Genome-wide association mapping of date palm fruit traits

Khaled M. Hazzouri, Muriel Gros-Balthazard, Jonathan M. Flowers, Dario Copetti, Alain Lemansour, Marc Lebrun, Khaled Masmoudi, Sylvie Ferrand, Michael I. Dhar, Zoë A. Fresquez, Ulises Rosas, Jianwei Zhang, Jayson Talag, Seunghee Lee, David Kudrna, Robyn F. Powell, Ilia J. Leitch, Robert R. Krueger, Rod A. Wing, Khaled M. A. Amiri () and Michael D. Purugganan ()
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Khaled M. Hazzouri: New York University Abu Dhabi, Saadiyat Island
Muriel Gros-Balthazard: New York University Abu Dhabi, Saadiyat Island
Jonathan M. Flowers: New York University Abu Dhabi, Saadiyat Island
Dario Copetti: University of Arizona
Alain Lemansour: UAE University
Marc Lebrun: CIRAD, UMR Qualisud
Khaled Masmoudi: UAE University
Sylvie Ferrand: New York University Abu Dhabi, Saadiyat Island
Michael I. Dhar: New York University Abu Dhabi, Saadiyat Island
Zoë A. Fresquez: New York University
Ulises Rosas: New York University
Jianwei Zhang: University of Arizona
Jayson Talag: University of Arizona
Seunghee Lee: University of Arizona
David Kudrna: University of Arizona
Robyn F. Powell: Kew, Richmond
Ilia J. Leitch: Kew, Richmond
Robert R. Krueger: United States Department of Agriculture-Agriculture Research Service
Rod A. Wing: University of Arizona
Khaled M. A. Amiri: UAE University
Michael D. Purugganan: New York University Abu Dhabi, Saadiyat Island

Nature Communications, 2019, vol. 10, issue 1, 1-14

Abstract: Abstract Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform genome-wide association studies (GWAS) of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor VIRESCENS gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crops, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.

Date: 2019
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DOI: 10.1038/s41467-019-12604-9

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