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

Abstract

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.

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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.

Abbreviations

rbcl :

Ribulose bisphosphate carboxylase large chain

matk :

Maturase K

SSR:

Simple sequence repeats

ISSR:

Inter simple sequence repeats

SCoT:

Start codon targeted

RAPD:

Randomly amplified polymorphic DNA

ITS:

Internal transcribed spacer

ML:

Maximum likelihood tree

TCS:

Transitive consistency score

DCA:

Dentrented correspondence analysis

GTR + G:

General time reversible + gamma distribution

AMOVA:

Analysis of molecular variance

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Acknowledgements

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).

Funding

None.

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Authors

Contributions

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.

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The authors declare that they have no conflict of interest.

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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). https://doi.org/10.1007/s40995-021-01085-5

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Keywords

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