly polymorphic SSR primers

(Figure 1, Table 3) were selected. PCR amplication was conducted

in thermal cycler (Bioer Life Eco, China) in a total volume of 25

μL, containing approximately 50 ng of genomic DNA, 2.5 μM of

each primer, green reaction buer including 1.5 mM MgCl

, 1U Taq

DNA polymerase (GoTaq, Promega, USA), and 2.5 mM of each

dNTP (Thermo Fisher Scientic, USA). Amplied DNA fragments

were separated on 2 % agarose gels using an electrophoresis unit

(Thermo Fisher Scientic, USA) and fragment sizes were estimated

by comparisons with 100 bp DNA ladder (GeneRuler, Thermo Fisher

Scientic, USA).

Data analysis

Genetic diversity parameters, including the number of alleles

(Na), eective alleles (Ne), Observed heterozygosity (Ho), expected

heterozygosity (He), Shannon’s index (I), and polymorphism

information content (PIC) were calculated using GenAlEx 6.5

(Peakall & Smouse, 2012) haploid and binary genetic loci and

DNA sequences. Both frequency-based (F-statistics, heterozygosity,

HWE, population assignment, relatedness. Principal coordinate

analysis (PCoA) was also performed in GenAlEx 6.5, while UPGMA

dendrogram was generated with MEGA 7.0 (Tamura et al., 2007)

which expands on the existing facilities for editing DNA sequence data

from autosequencers, mining Web-databases, performing automatic

and manual sequence alignment, analyzing sequence alignments to

estimate evolutionary distances, inferring phylogenetic trees, and

testing evolutionary hypotheses. Version 4 includes a unique facility to

generate captions, written in gure legend format, in order to provide

natural language descriptions of the models and methods used in the

analyses. This facility aims to promote a better understanding of the

underlying assumptions used in analyses, and of the results generated.

Another new feature is the Maximum Composite Likelihood (MCL.

Additional diversity indices, including major allele frequency,

and gene diversity, were obtained with PowerMaker v3.25 (Liu &

Muse, 2005). Population structure was assessed with STRUCTURE

software v2.3.4 using the ΔK methode (Evanno et al., 2005).

Results and discussion

Overall genetic diversity

The 24 SSR markers generated a total of 87 alleles, with an

average of 3.62 alleles per locus, demonstrating the eectiveness of the

Algerian pearl millet genotypes and (ii) examine the distribution of

allelic variation across distinct geographic zones.

Materials and methods

Plant material

Twenty-two pearl millet (Pennisetum glaucum [L.] R. Br.)

genotypes (Table 1) were collected from four contrasting Saharan

regions of Algeria-Tamanrasset (12 landraces), In Salah (8), Adrar

(1), and Oued Souf (1) representing distinct agro-climatic zones

(Table 2).

Table 1. Genotypes used in the present study.

Group

code

Name Origin and date of harvest

B1 TM-10Djf(3) In Salah (Djafou) - 2010

B2 TM-09Djf(3) In Salah (Djafou) - 2009

B3 TM-23Azzaoui AinSalah (Djafou) - 2023

B4 TM-21Lakhal(Fo) In Salah (Ouaini) - 2021

B5 TM-21SoumDjf In Salah (Djafou) - 2011

B6 TM-1-11FE(Fo) In Salah (Foggaret Ezzoua) - 2011

B7 TM-21NadjMed In Salah (Ouaini) - 2021

B8 TM-21Arialla(Liss) In Salah (Foggaret Ezzoua) - 2021

B9 TM-22Grenet Oued Souf - 2022

B10 TM-16NadjMed(Fo) Adrar (ex-Touat) - 2016

B11 TM-21HamdiZerga(Loc) Tamenrasset (Center) - 2021

B12 TM-21HamdiN/Tam(06) Tamenrasset (Niger) - 2021

B13 TM-16NadjMed(Mel) Tamenrasset (ex-Ahagar) - 2016

B14 TM-22Mham(4) Tamenrasset (India) - 2022

B15 TM-22Nasse(Mel) Tamenrasset (In M’guel) - 2022

B16 TM-22LaghnedjMed Tamenrasset (Abalessa) - 2022

B17 TM-22ZergaTaleb(Loc) Tamenrasset (In Dalag) - 2022

B18 TM-22LaghnedjAh(Mel) Tamenrasset (Abalessa) 2022

B19 TM-21Laghnedj(Mel) Tamenrasset (Abalessa) - 2021

B20 TM-22N/Tam(2) Tamenrasset (Niger) - 2022

B21 TM-21N/Tam(Soud) Tamenrasset (Niger) - 2021

B22 TM-21Zerga-Tam(Loc) Tamenrasset (Center) - 2021

The contrasting environmental conditions are expected to

inuence morphological and adaptative traits among landraces such

as plant height, panicle structure, seed color, and owering time,

reecting underlying genetic dierentiation, as suggested by previous

study on African pearl millet populations (Rhoné et al., 2020).

