Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop

Khaled M. Hazzouri, Jonathan M. Flowers, Hendrik J. Visser, Hussam S M Khierallah, Ulises Rosas, Gina M. Pham, Rachel S. Meyer, Caryn K. Johansen, Zoë A. Fresquez, Khaled Masmoudi, Nadia Haider, Nabila El Kadri, Youssef Idaghdour, Joel Malek, Deborah Thirkhill, Ghulam S. Markhand, Robert R. Krueger, Abdelouahhab Zaid, Michael D. Purugganan

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.

Original languageEnglish
Article number8824
JournalNature Communications
Volume6
DOIs
Publication statusPublished - 9 Nov 2015

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sequencing
fruits
genome
crops
polymorphism
Fruits
Middle East
Crops
Fruit
Genes
Polymorphism
Genome
Northern Africa
genes
Sudan
Phoenix (AZ)
Egypt
nucleotides
mutations
admixtures

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemistry(all)
  • Physics and Astronomy(all)

Cite this

Hazzouri, K. M., Flowers, J. M., Visser, H. J., Khierallah, H. S. M., Rosas, U., Pham, G. M., ... Purugganan, M. D. (2015). Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. Nature Communications, 6, [8824]. https://doi.org/10.1038/ncomms9824

Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. / Hazzouri, Khaled M.; Flowers, Jonathan M.; Visser, Hendrik J.; Khierallah, Hussam S M; Rosas, Ulises; Pham, Gina M.; Meyer, Rachel S.; Johansen, Caryn K.; Fresquez, Zoë A.; Masmoudi, Khaled; Haider, Nadia; El Kadri, Nabila; Idaghdour, Youssef; Malek, Joel; Thirkhill, Deborah; Markhand, Ghulam S.; Krueger, Robert R.; Zaid, Abdelouahhab; Purugganan, Michael D.

In: Nature Communications, Vol. 6, 8824, 09.11.2015.

Research output: Contribution to journalArticle

Hazzouri, KM, Flowers, JM, Visser, HJ, Khierallah, HSM, Rosas, U, Pham, GM, Meyer, RS, Johansen, CK, Fresquez, ZA, Masmoudi, K, Haider, N, El Kadri, N, Idaghdour, Y, Malek, J, Thirkhill, D, Markhand, GS, Krueger, RR, Zaid, A & Purugganan, MD 2015, 'Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop', Nature Communications, vol. 6, 8824. https://doi.org/10.1038/ncomms9824
Hazzouri, Khaled M. ; Flowers, Jonathan M. ; Visser, Hendrik J. ; Khierallah, Hussam S M ; Rosas, Ulises ; Pham, Gina M. ; Meyer, Rachel S. ; Johansen, Caryn K. ; Fresquez, Zoë A. ; Masmoudi, Khaled ; Haider, Nadia ; El Kadri, Nabila ; Idaghdour, Youssef ; Malek, Joel ; Thirkhill, Deborah ; Markhand, Ghulam S. ; Krueger, Robert R. ; Zaid, Abdelouahhab ; Purugganan, Michael D. / Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. In: Nature Communications. 2015 ; Vol. 6.
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abstract = "Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.",
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