Date Palm (Phoenix dactylifera L.) Cultivar Relationships Based on Chloroplast Genotyping


Date palm (Phoenix dactylifera L.) is a member of the genus Phoenix in Arecaceae family. It is the cultivated species in this genus with great economical and social importance in our country. We used three chloroplast regions of rbcLmatK, and trnHpsbA with the following aims: 1. To illustrate the cultivars phylogeny, 2. to identify nucleotide variations and identify the molecular events leading to these variations, and finally, 3. to provide DNA barcode for the studied cultivars. ILD (incongruence length difference test) heterogeneity test revealed that the genes used are not homogenous and produce different evolutionary signals, and the phylogenetic trees constructed by each of these genes differ in topology. A combined data were used to produce phylogenetic tree by SVDQuartets method, to consider evolutionary signals of all three genes together. The SVDQuartets tree and Bayesian-based phylogenetic tree obtained from BEAST were utilized to construct a condensed tree and produce divergence time by RASP program. Date palm cultivars were separated in two distinct major clades corresponding to their geographical distribution, Khuzestan province and Sistan and Baluchestan province. The present study produced some new information with regard to potential DNA barcodes for commercial date palms cultivation and threw light on the date of cultivar divergence in this area.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Availability of Data and Materials

The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.


rbcl :

Ribulose bisphosphate carboxylase large chain

matk :

Maturase K


Simple sequence repeats


Inter simple sequence repeats


Start codon targeted


Randomly amplified polymorphic DNA


Internal transcribed spacer


Maximum likelihood tree


Transitive consistency score


Dentrented correspondence analysis

GTR + G:

General time reversible + gamma distribution


Analysis of molecular variance


  1. Al-Qurainy F, Khan S, Al-Hemaid FM, AliMA TM, Ashraf M (2011) Assessing molecular signature for some potential date (Phoenix dactylifera L.) cultivars from Saudi Arabia, based on chloroplast DNA sequences rpoB and psbA-trnH. Int J Mol Sci 12:6871–6880.

    Article  Google Scholar 

  2. Bahraminejad A, Mohammadi-Nejad G (2015) Genetic diversity analysis of date palm (Phoenix dactylifera L.) genotypes using RAPD markers. Ann Res Rev Biol.

    Article  Google Scholar 

  3. Chao CT, Krueger RR (2007) The date palm (Phoenix dactylifera L.): overview of biology uses and cultivation. Hort Sci 42:1077–1082.

    Article  Google Scholar 

  4. Chou J, Gupta A, Yaduvanshi S, Davidson R, Nute M, Mirarab S, Warnow T (2015) A comparative study of SVDquartets and other coalescent-based species tree estimation methods. BMC Genom 16(10):S2

    Article  Google Scholar 

  5. Flowers JM, HazzouriK M, Gros-Balthazard M, Mo Z, Koutroumpa K, Perrakis A, Ferrand S, Khierallah HSM, Fuller DQ, Aberlenc F, Fournaraki C, Purugganan MD (2019) Cross-species hybridization and the origin of North African date palms. Proc Natl Acad Sci USA 116:1651–1658.

    Article  Google Scholar 

  6. Food and Agriculture Organization of the United Nations (2019)

  7. Gros-Balthazard M, Hazzouri KM, Flowers JM (2018) Genomic insights into date palm origins. Genes 9:502.

    Article  Google Scholar 

  8. Hammer Ø, Harper DA, Ryan PD (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontol Elect 4:9

    Google Scholar 

  9. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of Birds through DNA Barcodes. PLoS Biol 2:e312.

    Article  Google Scholar 

  10. Jain, S. M., & Johnson, D. V (2015) Date palm genetic resources and utilization. J. M. Al-Khayri (Ed.). Springer.

  11. Jaradat AA, Zaid A (2004) Quality traits of date palm fruits in a center of origin and center of diversity. Food Agric Environ 2:208–217

    Google Scholar 

  12. Jurado-Rivera JA, Vogler AP, Reid CA, Petitpierre E, Gómez-Zurita J (2009) DNA barcoding insect-host plant associations. Proc Biol Sci 276:639–648.

    Article  Google Scholar 

  13. Koohdar F, Sheidai M (2019) Molecular investigation in few spices of Dacocephalum in Iran: Species relationship, reticulation and divergence time. Ind Crops Prod 141:111758.