DNA extraction and PCR amplication

The experiment was conducted at the Ouamri experimental site

Médéa (36°12’18.2”N 2°31’30.0”E), under moderate sub-humid

climatic conditions. Seeds of each genotype (three per spike) were

Table 2. Environmental characteristics of the four collection sites in Algeria.

Study site Coordinates (DMS) Altitude (m) Rainfall (mm·yr⁻¹) Temp. (°C) Soil type

Tamanrasset 23°48′54″ N, 5°55′56″ E ~1,400 < 100 38–42 Sandy-loam

In Salah 27°11′53″ N, 2°27′47″ E ~270 < 30 > 45 Sandy-stony

Adrar 28°48′14″ N, 0°19′09″ E ~263 < 30 > 45 Sandy

Oued Souf 33°26′08″ N, 6°53′34″ E ~80 < 100 35–40 Sandy

This scientic publication in digital format is a continuation of the Printed Review: Legal Deposit pp 196802ZU42, ISSN 0378-7818.

Rev. Fac. Agron. (LUZ). 2025, 42(4): e254256 October-December. ISSN 2477-9409.

4-8 |

selected primers. Amplicons sizes ranged from 85 bp (IRD 46) to 378

bp (Xpsmp 2001), comparable to values reported in previous studies

(Chandra et al., 2020; Kumar et al., 2020; Gunguniya et al., 2023)

polymorphism data generated using 42 simple sequence repeat (SSR.

PIC values ranged from 0.043 (Xpsmp 2227) to 0.815 (Xpsmp 2070),

with a mean of 0.458 (Table 3). Nearly half of the markers (46 %) had

PIC > 0.50, conrming their high discriminatory power, consistent with

ndings in other pearl millet germplasm (Bougma et al., 2021).

The number of alleles per locus varied from 2 to 7, and loci with

higher allele numbers tended to show higher PIV values, conrming

the correlation between allelic richness and informativeness (Kumar

et al., 2020; Sangwan et al., 2019). The observed range was higher

than that reported for west African landraces (Singh et al., 2013;

Bougma et al., 2021; Makwana et al., 2021) but lower than values

found in more diverse international panels (Sangwan et al., 2019;

Gunguniya et al., 2023). Such dierences may reect germplasm

origin, marker choice, and resolution of electrophoresis techniques.

The number of eective alleles (Ne) ranged from 1.05 (Xpsmp

2227) to 6.12 (Xpsmp 2070), with an overall average of 2.42 (Table

3). These values indicate substantial genetic variation across loci. The

high Ne values correlate with genotypic diversity and are inuences

by the marker type and the resolution of the fragment separation

technique (Kuang et al., 2022). Lower values were obtained than

those reported by (Bougma et al., 2021).

Observed heterozygosity (Ho) averaged 0.411, ranging from 0.045

to 1.000, while expected heterozygosity (He) averaged 0.516, ranging

from 0.044 to 0.836. The high He values at several loci highlight

the considerable allelic richness of Algerian pearl millet, while the

variation in Ho indicated unequal distribution of heterozygotes

across loci. These results conrm the presence of substantial genetic

diversity. and in line with the cross-pollinating nature of pearl millet.

Similar results of heterozygosity have been reported in international

pearl millet panels (Chandra et al., 2020; Kumar et al., 2020; Rani

et al., 2024). Similar ranges have also been documented in regional

studies, particularly in west Africa and Sudan (Bashir et al., 2015;

Bougma et al., 2021). These agreement between regional reports and

our results conrms that substantial diversity is maintained across

dierent African pearl millet despite environmental constraints.

The xation index (F), indicating allelic xation within

populations, averaged 0.225 and ranged from -0.619 to 0.832. These

results suggest a moderate inbreeding level in the studied populations.

The variation in F values across loci reveals dierent evolutionary

pressures.

