oa Identification of gender-associated molecular markers in the date palm (Phoenix dactylifera) genome

Date palm (Phoenix dactylifera) is one of the most distributed and well-adapted fruit crops in the Middle East, and plays an important role in the history and diet of the Arab world. Dates constitute the primary exportable agricultural product in Qatar and current efforts are being made to improve its production. Over the years, clonal propagation has been used to maintain selected varieties with desirable morphological traits, leading to the establishment of uniform palm orchards. This, however, significantly reduces genetic diversity among palm plantations, making them potentially more susceptible to pests and diseases. Although research on date palm has increased over the past years, the genetic markers responsible for desirable agricultural traits, such as fruit color, fruit size, ripening time and gender remain unknown. In commercial plantations, one hundred fruit bearing female trees can be pollinated with a single non-bearing male tree. Still, half of the date palm offspring that is planted is expected to be male individuals. One of the biggest challenges that date production encounters is that female trees can only be distinguished after flowering, which occurs five to eight years after planting. Previous cytological studies have suggested the presence of heteromorphic sex chromosomes in date palm, however enzymatic approaches intended to anticipate gender determination have been unsuccessful. The recent genome sequencing of P. dactylifera in WCMC-Q, allowed the identification of a gender-linked genomic region. This single nucleotide polymorphism (SNP)-rich region was shown to segregate with gender, and is predicted to extend to 24 scaffolds. Only a limited amount of information about this region is currently available, and this study proposes the use of a deep-sequencing approach to significantly improve the date palm genome assembly, with an emphasis on the male/female segregating region. A bacterial artificial chromosome (BAC) library, with a 12x genome coverage and an average insert size of 125 Kb was constructed. BAC-end sequencing of at least 96 clones, associated with the polymorphic sex-linked region, will allow the generation of an optical and physical maps of the sex-determination region. This will be the first time that a full genetic map of a male/female region will be available for a plant. Our main goal is to ultimately generate molecular markers that have the potential to allow identification and selection of female trees before germination. Furthermore, standardization of this sequencing procedure, will also allow us to characterize other genomic regions associated with desirable commercial properties of these fruits. This in turn, will provide a valuable tool for the development of marker-assisted selection programs, for the improvement of date palm production.