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A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations in Phoenix dactylifera

Lisa S. Mathew, Michael A. Seidel, Binu George, Sweety Mathew, Manuel Spannagl, Georg Haberer, Maria F. Torres, Eman K. Al-Dous, Eman K. Al-Azwani, Ilhem Diboun, Robert R. Krueger, Klaus F.X. Mayer, Yasmin Ali Mohamoud, Karsten Suhre and Joel A. Malek
G3: Genes, Genomes, Genetics Early online May 8, 2015; https://doi.org/10.1534/g3.115.018341
Lisa S. Mathew
Weill Cornell Medical College in Qatar;
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Michael A. Seidel
Helmholtz Zentrum München;
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Binu George
Weill Cornell Medical College in Qatar;
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Sweety Mathew
Weill Cornell Medical College in Qatar;
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Manuel Spannagl
Helmholtz Zentrum München;
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Georg Haberer
Helmholtz Zentrum München;
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Maria F. Torres
Weill Cornell Medical College in Qatar;
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Eman K. Al-Dous
Weill Cornell Medical College in Qatar;
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Eman K. Al-Azwani
Weill Cornell Medical College in Qatar;
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Ilhem Diboun
Weill Cornell Medical College in Qatar;
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Robert R. Krueger
USDA-ARS National Clonal Germplasm Repository for Citrus & Dates;
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Klaus F.X. Mayer
Helmholtz Zentrum München;
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Yasmin Ali Mohamoud
Weill Cornell Medical College in Qatar;
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Karsten Suhre
Helmholtz Zentrum München; Weill Cornell Medical College in Qatar
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Joel A. Malek
Weill Cornell Medical College in Qatar;
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  • For correspondence: jom2042@qatar-med.cornell.edu
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Abstract

The date palm (Phoenix dactylifera L.) is one of the oldest cultivated trees and is intimately tied to the history of human civilization. There are hundreds of commercial cultivars with distinct fruit shapes, colors and sizes growing mainly in arid lands from the west of North Africa to India. The origin of date palm domestication is still uncertain and few studies have attempted to document genetic diversity across multiple regions. We conducted genotyping-by-sequencing on 70 female cultivar samples from across the date palm-growing regions, including four Phoenix species as outgroup. Here, for the first time we generate genome-wide genotyping data for 13,000 - 65,000 SNPs in a diverse set of date palm fruit and leaf samples. Our analysis provides the first genome-wide evidence confirming recent findings that the date palm cultivars segregate into two main regions of shared genetic background from North Africa and the Arabian Gulf. We identify genomic regions with high densities of geographically segregating SNPs and also observe higher levels of allele fixation on the recently described X-chromosome than on the autosomes. Our results fit a model with two centers of earliest cultivation including date palms autochthonous to North Africa. These results adjust our understanding of human agriculture history and will provide the foundation for more directed functional studies and a better understanding of genetic diversity in date palm.

  • date palm
  • domestication
  • genotyping-by-sequencing
  • plant sex chromosomes
  • population genetics
  • Received April 2, 2015.
  • Accepted May 5, 2015.
  • Copyright © 2015 Author et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Volume 9 Issue 12, December 2019

G3: Genes|Genomes|Genetics: 9 (12)

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A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations in Phoenix dactylifera

Lisa S. Mathew, Michael A. Seidel, Binu George, Sweety Mathew, Manuel Spannagl, Georg Haberer, Maria F. Torres, Eman K. Al-Dous, Eman K. Al-Azwani, Ilhem Diboun, Robert R. Krueger, Klaus F.X. Mayer, Yasmin Ali Mohamoud, Karsten Suhre and Joel A. Malek
G3: Genes, Genomes, Genetics Early online May 8, 2015; https://doi.org/10.1534/g3.115.018341
Lisa S. Mathew
Weill Cornell Medical College in Qatar;
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Michael A. Seidel
Helmholtz Zentrum München;
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Binu George
Weill Cornell Medical College in Qatar;
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Sweety Mathew
Weill Cornell Medical College in Qatar;
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Manuel Spannagl
Helmholtz Zentrum München;
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Georg Haberer
Helmholtz Zentrum München;
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Maria F. Torres
Weill Cornell Medical College in Qatar;
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Eman K. Al-Dous
Weill Cornell Medical College in Qatar;
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Eman K. Al-Azwani
Weill Cornell Medical College in Qatar;
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Ilhem Diboun
Weill Cornell Medical College in Qatar;
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Robert R. Krueger
USDA-ARS National Clonal Germplasm Repository for Citrus & Dates;
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Klaus F.X. Mayer
Helmholtz Zentrum München;
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Yasmin Ali Mohamoud
Weill Cornell Medical College in Qatar;
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Karsten Suhre
Helmholtz Zentrum München; Weill Cornell Medical College in Qatar
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Joel A. Malek
Weill Cornell Medical College in Qatar;
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  • For correspondence: jom2042@qatar-med.cornell.edu
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Citation

A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations in Phoenix dactylifera

Lisa S. Mathew, Michael A. Seidel, Binu George, Sweety Mathew, Manuel Spannagl, Georg Haberer, Maria F. Torres, Eman K. Al-Dous, Eman K. Al-Azwani, Ilhem Diboun, Robert R. Krueger, Klaus F.X. Mayer, Yasmin Ali Mohamoud, Karsten Suhre and Joel A. Malek
G3: Genes, Genomes, Genetics Early online May 8, 2015; https://doi.org/10.1534/g3.115.018341
Lisa S. Mathew
Weill Cornell Medical College in Qatar;
  • Find this author on Google Scholar
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  • Search for this author on this site
Michael A. Seidel
Helmholtz Zentrum München;
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Binu George
Weill Cornell Medical College in Qatar;
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Sweety Mathew
Weill Cornell Medical College in Qatar;
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Manuel Spannagl
Helmholtz Zentrum München;
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Georg Haberer
Helmholtz Zentrum München;
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Maria F. Torres
Weill Cornell Medical College in Qatar;
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Eman K. Al-Dous
Weill Cornell Medical College in Qatar;
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Eman K. Al-Azwani
Weill Cornell Medical College in Qatar;
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Ilhem Diboun
Weill Cornell Medical College in Qatar;
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Robert R. Krueger
USDA-ARS National Clonal Germplasm Repository for Citrus & Dates;
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Klaus F.X. Mayer
Helmholtz Zentrum München;
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Yasmin Ali Mohamoud
Weill Cornell Medical College in Qatar;
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Karsten Suhre
Helmholtz Zentrum München; Weill Cornell Medical College in Qatar
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Joel A. Malek
Weill Cornell Medical College in Qatar;
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  • For correspondence: jom2042@qatar-med.cornell.edu

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