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. Improvement of date production through date palm breeding is highly challenging due to the long regeneration times and the lack of knowledge about the genetic markers responsible for desirable agricultural traits. 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 planted from seeds are 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 different individuals from the commercial varieties Khalas, Deglet Noor and Medjool, 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 a complete physical and sequence map of the sex-determination region. Our main goal is to detect the critical mutation that gave rise to male and female separation. This is the firs time such level of detail in a dioecious plant will be achieved. 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.