Mapping and Sequencing of Sex Determination Genes in Phoenix Dactylifera
Authors: Torres Maria Fernanda , Mathew Lisa S. , Purchase Candice , Mohamoud Yasmin A. , Malek Joel A. 
Published: July 2019

Date palm (Phoenix dactylifera) is one of the most important crops in many arid land cultures. The date fruits are rich in essential nutrients, minerals, vitamins and fiber, making them a critical food source linked to the history of the Arab world. The most frequent method of propagation is by offshoots, which guarantees that the characteristics and quality of the fruit are maintained; however, it significantly reduces the genetic variability of the date palm plantations, making them extremely vulnerable to pests and diseases. During the past few years, advances on date palm research have provided some information about the molecular markers associated with different desirable agronomical traits, including gender and fruit color.

We recently showed that P. dactylifera employs and XY sex-chromosome system, and generated a genetic map that localized this gender determination locus to the lower arm of linkage group 12. Based on this initial information, we designed markers to screen a Bacterial Artificial Chromosome (BAC) library of a male P. dactylifera to sequence the X and Y alleles in date palm. A combination of approaches that include next-generation (Illumina) and Single Molecule, Real-Time (SMRT) Sequencing (PacBio) of more than one hundred BAC clones, have allowed us to map eighty markers to eleven larger DNA contigs, containing the corresponding female and male specific regions, spanning approximately 4Mb. However, multiple sequence gaps still exist within and between the sequenced region, and further analysis have indicated that the borders of most assembled contigs correspond to repetitive elements, which likely constitute a big portion of the unassembled DNA sequences. Non-recombining regions of sex chromosomes, particularly the Y chromosome, are highly repetitive due to degeneration, making it more challenging to design markers and extend the assembled sequences by chromosome walking.

These observations, led us to propose a parallel approach to complement and advance on the initial sequencing strategy. Date palm, and all other thirteen members of the genus Phoenix, are dioecious, with roughly half of the individuals planted from seed expected to be fruit-bearing female trees. The conservation of dioecy in this entire clade in the Palm family (Arecaceae) suggests that in the genus Phoenix, dioecy evolved before speciation. Therefore, we recently started using comparative genomics to analyze male and female individuals from the remaining thirteen Phoenix species, which has allowed us to narrow down the Y-specific region to a very small portion of the genome, containing only a few genes. Our latest findings are providing a new insight into the evolution of plant sex chromosomes and sex determination in date palm. Standardization and validation of new methodologies that allow for large-scale sequencing and analysis of polymorphisms in date palm, will provide valuable tools for the development of marker-assisted selection programs, for the improvement of date palm production. This will allow Qatar to diversify the varieties of dates it grows, and in the near future will allow us to test for the most desirable agricultural traits, which will significantly improve the quality of the fruit, making Qatar a more competitive date producer in the region.