Genetic Diversity of Iraqi Date Palms Revealed By Microsatellite Polymorphism

in Journal of the American Society for Horticultural Science

Genetic diversity in 30 date palm (Phoenix dactylifera L.) cultivars in Iraq representing 24 female and six male cultivars was investigated using 22 microsatellite [simple sequence repeat (SSR)] primers. The tested SSR markers showed a high level of polymorphism. A total of 188 alleles were detected at the 22 loci ranging from three to 21 with an average of 8.54 alleles per locus. The average of heterozygosity for all cultivars was 0.503; genetic distance among cultivars varied from 0.171 to 0.938 indicating diverse relationships. The cultivar Ghanami Akhder was highly divergent from ‘Ghnami Ahmer’, whereas ‘Jamal Al-Dean’ was very closely related to ‘Qitaz’. Unweighted pair group method arithmetic average ordered date palm cultivars into two main clusters. Principal coordinate analysis exhibited the similar clusters of cultivars as in the dendrogram.

Abstract

Genetic diversity in 30 date palm (Phoenix dactylifera L.) cultivars in Iraq representing 24 female and six male cultivars was investigated using 22 microsatellite [simple sequence repeat (SSR)] primers. The tested SSR markers showed a high level of polymorphism. A total of 188 alleles were detected at the 22 loci ranging from three to 21 with an average of 8.54 alleles per locus. The average of heterozygosity for all cultivars was 0.503; genetic distance among cultivars varied from 0.171 to 0.938 indicating diverse relationships. The cultivar Ghanami Akhder was highly divergent from ‘Ghnami Ahmer’, whereas ‘Jamal Al-Dean’ was very closely related to ‘Qitaz’. Unweighted pair group method arithmetic average ordered date palm cultivars into two main clusters. Principal coordinate analysis exhibited the similar clusters of cultivars as in the dendrogram.

Date palm (2n = 2x = 36) is considered of great socioeconomic importance in the Arabian region. The tree has been, and is still, at the center of comprehensive agricultural development. It is believed to have originated from Mesopotamia (Wrigley, 1995). The numbers of known date palm cultivars that are distributed all over the world are ≈5000 of which ≈600 are found in Iraq. Iraq is one of the largest date-producing countries in the world. Before 1991, Iraq was the largest producer of dates in the world (Food and Agriculture Organization of the United Nations, 2008) and had the largest date forest in the world (MacFarquhar, 2003). However, during the Gulf and Iran–Iraq wars, large numbers of date palm trees were destroyed.

Wars and sanctions imposed on Iraq have negatively affected both the production and natural genetic diversity of the crop in Iraq and inhibited the much-needed impetus to rebuild the date palm industry. Development of suitable DNA molecular markers for this crop may allow researchers to estimate genetic diversity, which will ultimately lead to the genetic conservation of date palm. The success of particular genetic conservation or breeding programs is dependent on understanding the amount and distribution of the genetic variation already present in the genetic pool (Jubrael et al., 2005). Morphological traits have been used to describe such genetic variation in date palm cultivars (Barreveld, 1993), which are mainly related to the fruit and influenced by the environment (Askari and Al-Khalifah, 2003; Sedra et al., 1993, 1998). In addition, biochemical studies, including isozyme and activity analyses of peroxidases, have been used to characterize date palms in Morocco and Tunisia (Baaziz, 1988; Baaziz and Saaidi, 1988; Bendiab et al., 1998; Majourhat et al., 2002; Ould Salem Mohamed et al., 2001). As such, analysis does not reflect precisely that polymorphisms occurred (Al-Jibouri and Adham, 1990).

