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Open Access Highly Accessed Research article

A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms

Lisa S Mathew1, Manuel Spannagl2, Ameena Al-Malki3, Binu George1, Maria F Torres4, Eman K Al-Dous1, Eman K Al-Azwani1, Emad Hussein5, Sweety Mathew1, Klaus FX Mayer2, Yasmin Ali Mohamoud1, Karsten Suhre6 and Joel A Malek146*

Author Affiliations

1 Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar

2 MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany

3 Biotechnolgy Centre, Ministry of Environment, Doha, Qatar

4 Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar

5 Agricultural Affairs Department, Ministry of Environment, Doha, Qatar

6 Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar

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BMC Genomics 2014, 15:285  doi:10.1186/1471-2164-15-285

Published: 15 April 2014



The date palm is one of the oldest cultivated fruit trees. It is critical in many ways to cultures in arid lands by providing highly nutritious fruit while surviving extreme heat and environmental conditions. Despite its importance from antiquity, few genetic resources are available for improving the productivity and development of the dioecious date palm. To date there has been no genetic map and no sex chromosome has been identified.


Here we present the first genetic map for date palm and identify the putative date palm sex chromosome. We placed ~4000 markers on the map using nearly 1200 framework markers spanning a total of 1293 cM. We have integrated the genetic map, derived from the Khalas cultivar, with the draft genome and placed up to 19% of the draft genome sequence scaffolds onto linkage groups for the first time. This analysis revealed approximately ~1.9 cM/Mb on the map. Comparison of the date palm linkage groups revealed significant long-range synteny to oil palm. Analysis of the date palm sex-determination region suggests it is telomeric on linkage group 12 and recombination is not suppressed in the full chromosome.


Based on a modified gentoyping-by-sequencing approach we have overcome challenges due to lack of genetic resources and provide the first genetic map for date palm. Combined with the recent draft genome sequence of the same cultivar, this resource offers a critical new tool for date palm biotechnology, palm comparative genomics and a better understanding of sex chromosome development in the palms.

Sex chromosome; Genotyping by sequencing; Comparative genomics