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Next-generation sequencing has enabled the sequencing of the date palm chloroplast (Yang et al., 2010; Sabir et al., 2014), mitochondria (Fang et al., 2012; Sabir et al., 2014) and nuclear genomes (Al-Dous et al., 2011; Al-Mssallem et al., 2013). Following the sequencing of ‘Hallas’, a Saudi cultivar, assembly of many additional cultivars has been completed (Hazzouri et al., 2015). A genetic map has been constructed using c.4000 markers based on a genotype sequencing approach of ‘Hallas’ seedlings (Mathew et al., 2014). The map spans almost 1300 cM, with an average of 1.9 cM per 1 Mb in the genomic sequence. Detailed analysis of many cultivars has revealed elevated inbreeding in some cultivars, detected by long stretches of homozygosity (Hazzouri et al., 2015). In some cultivars, e.g. ‘Ajwa’ and ‘Medjool’, up to 25% of the genomic segments are homozygous. Since date is dioecious and therefore an obligate cross-pollinator, this inbreeding may be due to repeated crosses while selecting for specific traits or by crosses in small populations with limited genepools in isolated oases.

Sequencing of several female cultivars and males that originated from repeated backcrosses to these cultivars enabled the detection of a polymorphism associated with sex and identification of a specific region in the date palm genome responsible for sex determination. This locus functions as an XY inheritance system where the female is homogametic and the male is heterogametic (Al-Dous et al., 2011). Sex-specific markers that are heterozygous only in males support a non-recombining sex-related region (Cherif et al., 2013). The sex-determining region is located in linkage group 12 of the genetic map and spans across c.26 cM (Mathew et al., 2014). The markers enable identification of sex in very young seedlings (Bekheet and Hanafy, 2011; Al-Mahmoud et al., 2012; Dakhlaoui-Dkhil et al., 2013; Awan et al., 2017) and can be valuable for breeding programmes.

During date cultivation in the desert oases, traditional selection for fruit quality together with vegetative propagation resulted in narrowing the genetic variation. Until recently, it was difficult to accurately identify the origin of domestication and the wild progenitors. Date palm germplasm can be divided into two pools: an eastern one from Asia and a Western one originated in Africa, with many admixture cultivars. The highest admixture levels occur in the geographically intermediate areas, mainly east Africa, i.e. Egypt and Sudan (Hazzouri et al., 2015; Mathew et al., 2015; Zehdi-Azouzi et al., 2015). A similar East–West structure of the germplasm was also found using male-specific SSR markers (Cherif et al., 2013) and chloroplast SSR markers (Zehdi-Azouzi et al., 2015). However, the chloroplasts markers, representing maternal inheritance, were not always related to the geographical origin, particularly in Africa. This pattern may suggest ancient movements of female genotypes from the east and their pollination with local western males. A further secondary structure within the western germplasm cluster was found in south-eastern Nigerian populations (Zango et al., 2017). The recent discovery of a wild date palm population in Oman (Gros-Balthazard et al., 2017) further confirms the eastern origin of date palm and its early cultivation.

Several studies have characterized the gene and protein expression patterns of different date palm tissues to form a catalogue of gene expression (Zhang et al., 2012). The date palm is unique in the accumulation of sugar in its pulp. Focusing especially on fruit development Bourgis et al. (2011), Yin et al. (2012) and Marondedze et al. (2014) detected genes and proteins that function in important pathways. Carbohydrate metabolism and especially sugar synthesis were specifically induced during fruit ripening (Yin et al., 2012). Comparison of gene expression during oil palm (accumulating oil) and date palm fruit development and fruit ripening detected induction of different metabolic pathways in the two species (Bourgis et al., 2011).

Date palms tolerate abiotic stresses, i.e. drought and salinity; however, some cultivars are more sensitive than others to these stresses (Al Kharusi et al., 2017). Salinity stress was studied at the gene expression level (Radwan et al., 2015; Yaish et al., 2015, 2017b). Following salinity stress, expression patterns of many transcripts in roots and leaves were modified. Moreover, the level of at least 54 and 25 microRNAs were affected by the salinity stress in leaves and roots, respectively (Yaish et al., 2015). Changes were also detected at the proteomic level as a result of biotic, salinity and drought stress (El Rabey et al., 2016). These analyses provide candidate genes and pathways that are associated with responses to saline conditions and will provide basic data for further characterization of salt stress-responsive genes in date palms. Part of the tolerance of salinity might involve Na⁺ exclusion in the leaves and regulation of oxidative damage and photosynthesis (Al Kharusi et al., 2017). Analysis of the endophytic microbiome of date palm root suggests an important role of microbes in the tolerance of dates to salt stress (Yaish et al., 2017a).