A genome-wide survey of date palm cultivars supports two major subpopulations in Phoenix dactylifera

Lisa Sara Mathew, Michael A. Seidel, Binu George, Sweety Mathew, Manuel Spannagl, Georg Haberer, Maria F. Torres, Eman Aldous, Eman K. Al-Azwani, Ilhem Diboun, Robert R. Krueger, Klaus F.X. Mayer, Yasmin Ali Mohamoud, Karsten Suhre, Joel Malek

Research output: Contribution to journalArticle

18 Citations (Scopus)

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 genomewide 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.

Original languageEnglish
Pages (from-to)1429-1438
Number of pages10
JournalG3: Genes, Genomes, Genetics
Volume5
Issue number7
DOIs
Publication statusPublished - 2015

Fingerprint

Genome
Northern Africa
Single Nucleotide Polymorphism
Civilization
Western Africa
Phoeniceae
Surveys and Questionnaires
X Chromosome
Agriculture
India
Fruit
Color
History
Alleles

Keywords

  • Date palm
  • Domestication
  • Genotyping-bysequencing
  • Plant sex chromosomes
  • Population genetics

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

A genome-wide survey of date palm cultivars supports two major subpopulations in Phoenix dactylifera. / Mathew, Lisa Sara; Seidel, Michael A.; George, Binu; Mathew, Sweety; Spannagl, Manuel; Haberer, Georg; Torres, Maria F.; Aldous, Eman; Al-Azwani, Eman K.; Diboun, Ilhem; Krueger, Robert R.; Mayer, Klaus F.X.; Ali Mohamoud, Yasmin; Suhre, Karsten; Malek, Joel.

In: G3: Genes, Genomes, Genetics, Vol. 5, No. 7, 2015, p. 1429-1438.

Research output: Contribution to journalArticle

Mathew, LS, Seidel, MA, George, B, Mathew, S, Spannagl, M, Haberer, G, Torres, MF, Aldous, E, Al-Azwani, EK, Diboun, I, Krueger, RR, Mayer, KFX, Ali Mohamoud, Y, Suhre, K & Malek, J 2015, 'A genome-wide survey of date palm cultivars supports two major subpopulations in Phoenix dactylifera', G3: Genes, Genomes, Genetics, vol. 5, no. 7, pp. 1429-1438. https://doi.org/10.1534/g3.115.018341
Mathew, Lisa Sara ; Seidel, Michael A. ; George, Binu ; Mathew, Sweety ; Spannagl, Manuel ; Haberer, Georg ; Torres, Maria F. ; Aldous, Eman ; Al-Azwani, Eman K. ; Diboun, Ilhem ; Krueger, Robert R. ; Mayer, Klaus F.X. ; Ali Mohamoud, Yasmin ; Suhre, Karsten ; Malek, Joel. / A genome-wide survey of date palm cultivars supports two major subpopulations in Phoenix dactylifera. In: G3: Genes, Genomes, Genetics. 2015 ; Vol. 5, No. 7. pp. 1429-1438.
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