DNA marker analysis in date palm is recently in the development stage. Askari and Al-Khalifah (2003) analyzed the genetic diversity among 13 different cultivars using random amplified polymorphic DNA (RAPD) markers. Similar reports are published for North African cultivars (Hussein et al., 2002; Sedra et al., 1998). Amplified fragment length polymorphism (AFLP) markers (Vos et al., 1995) were also been used for genetic fingerprinting and mapping for this crop. Jubrael et al., (2005) and Khierallah et al. (2011) used AFLP fingerprinting to characterize a number of Iraqi date palm cultivars. Microsatellites, also known as SSR, are ideal DNA markers for population studies and genetic mapping as a result of their abundance, high level of polymorphism, dispersion throughout diverse genomes, ease to assay by polymerase chain reaction (PCR), and ease to disseminate among laboratories (Udupa and Baum, 2001). Microsatellite markers were used for investigation of genetic diversity in date palm (Billotte et al., 2004). Zehdi et al. (2004) applied these markers to characterize Tunisian cultivars, whereas Al-Ruqaishi et al. (2008) used these primers to screen and analyze the genetic diversity among clonal genotypes of Omani cultivars. Recently, many researchers in date palm-producing countries have used SSR markers to genotype cultivars. Elshibli and Korpelainen (2008) investigated genetic diversity in Sudan germplasm representing 37 female and 23 male accessions using 16 SSR primers. In Qatar, Ahmed and Al-Qaradawi (2009) used 10 primers to analyze genetic diversity among 15 cultivars. Akkak et al. (2009) developed 17 additional microsatellite markers. Hamwieh et al. (2010) developed 1000 SSR markers in date palm, mining genome sequencing data for this vital crop. The aim of this study is intended to characterize the genotype for 30 Iraqi important date palm cultivars using SSR markers.

Materials and Methods

Plant materials.

Leaves were collected from 30 well-defined reference Iraqi date palm cultivars grown in date palm stations belong to the Ministry of Agriculture (Table 1). Twenty-two female cultivar samples were collected from Al-Mahaweel Date Palm Station, Hilla Governorate, 80 km south of Baghdad. The remaining eight cultivar samples were collected from Al-Za'afarania Date Palm Station, Baghdad (Fig. 1). Total genomic DNA was extracted from young and healthy leaves according to the procedure mentioned by Benito et al. (1993) with minor modifications. After purification, the resultant DNA was quantified on 1% agarose gel electrophoresis as described by Sambrook et al. (1989).

Table 1.

Names, gender, and sources of collection of 30 date palm cultivars grown in Iraq.

Table 1.
Fig. 1.
Fig. 1.

Sample collection sites of date palm in Iraq.

Citation: Journal of the American Society for Horticultural Science J. Amer. Soc. Hort. Sci. 136, 4; 10.21273/JASHS.136.4.282

Microsatellite amplification.

A total of 33 date palm-specific primer pairs were tested; 16 of them were developed by Billotte et al. (2004) and 17 were developed by Akkak et al. (2009) as indicated in Table 2. PCR was performed in a total mixture of 20 μL containing: 13.9 μL H2O, 50 ng of total cellular DNA (2 μL) as template, 1 μL/PCR buffer (Roche, Mannheim, Germany), 1 μL of 0.2 mm of dNTP PCR mix (Roche), 0.1 μL (0.625 U) of Taq DNA polymerase (Roche) and1 μL of 0.2 mm of each primer using forward primer end labeled (6FAM, NED, or TET). Amplifications were performed in a thermocycler (Applied Biosystems, Carlsbad, CA) under the following conditions: a denaturation step of 5 min at 95 °C followed by 35 cycles of 30 s at 95 °C, 1 min at 52 °C and 1 min at 72 °C, and a final extension step at 72 °C for 7 min. At the testing stage, amplification products were separated by electrophoresis according to their molecular weight in 1.4% agarose gels and then detected by staining with ethidium bromide as described by Sambrook et al. (1989). The DNA profiles were visualized on an ultraviolet transilluminator and documented by using a gel documentation system (Alpha Innotech Imaging Station; Cell Biosciences, Santa Clara, CA). For final analyses, 2 μL of amplified DNA (diluted to 1/10) and 8 μL of (Rox) DNA standard size (Applied Biosystems) were loaded into 96-well plates. Genotyping was carried out using an automatic DNA analyzer (Model 3100; Applied Biosystems). Amplifications were performed at least twice and only reproducible products were taken into account for further data analysis.

Table 2.

Name, motif repeat, and sequence of 33 simple sequence repeat primers used for genotyping 30 Iraqi date palm cultivars.