Genetic diversity by region

Signicant dierences were observed among the four studied

regions (Table 4). Tamanrasset and In Salah displayed the highest

genetic diversity, with 78 and 71 alleles detected, respectively, along

with several private and rare alleles, conrming their roles as major

Table 3. Number of Alleles, Major Allele Frequency, Heterozygosity, Genetic diversity, polymorphic information content and genetic

dierentiation by locus.

Primers

Amplicon size

(bp)

MAF

PIC

Xpsmp 2008 194-265 7.000 3.33 0.349 0.524 0.700 0.642 0.259

Psmp 2214 236-267 3.000 1.68 0.750 0.227 0.406 0.370 0.446

Xpsmp 2019 241-270 3.000 2.60 0.500 1.000 0.616 0.542 -0.619

Xpsmp 2237 265-295 3.000 2.38 0.524 0.222 0.580 0.497 0.622

Psmp 2247 207-214 2.000 1.37 0.841 0.045 0.268 0.232 0.832

Xpsmp 2048 210-282 6.000 2.85 0.533 0.400 0.649 0.608 0.393

Psmp 2249 152-188 4.000 1.45 0.818 0.136 0.309 0.280 0.564

Xpsmp 2063 163-270 6.000 4.85 0.295 0.909 0.794 0.764 -0.138

Xpsmp 2043 138-158 3.000 2.36 0.545 0.364 0.577 0.499 0.376

Xpsmp 2070 174-251 7.000 6.12 0.214 0.762 0.836 0.815 0.097

Xpsmp 2201 330-368 4.000 1.63 0.765 0.394 0.386 0.353 -0.012

Psmp 2202 132-149 2.000 1.89 0.621 0.576 0.471 0.360 -0.216

Psmp 2206 190-210 4.000 2.83 0.523 0.439 0.646 0.599 0.327

Psmp 2219 268-275 2.000 1.90 0.614 0.136 0.474 0.362 0.716

Psmp 2220 145-175 3.000 1.98 0.667 0.429 0.495 0.441 0.143

Xpsmp 2227 200-220 2.000 1.05 0.977 0.045 0.044 0.043 -0.016

Psmp 2231 260-279 2.000 1.82 0.659 0.409 0.449 0.348 0.097

IRD 12 190-210 2.000 1.71 0.705 0.591 0.416 0.330 -0.413

IRD 46 85-122 4.000 1.41 0.833 0.258 0.292 0.274 0.126

Xpsmp 2267 131-202 4.000 2.37 0.598 0.412 0.578 0.530 0.297

Xpsmp 2090 148-186 4.000 2.88 0.474 0.684 0.652 0.592 -0.040

Xpsmp 2248 145-184 2.000 1.95 0.579 0.211 0.488 0.369 0.574

Xpsmp 2001 193-378 5.000 3.34 0.465 0.579 0.700 0.660 0.182

Xpsmp 2076 148-169 3.000 2.31 0.556 0.111 0.568 0.489 0.808

Mean 3.625 2.42 0.600 0.411 0.516 0.458 0.225

Number of allele,

Number of eective allele,

Major allele frequency,

Heterozygosity,

Genetic diversity,

Polymorphic information content,

Fixation index

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Kirouani et al. Rev. Fac. Agron. (LUZ). 2025, 42(4): e254256

5-8 |

reservoirs of genetic diversity. By contrast, Oued Souf presented only

49 alleles, with reduced heterozygosity and no private alleles. Adrar

had the lowest diversity, with 45 alleles, low Shannon’s index, and

a decit of heterozygotes, reecting possible genetic erosion and

isolation. These results conrm that southern populations maintain

richer and more diverse germplasm than northern desert regions. The

presence of private alleles in the south suggests long-term adaptation

and restricted gene ow, while the reduced diversity in the north

points to genetic narrowing, possibly due to farmer selection practices

or limited seed exchange. Such geographic structuring of diversity

has also been reported in west African landraces (Bashir et al., 2015;

Bougma et al., 2021).

Table 4. Genetic diversity of landraces of Pearl millet according

to geographic origin.

