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; Michael D. Purugganan

doi:10.1038/s41467-019-12604-9

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

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73 Scopus citations

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.

Original language	English (US)
Article number	4680
Journal	Nature communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-12604-9
State	Published - Dec 1 2019

ASJC Scopus subject areas

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

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Hazzouri, K. M., Gros-Balthazard, M., Flowers, J. M., Copetti, D., Lemansour, A., Lebrun, M., Masmoudi, K., Ferrand, S., Dhar, M. I., Fresquez, Z. A., Rosas, U., Zhang, J., Talag, J., Lee, S., Kudrna, D., Powell, R. F., Leitch, I. J., Krueger, R. R., Wing, R. A., ... Purugganan, M. D. (2019). Genome-wide association mapping of date palm fruit traits. Nature communications, 10(1), Article 4680. https://doi.org/10.1038/s41467-019-12604-9

Hazzouri, KM, Gros-Balthazard, M, Flowers, JM, Copetti, D, Lemansour, A, Lebrun, M, Masmoudi, K, Ferrand, S, Dhar, MI, Fresquez, ZA, Rosas, U, Zhang, J, Talag, J, Lee, S, Kudrna, D, Powell, RF, Leitch, IJ, Krueger, RR, Wing, RA, Amiri, KMA & Purugganan, MD 2019, 'Genome-wide association mapping of date palm fruit traits', Nature communications, vol. 10, no. 1, 4680. https://doi.org/10.1038/s41467-019-12604-9

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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.",

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AU - Lebrun, Marc

AU - Masmoudi, Khaled

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AU - Fresquez, Zoë A.

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AU - Talag, Jayson

AU - Lee, Seunghee

AU - Kudrna, David

AU - Powell, Robyn F.

AU - Leitch, Ilia J.

AU - Krueger, Robert R.

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AU - Amiri, Khaled M.A.

AU - Purugganan, Michael D.

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Genome-wide association mapping of date palm fruit traits

Abstract

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