Table 2.

Simple sequence repeat genotyping.

Electropherogram data were analyzed by using Foundation Data Collection software (Genetic Analyser Data Collection Version 2.0; Applied Biosystems). Allele size scoring was performed by Gene Mapper software (Version 3.7; Applied Biosystems). The Jaccard similarity matrix (Jaccard, 1908) was used for cluster analysis using the unweighted pair group method arithmetic average to study the genetic relationships among the cultivars. Jaccard similarity index, major allele frequency, heterozygosity, gene diversity, and polymorphism information content estimation were done using a software package (PowerMarker Version 1.31; Liu and Muse 2005). The phylogenetic diagram was drawn by PAST software [Version 1.91 (Hammer et al., 2001)] on the basis of Hamming similarity index with 100 bootstrap. Principal coordinate analysis (PCA) was performed according to Euclidean similarity index using the PAST software.

Results

The 33 primer pairs of Akkak et al. (2009) and Billotte et al. (2004) were tested for their ability to generate expected SSR banding patterns in Iraqi date palms. A total of 22 primers showed polymorphic bands among the 30 cultivars (24 female and six male) successfully (Table 3).

Table 3.

Major allele frequency, number of genotypes showed polymorphic bands, number of alleles generated, heterozygosity, gene diversity, and polymorphism information content (PIC) estimated by 22 simple sequence repeat markers in 30 Iraqi date palm cultivars.

Table 3.

The genetic diversity was widely varied among cultivars ranging from 0.168 to 0.923 at loci mPdCIR057 and PDCAT 18, respectively, with an average of 0.695. The 22 primers resulted in a total of 188 alleles and ranged from three to 21 alleles with an average of 8.545 alleles per locus. However, the major allele frequency ranged from 0.140 to 0.909 for PDCAT18 and mPdCIR057, respectively, with an average of 0.436. High levels of heterozygosity were detected in female cultivars with an average of 0.503 (Table 3). Genetic distance among cultivars varied from 0.171 to 0.938 indicating diverse relationships. The cultivar Ghanami Akhder is highly divergent from ‘Ghanami Ahmer’, whereas ’Jamal Al-Dean’ was very closely related to ‘Qitaz’. Genetic relationships among the 30 cultivars based on 22 microsatellite loci with bootstrapping values is shown in Figure 2. Cluster analysis revealed the presence of two major clusters denoted A and B. Cluster A consisted of three cultivars (Khekri, Barhi, and Smeasmi), whereas Cluster B consisted of three subclusters (denoted as B1, B2, and B3). Subcluster B1 consisted of 10 cultivars (Shwethi Asfar, Baw Adem, Deari, Ghulami, Zahdi, Meer Haj, Greatli, Usta Umran, Um Al-Blaliz, and Khestawi). Subcluster B2 consisted of four cultivars (Buliani, Maktom Asfar, Shwethi Ahmer, and Chipchab). Subcluster B3 consisted of 11 cultivars (Bream, Leelwi, Tabarzal, Ashrasi, Helawi, Um Al-Dihen, Guntar, Qul Husaini, Khadrawi, Jamal Al-Dean, and Qitaz). The two male cultivars, Ghanami Akhder and Ghnami Ahmer, were highly divergent from other cultivars and within each other and were not involved in any cluster (Fig. 2).

Fig. 2.
Fig. 2.

Genetic relationships among 30 Iraqi date palm cultivars based on 22 microsatellite loci with 100 bootstrap.

Citation: Journal of the American Society for Horticultural Science J. Amer. Soc. Hort. Sci. 136, 4; 10.21273/JASHS.136.4.282

Data were analyzed using PCA based on 22 SSR loci representing 57% of the total variation. The results of the first two PC1 and PC2 axes exhibited the similar clusters of cultivars as in the dendrogram (Fig. 3).

Fig. 3.
Fig. 3.

Principal coordinate analysis (PCA) of 30 Iraqi date palm cultivars based on 22 microsatellite loci.

