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.

Citation
Hazzouri, K. M., Gros-Balthazard, M., Flowers, J. M., Copetti, D., Lemansour, A., Lebrun, M., … Purugganan, M. D. (2019). Genome-wide association mapping of date palm fruit traits. Nature Communications, 10(1). doi:10.1038/s41467-019-12604-9

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.

Publisher
Springer Nature

Journal
Nature communications

DOI
10.1038/s41467-019-12604-9

Additional Links
http://www.nature.com/articles/s41467-019-12604-9https://www.nature.com/articles/s41467-019-12604-9.pdf

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