Region Na Naa Ne He Ho I PIC Pa Ra

Adrar 43 1.79 1.64 0.30 0.43 0.45 0.24 0 0

In Salah 71 3.00 2.23 0.47 0.44 0.81 0.41 2 2

OuedSouf 31 1.29 1.27 0.11 0.18 0.17 0.09 0 0

Tamenrast 78 3.25 2.21 0.50 0.40 0.86 0.44 7 5

Na = Number of Alleles, Naa = Number of average alleles, Ne = Number of eective alleles =

1 / (Sum pi^2), He = Gene diversity = 1 - Sum pi^2 Where pi is the frequency of the i

allele for

the population, Ho = Observed Heterozygosity = No. of Hets / N, I = Shannon’s Information

Index = -1* Sum (pi * Ln (pi)), PIC = Polymorphic Information Content, Pa = Private allele,

Ra = Rare allele.

Cluster Analysis and PCoA

Based on 24 SSR markers, UPGMA analysis (Figure 1) grouped

the 66 pearl millet accessions into ve clusters. The rst cluster

(Blue) included most accessions from Tamanrasset and In Salah

which were closely associated with several Nigerian genotypes,

highlighting historical connections and gene ow across Sahelian

trade and pastoral routes. A second cluster (Red) was formed by the

Indian accessions, which remained distinct but showed partial anity

with some Tamenrasset lines, suggesting either introductions of Asian

germplasm into Algeria or convergent adaption to arid environments.

A third cluster (Green) contains only Oued Souf accessions, which

form a distinct group likely due to their geographical isolation

near Tunisia and their reduced genetic base. Meanwhile, cluster

4 (Black), included genotypes from Abalessa, Hoggar, In Saleh,

and Adrar, showing more genetic convergence, possibly to local

adaptation or shared ancestry within the region. Finally, cluster 5

(Light blue) grouped only In Saleh accessions, emphasizing their

genetic distinctiveness, probably due to long-term isolation and local

adaptation. As highlighted in similar studies Burkina Faso (Bougma

et al., 2021; Sawadogo et al., 2015) and Sudan (Bashir et al., 2015),

the sharing of seeds through inheritance and informal exchange

often result in the same populations appearing in multiple regions.

This widespread practice, as explained by Mariac et al. (2006); Vom

Brocke et al. (2003), contributes to low genetic dierentiation due to

ongoing gene ow. However, Stich et al. (2010) noted that regional

similarity can also arise from climatic selection pressures, which over

time may narrow genetic diversity.

Genetic distance analysis conrmed these patterns, with values

ranging from 0.23 between Tamanrasset and In Salah to 0.52 between

Tamanrasset and Oued Souf. This demonstrates greater similarity

among neighboring southern regions and stronger divergence between

the geographically distant northern and southern populations.

Figure 1. Dendrogram of 66 pearl millet accessions based on

banding pattern analysis of 24 SSR markers using

Nei 1983 UPGMA method. B1, B2, B3, B5 = In Salah

(Djafou). B4, B7 = In Salah (Ouaini). B6, B8 = In Salah

(Foggaret Ezzoua). B9 = Oued Souf. B10 = Adrar.

B11, B22 = Tamanrasset (Center). B12, B20, B21 =

Tamanrasset (from Niger). B13 = Tamanrasset (Hoggar).

B14 = Tamanrasset (from India). B15 = Tamanrasset (In

M’guel). B16, B18, B19 = Tamanrasset (Abalessa). B17 =

Tamanrasset (In Dalag).

Interestingly, high divergence was also observed within

Tamanrasset between sites such as the center, Hoggar, and In Dalag,

pointing to localized dierentiation even within a single region. The

information available on genetic distances can be used to predict

hybrid performance, as is done previously (Gupta et al., 2018).

Principal Coordinates Analysis (PCoA) supported the dendrogram

results, explaining 44.10 % of total variation across the rst three axes

(21.45 %, 9,69 % and 8.96 %, respectively) (Figure 2). PCoA clearly

separated Nigerien and Indian accessions from Algerian landraces,

while most accessions from Tamanrasset and In Salah clustered

close to Nigerien lines. In contrast, Oued Souf and Adrar occupied

marginal positions on the scatter plot, conrming their isolation and

limited variability.

Analysis of molecular variance (AMOVA) revealed that 66

% of the total variation occurred within individuals, 20 % among

individuals, and only 14 % among populations. This result suggests

that pearl millet exhibits high intra-individual heterozygosity, likely

due its outcrossing nature and extensive gene ow, which allows the

maintenance of genetic diversity at the individual level rather than

between groups. This ndings align with those presented earlier

(Ramya et al., 2018; Bhardwaj et al., 2018; Chandra et al., 2020)95

maintainer (B line, and further reinforce the idea that intrapopulation

variation plays a dominant role in the genetic structure of pearl millet.

