SignificanceDate palm (Phoenix dactylifera L.) is one of the oldest tree crop species in the world and is a major fruit crop of arid regions of the Middle East and North Africa. We use whole-genome sequence data from a large sample of P. dactylifera and its wild relatives to show that hybridization between date palms and Phoenix theophrasti Grueter—a species endemic to the Eastern Mediterranean—is associated with the diversification of date palm.

Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.

Date Palm is a major environmental and economic factor in arid climates in many countries around the world. Microsatellite markers have been proven to be very powerful in plant genome analysis because they are locus-specific, codominant, highly polymorphic and highly reproducible. In date palm only few microsatellite markers have been developed so far. Recently, the Cornell Medical College in Qatar issued a draft assembly of the date palm genome ('Khalas') generated by whole genome shotgun next generation DNA sequencing. In this paper, we analyzed the microsatellite motifs across the date palm genome. The results indicated that the most abundant type of microsatellite repeats are dinucleotide repeats (52442 motifs) followed by trinucleotide (28503 motifs) and pentanucleotide repeats (12873 motifs). The frequencies of tetra-nucleotide and hexa-nucleotide repeats were less across the genome (5555 and 5810 motifs, respectively). The most common type of dinucleotide repeat was GA (48.7%) followed by AT (37%). Out of 28645 trinucleotide repeats, TAA and GAA repeats were the most abundant repeats (28.1 and 27.1%) respectively. More than 1090 new microsatellite markers could be designed. The primary test for 50 primer pairs revealed that 28 (56%) were functional and 19 (38%) yielded polymorphic PCR products. We wish that the results of our study will be a starting point for researchers making use of the markers for genetic mapping and diversity analysis of date palm.

Genetic diversity in 30 date palm (Phoenix dactylifera L.) cultivars in Iraq representing 24 female and six male cultivars was investigated using 22 microsatellite [simple sequence repeat (SSR)] primers. The tested SSR markers showed a high level of polymorphism. A total of 188 alleles were detected at the 22 loci ranging from three to 21 with an average of 8.54 alleles per locus. The average of heterozygosity for all cultivars was 0.503; genetic distance among cultivars varied from 0.171 to 0.938 indicating diverse relationships. The cultivar Ghanami Akhder was highly divergent from ‘Ghnami Ahmer’, whereas ‘Jamal Al-Dean’ was very closely related to ‘Qitaz’. Unweighted pair group method arithmetic average ordered date palm cultivars into two main clusters. Principal coordinate analysis exhibited the similar clusters of cultivars as in the dendrogram.

Iraq is the birthplace of the date palm, and historically it was the domestication center of this crop. Moreover, for some years, Iraq was the largest producer of dates in the world. Many factors negatively have affected both the production and natural genetic diversity of the crop. However, efforts are being made by the Iraqi authorities and researchers alike to compensate for the serious damage the date palm sector has experienced over the past 30 years. New approaches have been introduced including biotechnology, grove management, pest control, and industrial practices. Production limitations have been diagnosed and constraints are on their way to be resolved. Date palm plantations are under stress from many biotic and abiotic factors including key insect pests like dubas bug, lesser date moth, trunk and stalk borers, and Old World date mite. Date palm diseases cause serious damages to date palm trees especially where stress factors are present such as palm weakness, soil salinity, high water table, borers, and tree aging. The use of plant tissue culture to support propagation by offshoots is necessary and started in the early 1980s. Both direct organogenesis and callus induction with subsequent asexual embryo formation protocols were achieved. Approximately, 600 date palm cultivars were grown in Iraq before 1980; however, currently their number is reduced to 500. Morphological