Citation: Journal of the American Society for Horticultural Science J. Amer. Soc. Hort. Sci. 136, 4; 10.21273/JASHS.136.4.282

Discussion

It is well known that Iraq is one of the richest countries in the diversity of date palm cultivars with an estimated number of 600 cultivars. Discrimination between cultivars is based on phenotypic differences, which are often influenced by the environment. In this study, microsatellite genotyping was used to examine the genetic diversity and genetic relationships among 30 cultivars grown widely in Iraq. Although the frequency of microsatellite varies among species, they are abundant, dispersed throughout the genome, and show higher levels of polymorphism than other genetic markers. These features, coupled with their ease of detection, had suggested being useful molecular markers. Their potential for automation and inheritance in a codominant manner are additional advantages when compared with other types of molecular tools (Holton, 2001). The microsatellites examined in this study were highly polymorphic possessing a great number of alleles (188 alleles) distributed in 30 date palm cultivars. The number of detected alleles per locus in this study (8.54) was higher than 7.6 alleles per locus that scored by Zehdi et al. (2004) in 46 date palm cultivars cultivated in Tunisia and those studied by Ahmed and Al-Qaradawi (2009) representing 15 cultivars grown in Qatar. The mean heterozygosity value detected in the Iraqi cultivars was 0.503, indicating the presence of higher genetic diversity. Date palm growers believe that ‘Ghanami Akhder’ and ‘Ghnami Ahmer’ are two clones belonging to the same cultivar. The present investigation revealed high divergence between those two cultivars, thus suggesting they are independent cultivars and confirming the results of Al-Khateeb and Jubrae (2006) who used RAPD markers for the same purpose.

Jubrael et al. (2005) and Khierallah et al. (2011) suggested a common genetic basis among date palm genotypes despite the differences in fruit characters and tree morphology. Other authors reported similar results in Tunisian date palm (Sedra et al., 1998; Zehdi et al., 2004). The long history of date palm domestication with an unknown origin (Wrigley, 1995) and the nature of date palm culture may have played an important role in the composition of date palm genomes (Elshibli and Korpelainen, 2008). New cultivars may appear as a result of the continuous selection carried out by farmers after sexual reproduction. Exchange of propagules, which are a mixture of vegetative and seed-propagated materials, is conducted between farmers. All of these processes together may result in a mixed genome in date palm within the country (Elshibli and Korpelainen, 2008).

Results of the present study using SSR analysis showed a high level of polymorphism among Iraqi cultivars. However, the cultivar nomenclature and classification in Iraq still remains to be based on fruit characters, including morphological, physical, and chemical traits.

In conclusion, Iraqi date palm germplasm requires further investigation and adoption of proper markers that may assist in identifying the economically and agronomically important cultivars.

Literature Cited

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    • Export Citation
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    • Search Google Scholar
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    • Search Google Scholar
    • Export Citation
  • UdupaS.M.BaumM.2001High mutation rate and mutational bias at (TAA)n microsatellite loci in chickpea (Cicerarietinum L.)Mol. Genet. Genomics26510971103

    • Search Google Scholar
    • Export Citation
  • VosP.HogersR.BleekerM.ReijansM.Van de LeeT.HornesM.FrijtersA.PotJ.PelemanJ.KuiperM.ZabeauM.1995AFLP a new technique for DNA fingerprintingNucleic Acids Res.2344074414

    • Search Google Scholar
    • Export Citation
  • WrigleyG.1995Date palm (Phoenix dactylifera L.)399403SmarttJ.SimmondsN.W.The evolution of crop plantsLongmanLondon, UK

  • ZehdiS.TrifiM.BillotteN.MarakchiM.PintaudJ.C.2004Genetic diversity of Tunisian date palms (Phoenix dactylifera L.) revealed by nuclear microsatellite polymorphismHereditas141278287

    • Search Google Scholar
    • Export Citation

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Contributor Notes

This project was supported by a grant from Tottori University and funds from BMZ (Bundesministerium fur Wirtschaftliche Zusammenarbeit und Entwicklung), Germany, and the State Board of the Agriculture Research, Ministry of Agriculture, Iraq.We acknowledge the technical support of A. Sabbagh (International Center for Agricultural Research in the Dry Areas, Aleppo, Syria).