    Article  Google Scholar 

  14. Kress WJ, Erickson DL, Swenson NG, Thompson J, Uriarte M et al (2010) Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a puerto rican forest dynamics plot. PLoS ONE 5:e15409.

    Article  Google Scholar 

  15. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  Google Scholar 

  16. Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S (2015) Plant DNA barcoding: from gene to genome. Biol Rev 90:157–166

    Article  Google Scholar 

  17. Marsafari M, Mehrabi AA (2013) Molecular identification and genetic diversity of iranian date palm (Phoenix dactylifera L.) cultivars using ISSR and RAPD markers. Aust J Crop Sci 7:1160

    Google Scholar 

  18. Mohamoud YA, Mathew LS, Torres MF et al (2019) Novel subpopulations in date palm (Phoenix dactylifera) identified by population-wide organellar genome sequencing. BMCGenom 20:498.

    Article  Google Scholar 

  19. Naeem A, Khan AA, Cheema HMN, Khan IA, Buerkert A (2014) DNA barcoding for species identification in the Pal+mae family. Genet Mol Res 13:10341–10348.

    Article  Google Scholar 

  20. Nemati Z, Zeinalabedini M, Majidian P, Eftekharian Jahromi A, Kiani D (2014) Phylogenetic relationships among Iranian and Spanish date palms (Phoenix dactylifera L.) revealed by microsatellite markers. J Hortic Sci Biotechnol 89:115–120.

    Article  Google Scholar 

  21. Partovi R, Iranbakhsh A, Sheidai M, Ebadi M (2020) Population genetic studies in wild olive (Olea cuspidata) by molecular barcodes and SRAP molecular markers. Caryologia.

    Article  Google Scholar 

  22. Saboori S, Noormohammadi Z, Sheidai M, Marashi S (2019) SCoT molecular markers and genetic fingerprinting of date palm (Phoenix dactylifera L.) cultivars. Genet Resour Crop Evol 67:73–82.

    Article  Google Scholar 

  23. Saboori S, Noormohammadi Z, Sheidai M, Marashi S (2020) Insight into date palm diversity: genetic and morphological investigations. Plant Mol Biol Rep.

    Article  Google Scholar 

  24. Shapcott A, Forster PI, Guymer GP, McDonald WJF, Faith DP, Erickson D et al (2015) Mapping biodiversity and setting conservation priorities for SE Queensland’s rainforests using DNA barcoding. PLoS ONE 10:e0122164.

    Article  Google Scholar 

  25. Sheidai M, Darini S, Talebi SM, Koohdar F, Ghasemzadeh-Baraki S (2019) Molecular systematic study in the genus Linum (Linaceae) in Iran. Acta Bot Hung 61:421–434.

    Article  Google Scholar 

  26. Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4.0b10.

  27. Tabaripoor R, Sheidai M, Talebi SM, Noormohammadi Z (2016) Population genetic diversity and structure in Ziziphora tenuior L.: identification of potential gene pools. Genetika 48:565–578.

    Article  Google Scholar 

  28. Zohary D, Hopf M (2000) Domestication of plants in the old world: the origin and spread of cultivated plants in West Asia, Europe and the Nile Valley (No. Ed. 3). Oxford University Press. ISBN:9780199549061

Download references


We acknowledge Science and Research Branch, Islamic Azad University for providing laboratory. We thank the Iran National Science Foundation (INSF), for partial financial support of this Project (No. 97010700).



Author information




Z.N. and M.Sh: conceptualization of the project; M.Sh.: analyses of data; S.S: data collection and lab work; S.M.: providing samples. The authors accept responsibility for releasing this material. All authors have read and approved the manuscript.

Corresponding authors

Correspondence to Zahra Noormohammadi or Masoud Sheidai.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Consent for Publication

The authors accept responsibility for releasing this material.

Supplementary Information

Below is the link to the Supplementary Information.

Supplementary Information 1 (DOC 59 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Saboori, S., Noormohammadi, Z., Sheidai, M. et al. Date Palm (Phoenix dactylifera L.) Cultivar Relationships Based on Chloroplast Genotyping. Iran J Sci Technol Trans Sci 45, 833–840 (2021).

Download citation


  • Date palm
  • DNA barcode
  • Deep coalescence
  • Chloroplast genes