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G3 (Bethesda). 2015 May 8;5(7):1429-38. doi: 10.1534/g3.115.018341.

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

Author information

1
Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
2
MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
3
Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
4
Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
5
USDA-ARS National Clonal Germplasm Repository for Citrus and Dates, University of California, Riverside, California 92507.
6
MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
7
Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar jom2042@qatar-med.cornell.edu.

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 the 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.

KEYWORDS:

date palm; domestication; genotyping-by-sequencing; plant sex chromosomes; population genetics

PMID:
25957276
PMCID:
PMC4502377
DOI:
10.1534/g3.115.018341
[Indexed for MEDLINE]
Free PMC Article

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