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

BMC Genomics

Joel A Malek⁶  Karsten Suhre⁶  Yasmin Ali Mohamoud¹  Klaus FX Mayer²  Sweety Mathew¹  Emad Hussein⁴  Eman K Al-Azwani¹  Eman K Al-Dous¹  Maria F Torres³  Binu George¹  Ameena Al-Malki⁵  Manuel Spannagl²  Lisa S Mathew¹ 

[1] Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar;MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany;Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar;Agricultural Affairs Department, Ministry of Environment, Doha, Qatar;Biotechnolgy Centre, Ministry of Environment, Doha, Qatar;Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar

关键词: Comparative genomics;    Genotyping by sequencing;    Sex chromosome;   

Others  :  1217471
DOI  :  10.1186/1471-2164-15-285

 received in 2013-12-27, accepted in 2014-04-04,  发布年份 2014

【 摘 要 】

Background

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.

Results

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.

Conclusions

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.

【 授权许可】

   
2014 Mathew et al.; licensee BioMed Central Ltd.

【 图 表 】

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