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 A. Malek, Deborah Thirkhill, Ghulam S. Markhand, Robert R. Krueger, Abdelouahhab Zaid and Michael D. Purugganan ()
Additional contact information
Khaled M. Hazzouri: Center for Genomics and Systems Biology, New York University Abu Dhabi
Jonathan M. Flowers: Center for Genomics and Systems Biology, New York University Abu Dhabi
Hendrik J. Visser: Date Palm Research and Development Unit, United Arab Emirates University
Hussam S. M. Khierallah: Date Palm Research Unit, College of Agriculture, PO Box 47054, University of Baghdad
Ulises Rosas: Center for Genomics and Systems Biology, 12 Waverly Place, New York University
Gina M. Pham: Center for Genomics and Systems Biology, 12 Waverly Place, New York University
Rachel S. Meyer: Center for Genomics and Systems Biology, New York University Abu Dhabi
Caryn K. Johansen: Center for Genomics and Systems Biology, 12 Waverly Place, New York University
Zoë A. Fresquez: Center for Genomics and Systems Biology, 12 Waverly Place, New York University
Khaled Masmoudi: International Center for Biosaline Agriculture, Academic City, Al Ruwayyah 2
Nadia Haider: Department of Molecular Biology and Biotechnology
Nabila El Kadri: Technical Center of Dates, Ministry of Agriculture
Youssef Idaghdour: New York University Abu Dhabi
Joel A. Malek: Genomics Core Laboratory, Weill Cornell Medical College in Qatar
Deborah Thirkhill: Arizona State University Date Palm Collection, Arizona State University Tempe
Ghulam S. Markhand: Date Palm Research Institute (DPRI), Shah Abdul Latif University
Robert R. Krueger: United States Department of Agriculture
Abdelouahhab Zaid: Date Palm Research and Development Unit, United Arab Emirates University
Michael D. Purugganan: Center for Genomics and Systems Biology, New York University Abu Dhabi

Nature Communications, 2015, vol. 6, issue 1, 1-11

Abstract: 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.

Date: 2015
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DOI: 10.1038/ncomms9824

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