Corresponding author. E-mail: khierallah70@yahoo.com.

  • View in gallery

    Sample collection sites of date palm in Iraq.

  • View in gallery

    Genetic relationships among 30 Iraqi date palm cultivars based on 22 microsatellite loci with 100 bootstrap.

  • View in gallery

    Principal coordinate analysis (PCA) of 30 Iraqi date palm cultivars based on 22 microsatellite loci.

  • AhmedT.Al-QaradawiA.2009Molecular phylogeny of Qatari date palm genotypes using simple sequence repeat markerBiotechnology8126131

  • AkkakA.ScariotV.DorelloT.BoccacciP.BeltramoC.BottaR.2009Development and evaluation of microsatellite markers in (Phoenix dactylifera L.) and their transferability to other Phoenix speciesBiol. Plant.53164166

    • Search Google Scholar
    • Export Citation
  • Al-JibouriA.A.M.AdhamK.M.1990Biochemical classification of date palm male cultivarsJ. Hort. Sci.65725729

  • Al-KhateebT.A.JubraelJ.M.2006The use of RAPD markers for sex and male cultivars identification in (Phoenix dactylifera L.) in IraqActa Hort.736162170

    • Search Google Scholar
    • Export Citation
  • Al-RuqaishiI.A.DaveyM.AldersonP.MayesS.2008Genetic relationships and genotype tracing in date palm (Phoenix dactylifera L.) in Oman based on microsatellite markersPlant Genet. Resources617072

    • Search Google Scholar
    • Export Citation
  • AskariE.Al-KhalifahN.S.2003Molecular phylogeny of date palm (Phoenix dactylifera L.) cultivars from Saudi Arabia by DNA fingerprintingTheor. Appl. Genet.10712661270

    • Search Google Scholar
    • Export Citation
  • BaazizM.1988The activity and preliminary characterisation of peroxidases in leaves of cultivars of date palm (Phoenix dactylifera L.)New Phytol.111403411

    • Search Google Scholar
    • Export Citation
  • BaazizM.SaaidiM.1988Preliminary identification of date palm cultivars by esterase isoenzymes and peroxidase activitiesCan. J. Bot.668993

    • Search Google Scholar
    • Export Citation
  • BarreveldW.H.1993Date palm productsFAO Agr. Serv. Bul. 101Food and Agriculture Organization of the United NationsRome, Italy

  • BendiabK.BaazizM.MajourhatK.1998Preliminary date palm cultivar composition of moroccan palm groves as revealed by leaf isozyme phenotypesBiochem. Syst. Ecol.267182

    • Search Google Scholar
    • Export Citation
  • BenitoC.FigueirasA.M.ZaragozalC.GallegoF.J.Dela PenalA.1993Rapid identification of Trijticeaegeno types from single seed using the polymerase chain reactionJ. Plant Mol. Biol.21181183

    • Search Google Scholar
    • Export Citation
  • BillotteN.MarseillacN.BrottierP.NoyerJ.L.Jacquemoud ColletJ.P.MoreauC.CouvreurT.ChevallierM.H.PintaudJ.C.RisterucciA.M.2004Nuclear microsatellite markers for the date palm (Phoenix dactylifera L.): Characterization and utility across the genus Phoenix and in other palm generaMol. Ecol. Notes4256258

    • Search Google Scholar
    • Export Citation
  • ElshibliS.KorpelainenH.2008Microsatellite markers reveal high genetic diversity in date palm (Phoenix dactylifera L.) germplasm from SudanGenetica134251260

    • Search Google Scholar
    • Export Citation
  • Food and Agriculture Organization of the United Nations2008Food and Agriculture Organization statistical databases (FAOSTAT)12 Feb. 2011. <http://faostat.fao.org/site/339/default.aspx>

    • Export Citation
  • HammerØ.HarperD.A.T.RyanP.D.2001PAST: Palaeontological statistics software package for education and data analysisPalaeontol. Electronica419

    • Search Google Scholar
    • Export Citation
  • HamwiehA.FarahJ.MoussallyS.Al-Sham'aaK.AlmerK.KhierallahH.UdupaS.LababidiS.MalekJ.AaouineandM.BaumM.2010Development of 1000 microsatellite markers across the date palm (Phoenix dactylifera L.) genomeActa Hort.882269277

