Genome-wide association mapping of date palm fruit traits

Authors: HAZZOURI, K - New York University; GROS-BALTHAZARD, M - New York University; FLOWERS, J - New York University; COPETTI, D - University Of Arizona; LEMANSOUR, A - United Arab Emirates; LEBRUN, M - Cirad, France; MASMOUDI, K - United Arab Emirates; FERRAND, S - New York University; DHAR, M - New York University; FRESQUEZ, S - New York University; ROAS, U - New York University; ZHANG, J - University Of Arizona; TALAG, J - University Of Arizona; LEE, S - University Of Arizona; KUDRNA, D - University Of Arizona; POWELL, R - Royal Botanical Gardens; LEITCH, I - Royal Botanical Gardens; Krueger, Robert; WING, R - King Abdullah University Of Science And Technology; AMIRI, K - United Arab Emirates; PURUGGANAN, M - New York University

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2019
Publication Date: 10/15/2019
Citation: Hazzouri, K.M., Gros-Balthazard, M., Flowers, J.M., Copetti, D., Lemansour, A., Lebrun, M., Masmoudi, K., Ferrand, S., Dhar, M.I., Fresquez, S., Roas, U., Zhang, J., Talag, J., Lee, S., Kudrna, D., Powell, R.F., Leitch, I.J., Krueger, R., Wing, R., Amiri, K.M., Purugganan, M.D. 2019. Genome-wide association mapping of date palm fruit traits. Nature Communications. https://doi.org/10.1038/s41467-019-12604-9.
DOI: https://doi.org/10.1038/s41467-019-12604-9

Interpretive Summary: Date palm (Phoenix dactylifera) is an important fruit crop in the Middle East and North Africa. This paper describes the association between various parts of the genome and date fruit quality traits. An improved reference genome was developed and used in conjunction with high density SNP data from whole genome resequencing of a large mapping population to perform GWAS mapping of 21 fruit traits. Associations of specific areas of the genome were confirmed for date fruit color and sugar composition and were correlated with similar findings in other fruit crops.

Technical Abstract: Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa, and like many perennial species, little is known about the genetics of their domestication and diversification. To facilitate genetic mapping of important date palm fruit traits, we developed an improved reference genome sequence for P. dactylifera using long reads from single-molecule, real-time (SMRT) technology that is 772.3 Mb in length, has a contig N50 of 897.2 Kb, and 28,595 high-confidence gene models. We use this assembly in conjunction with high density SNP data from whole genome re-sequencing of a large mapping population to perform GWAS mapping of the date palm sex determining region and 21 fruit traits. We confirmed an association between an R2R3-MYB transcription factor (VIRESCENS) and fruit color variation and propose a model for date palm fruit color based on sequence variation at this locus, including a retrotransposon insertion polymorphism in exon 3 and a start codon mutation. We also report a significant GWAS peak for fruit sugar composition, and analysis of gene expression and enzyme activity between varieties suggests that deletion polymorphisms in these multiple linked invertase loci are associated with sugar composition in date palm fruits. Homologues of R2R3-MYB transcription factors and invertase have been implicated in fruit color and sugar composition traits in fruits of other crop species, demonstrating the importance of parallel evolution in domestication and the evolution of crop species.