The results of this study provide essential baseline information for

the genetic improvement and conservation of pearl millet in Algeria.

The detection of signicant genetic dierentiation among regional

populations indicates the presence of locally adapted alleles that

could be exploited in breeding programs targeting drought tolerance,

earliness, and yield stability under arid and semi-arid conditions.

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Rev. Fac. Agron. (LUZ). 2025, 42(4): e254256 October-December. ISSN 2477-9409.

6-8 |

Figure 2. Principal component analysis (PCoA) using 24 SSR

markers of 66 accessions from four dierent regions

(In Salah, Oued Souf, Adrar and Tamanrasset) based

on Euclidean distance estimates.

The identication of genetically distinct groups also supports

the strategic selection of parental lines to broaden the genetic base

of national breeding materials. Moreover, the molecular proles

generated here can serve as a reference for germplasm conservation

and management, guiding the establishment of a representative

national core collection - how is a small subset that minimizes

genetic redundancy while preserving the maximum genetic diversity

and it is crucial for the ecient management and utilization

of germplasm resources - and facilitating the integration of Algerian

landraces into regional and international genetic resource networks.

Structure Analysis

Structure analysis identied four genetic subpopulations (K= 4),

The bar plot (Figure 3) showed that the rst subpopulation (red)

grouped accessions from Tamanrasset and India, suggesting a

historical exchange of germplasm or convergent adaptation to arid

environments. Subpopulation 2 (green) grouped accessions from

In Salah and Abalessa, and showed the highest level of admixture,

reecting its central geographic location, and possible role as a zone of

gene ow. Subpopulation 3 (blue) encompassed a broader combination

of accessions from regions such as Hoggar, In Dalag, Djafou, Adrar

and Niger. A low level of admixture was in some Adrar accessions

within this group. Subpopulation 4 (yellow) included individuals form

Oued Souf, In M’guel, Djafou, and some from Niger, reecting a high

level of shared ancestry among geographically distant populations.

The result indicates that, despite its geographical isolation, Oued Souf

may have received genetic material through historical seed exchange

or migration. These ndings are largely consistent with the results

obtained from the UPGMA dendrogram and PCoA analysis, which

also showed overlapping genetic relationships between Tamanrasset,

In Salah, and Niger. However, STRUCTURE analysis adds new

insight by showing that Oued Souf is not genetically distinct, but

rather part of a mixed gene pool.

Conclusions

The results reveal substantial genetic variability, with greater allele

richness and heterozygosity in Tamanrasset and In Salah compared with

the narrower diversity in Oued Souf and Adrar. This regional dierentiation

provides useful information for identifying genetically distant parental

lines and strengthening breeding programs aimed at adaptation to arid

conditions. The predominance of genetic variance within individuals

conrms pearl millet’s outcrossing nature and underscores the need

to preserve intra-population diversity through targeted conservation

strategies. Overall, this study enhances the understanding of Algerian

pearl millet diversity and contributes to regional eorts for crop

improvement and food security in dryland environments.

Figure 3. Bar diagram for 66 accessions arranged based on inferred

ancestry at K = 4; Color codes represent the four

subpopulations. Values in the left indicate the membership

coecient (Q). Proportions of colors in each bar indicate the

allelic aliation of the sub-populations. 1-2-3 (B1), 4-5-6

(B2), 7-8-9 (B3), 10-11-12 (B4), 13-14-15 (B5), 16-17-18

(B6), 19-20-21 (B7), 22-23-24 (B8), 64-65-66 (B9), 25-26-

27 (B10), 28-29-30 (B11), 55-56-57 (B12), 31-32-33 (B13),

61-62-63 (B14), 34-35-36 (B15), 37-38-39 (B16), 40-41-42

(B17), 43-44-45 (B18), 46-47-48 (B19), 49-50-51 (B20), 52-

53-54 (B21), 58-59-60 (B22).

Acknowledgment and funding

The authors sincerely thank the technical sta of the Ouamri

experimental station (Médéa) for their assistance with eld

management and sampling.

Funding source

This research was nancially supported by the the national bank

of Tunis (Tunisia) and the Ministry of higher education and scientic

research of Algeria.

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8-8 |