Genomic Insights into Date Palm Origins

Abstract

With the development of next-generation sequencing technology, the amount of date palm (Phoenix dactylifera L.) genomic data has grown rapidly and yielded new insights into this species and its origins. Here, we review advances in understanding of the evolutionary history of the date palm, with a particular emphasis on what has been learned from the analysis of genomic data. We first record current genomic resources available for date palm including genome assemblies and resequencing data. We discuss new insights into its domestication and diversification history based on these improved genomic resources. We further report recent discoveries such as the existence of wild ancestral populations in remote locations of Oman and high differentiation between African and Middle Eastern populations. While genomic data are consistent with the view that domestication took place in the Gulf region, they suggest that the process was more complex involving multiple gene pools and possibly a secondary domestication. Many questions remain unanswered, especially regarding the genetic architecture of domestication and diversification. We provide a road map to future studies that will further clarify the domestication history of this iconic crop.

Origins and insights into the historic Judean date palm based on genetic analysis of germinated ancient seeds and morphometric studies

“…Phoenicia, a maritime trading nation occupying the coastal areas of modern northern Israel, Lebanon, and Syria (1500 to 300 BCE), was also historically associated with cultivation and trade of date palms (32). We can speculate that later west to east germplasm exchanges to this region may have been associated with domesticated varieties originating in Phoenician City States in North African (e.g., Carthage in present-day Tunisia) (32), where oasis agriculture appeared relatively late in the archaeological record (3).…”

Novel subpopulations in date palm (Phoenix dactylifera) identified by population-wide organellar genome sequencing

“…The subpopulations show strong distinction between North African (Western) and Arabian Gulf (Eastern) cultivars while admixture is observed in cultivars from Egypt, Sudan and the Middle East. High genetic diversity in the North Africa subpopulation argues against it simply a result of colonization from a middle-east population [8] though studies have shown a significant portion of the North Africa date palm genome likely originates from the Arabian Gulf date palm [3, 4, 10]. Despite these results, many have suggested that the date palm was originally domesticated in the region of modern day Iraq as the historical record of date palm is richest in that region [11].…”

Integration of ethnobotany and population genetics uncovers the agrobiodiversity of date palms of Siwa Oasis (Egypt) and their importance to the evolutionary history of the species

“…Date palms were domesticated at least in the Persian Gulf region, followed by diffusion to North Africa (for review, Gros-Balthazard et al, 2018). A recent study, based on whole-genome re-sequencing data, indicated that North African date palms have been introgressed by the Aegean Phoenix theophrasti, and today, about 5-18% of their genome originates from this wild relative or a P. theophrasti-like population (Flowers et al, 2019).…”

“…Date palms exist mostly as either cultivated or feral (i.e. uncultivated but derived from cultivated palms) domesticated forms (for review, Gros-Balthazard et al, 2018). Only a few relictual populations of its wild progenitor are known today in Oman (Gros-Balthazard et al, 2017), even though Tuaregs of the Tassili n'Ajjer (Algeria) consider it to be wild in their gardens (Battesti, 2004).…”