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 Anthony 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 Anthony Wing, Khaled M A AmiriMichael D Purugganan

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74 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)
Journal	Nature communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-12604-9
State	Published - Oct 17 2019

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We are very grateful to Dr. Ahmed Mohammed Saif Al-Falasi for allowing us access to his date palm farm. Without his generosity and dedication to date palm culture, this research would not have been possible. We are also grateful to the United Arab Emirates Ministry of Environment and Water for allowing us use of their farm. We would like to thank Jae Young Choi, Adrian Platts, Katherine Dorph, Ziyi Mo, Marc Arnoux, Nizar Drou, Fayizal Kunhi, Nasser Al-Ansari, Hussam Khierallah, H. Jorik Visser, and the USDA-ARS staff at Thermal, CA, and the staffs at UAE MOEW and Al-Falasi Farms for help in various aspects of this work. This study was funded in part by grants from the UAE Ministry of Presidential Affairs to Khalifa Center for Genetic Engineering and Biotechnology, and the New York University Abu Dhabi Research Institute, the US National Science Foundation Plant Genome Research Program and the Zegar Family Foundation to M.D.P. U.R. was funded by UNAM-PAPIIT grant IN211319.

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10.1038/s41467-019-12604-9

https://repository.kaust.edu.sa/bitstream/10754/660044/1/s41467-019-12604-9.pdf

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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). https://doi.org/10.1038/s41467-019-12604-9

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title = "Genome-wide association mapping of date palm fruit traits.",

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.",

author = "Hazzouri, {Khaled M} and Muriel Gros-Balthazard and Flowers, {Jonathan M} and Dario Copetti and Alain Lemansour and Marc Lebrun and Khaled Masmoudi and Sylvie Ferrand and Dhar, {Michael I} and Fresquez, {Zo{\"e} A} and Ulises Rosas and Jianwei Zhang and Jayson Talag and Seunghee Lee and David Kudrna and Powell, {Robyn F} and Leitch, {Ilia J} and Krueger, {Robert R} and Wing, {Rod Anthony} and Amiri, {Khaled M A} and Purugganan, {Michael D}",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We are very grateful to Dr. Ahmed Mohammed Saif Al-Falasi for allowing us access to his date palm farm. Without his generosity and dedication to date palm culture, this research would not have been possible. We are also grateful to the United Arab Emirates Ministry of Environment and Water for allowing us use of their farm. We would like to thank Jae Young Choi, Adrian Platts, Katherine Dorph, Ziyi Mo, Marc Arnoux, Nizar Drou, Fayizal Kunhi, Nasser Al-Ansari, Hussam Khierallah, H. Jorik Visser, and the USDA-ARS staff at Thermal, CA, and the staffs at UAE MOEW and Al-Falasi Farms for help in various aspects of this work. This study was funded in part by grants from the UAE Ministry of Presidential Affairs to Khalifa Center for Genetic Engineering and Biotechnology, and the New York University Abu Dhabi Research Institute, the US National Science Foundation Plant Genome Research Program and the Zegar Family Foundation to M.D.P. U.R. was funded by UNAM-PAPIIT grant IN211319.",

year = "2019",

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day = "17",

doi = "10.1038/s41467-019-12604-9",

language = "English (US)",

volume = "10",

journal = "Nature communications",

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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. https://doi.org/10.1038/s41467-019-12604-9

TY - JOUR

T1 - Genome-wide association mapping of date palm fruit traits.

AU - Hazzouri, Khaled M

AU - Gros-Balthazard, Muriel

AU - Flowers, Jonathan M

AU - Copetti, Dario

AU - Lemansour, Alain

AU - Lebrun, Marc

AU - Masmoudi, Khaled

AU - Ferrand, Sylvie

AU - Dhar, Michael I

AU - Fresquez, Zoë A

AU - Rosas, Ulises

AU - Zhang, Jianwei

AU - Talag, Jayson

AU - Lee, Seunghee

AU - Kudrna, David

AU - Powell, Robyn F

AU - Leitch, Ilia J

AU - Krueger, Robert R

AU - Wing, Rod Anthony

AU - Amiri, Khaled M A

AU - Purugganan, Michael D

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We are very grateful to Dr. Ahmed Mohammed Saif Al-Falasi for allowing us access to his date palm farm. Without his generosity and dedication to date palm culture, this research would not have been possible. We are also grateful to the United Arab Emirates Ministry of Environment and Water for allowing us use of their farm. We would like to thank Jae Young Choi, Adrian Platts, Katherine Dorph, Ziyi Mo, Marc Arnoux, Nizar Drou, Fayizal Kunhi, Nasser Al-Ansari, Hussam Khierallah, H. Jorik Visser, and the USDA-ARS staff at Thermal, CA, and the staffs at UAE MOEW and Al-Falasi Farms for help in various aspects of this work. This study was funded in part by grants from the UAE Ministry of Presidential Affairs to Khalifa Center for Genetic Engineering and Biotechnology, and the New York University Abu Dhabi Research Institute, the US National Science Foundation Plant Genome Research Program and the Zegar Family Foundation to M.D.P. U.R. was funded by UNAM-PAPIIT grant IN211319.

PY - 2019/10/17

Y1 - 2019/10/17

N2 - 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.

AB - 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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UR - http://www.nature.com/articles/s41467-019-12604-9

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U2 - 10.1038/s41467-019-12604-9

DO - 10.1038/s41467-019-12604-9

M3 - Article

C2 - 31615981

SN - 2041-1723

VL - 10

JO - Nature communications

JF - Nature communications

IS - 1

ER -

Genome-wide association mapping of date palm fruit traits.

Abstract

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