    • Search Google Scholar
    • Export Citation
  • HoltonT.A.2001Plant gnotyping by analysis of microsatellites1527HenryR.J.Plant genotyping: The DNA fingerprinting of plantsCABICambridge, UK

    • Search Google Scholar
    • Export Citation
  • HusseinE.H.AdawyS.S.El-KhishinD.MoharamH.El-ItribyH.2002Genetic variability studies and molecular fingerprinting of some Egyptian date palm (Phoenix dactylifera L.) cultivars. I. A preliminary study using RAPD markersArab J. Biotechnol.5217224

    • Search Google Scholar
    • Export Citation
  • JaccardP.1908Nouvel le srescherchessur la distribution floraleBulletin de la Socieìteì vaudoise des sciences naturelles44223270

  • JubraelJ.M.S.UdupaS.BaumM.2005Assessment of AFLP-based genetic relationships among date palm (Phoenix dactylifera L.) varieties of IraqJ. Amer. Soc. Hort. Sci.130442447

    • Search Google Scholar
    • Export Citation
  • KhierallahH.S.BaderS.M.BaumM.HamwiehA.2011Assessment of genetic diversity for some Iraqi date palms (Phoenix dactylifera L.) using AFLP markersAfr. J. Biotechnol.in press

    • Search Google Scholar
    • Export Citation
  • LiuK.MuseS.V.2005PowerMarker: Integrated analysis environment for genetic marker dataBioinformatics2121282129

  • MacFarquharN.2003Forbidden fruit: Iraq dates hit by war and sanctions1 July 2010. <http://www.iht.com/ articles/83194.html>

    • Export Citation
  • MajourhatK.BendiabK.MedraouiL.BaazizM.2002Diversity of leaf peroxidases in date palm (Phoenix dactylifera L.) as in an example of marginal (seedling derived) palm grovesSci. Hort.953138

    • Search Google Scholar
    • Export Citation
  • Ould Salem MohamedA.TrifiM.SakkaH.RhoumaA.MarrakchiM.2001Genetic inheritance analysis of four enzymes in date palm (Phoenix dactylifera L.)Genet. Resources Crop Evol.48361368

    • Search Google Scholar
    • Export Citation
  • SambrookJ.FritschE.F.ManiatisT.1989Molecular cloning: A laboratory manual2nd EdCold Spring Harbor Laboratory PressCold Spring Harbor, NY

    • Export Citation
  • SedraM.H.El-FilaliH.FriraD.1993Observarions sur quelques caracteristiques phenotypiques et agronomiques du fruit des varietes et clones du palmier dattier selectionnesAl-Awami82105120

    • Search Google Scholar
    • Export Citation
  • SedraM.H.LashermesP.TrouslotM.HamonS.1998Identification and genetic diversity analysis of date palm (Phoenix dactylifera L.) varieties of Morocco using RAPD markersEuphytica1037582

    • Search Google Scholar
    • Export Citation
  • UdupaS.M.BaumM.2001High mutation rate and mutational bias at (TAA)n microsatellite loci in chickpea (Cicerarietinum L.)Mol. Genet. Genomics26510971103

    • Search Google Scholar
    • Export Citation
  • VosP.HogersR.BleekerM.ReijansM.Van de LeeT.HornesM.FrijtersA.PotJ.PelemanJ.KuiperM.ZabeauM.1995AFLP a new technique for DNA fingerprintingNucleic Acids Res.2344074414

    • Search Google Scholar
    • Export Citation
  • WrigleyG.1995Date palm (Phoenix dactylifera L.)399403SmarttJ.SimmondsN.W.The evolution of crop plantsLongmanLondon, UK

  • ZehdiS.TrifiM.BillotteN.MarakchiM.PintaudJ.C.2004Genetic diversity of Tunisian date palms (Phoenix dactylifera L.) revealed by nuclear microsatellite polymorphismHereditas141278287

    • Search Google Scholar
    • Export Citation
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