Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations

Abstract

Background and aims: Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species.

Methods: Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite.

Key results: Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species.

Conclusions: This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool.

Keywords: Arecaceae; Date palm; Phoenix dactylifera; SSR markers.; genetic diversity; genetic structure; nuclear microsatellite; plastid minisatellite.

Fig. 1.

Origin of the 295 date palm accessions classified into ten groups and two regions: I and II as defined according to their spatial and genetic proximity. Region I, Mauritania, Algerian, Morocco, Tunisia and Egypt; region II, Djibouti, Oman, the UAE, Iraq and Pakistan. The colours correspond to the genetic clusters defined by STRUCTURE analysis, with cluster I in green and cluster II in red.

Fig. 2.

Inferred population structure for K = 2 to K = 6 as the presumed number of sub-populations within the date palm collection, including 295 accessions. The bar plot chart, generated by DISTRUCT, depicts classifications with the highest probability among assumed clusters in the date palm groups. Each individual is represented by a vertical bar, partitioned into coloured segments representing the proportion of the individual’s genome in the K clusters. The date palm groups are separated by a black line.

Fig. 3.

Frequencies of the occidental (red column charts) and oriental (green column charts) chlorotypes.

Fig. 4.

NJ clustering of geographic groups based on D_AS genetic distance values, as well as the distribution of the genetic clusters within each of them. The colours correspond to genetic clusters defined by the STRUCTURE analysis, as reported in Fig. 1 with cluster I in green and cluster II in red (pie charts). The numbers next to the nodes indicate bootstrap support percentages in 1000 pseudoreplicates.

Fig. 5.

Discriminant analysis of principal components (DAPC) on SSR data of genotypes. The colours of the groups correspond to the geographic groups. Axes 1 and 2 explain 83 % of the total variance (shaded vertical bars in the eigenvalue histogram). Maur, Mauritania; Mc, Morocco; Al, Algeria; Tn, Tunisia; Eg, Egypt; Dj, Djibouti; Ir, Iraq; Om, Oman; Pak, Pakistan.