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. AmiriMichael D. Purugganan

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Article number4680
JournalNature communications
Issue number1
StatePublished - Dec 1 2019

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy


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