Genotyping-by-sequencing identifies date palm clone preference in agronomics of the State of Qatar

Abstract

Understanding the genetic diversity in a crop population is key to its targeted breeding for desired traits, such as higher yields, better fruit quality and resistance to disease and changing climates. Date fruits represent a major crop in the Middle East and are key to achieving future food independence in arid countries like Qatar. We previously determined the genome of the date palm Phoenix dactylifera and showed that date palm trees world-wide divide into two distinct subpopulations of Eastern and Western origins. Here we applied a resource of SNPs from 179 commercially available date fruits to assess the genetic diversity of date palm trees grown in the State of Qatar. We found that palm trees in Qatar are mainly of Eastern origin, and that their genetic diversity doesn't associate with regions of the State. Together with targeted genetic assays, our resource can be used in the future for date palm cultivar identification, to aid selecting suitable cultivars for targeted breeding, to improve a country's date palm genetic diversity, and to certify the origin of date fruits and trees.

Fig 1. A rooted hierarchical cluster tree showing the relationship between 179 Phoenix dactylifera cultivars and samples from 19 other Phoenix species using 13,803 markers.

The edge length represents the (1-Identity-by-state) distances. The highlighted clusters in the tree are samples from other Phoenix Species (yellow background), Eastern cultivars originating from the Arabian Gulf (white background) and Western cultivars originating from North Africa (blue background). Colored labels indicate that these variants have already been classified in our previous work [22]. Green labels indicate previously identified Eastern cultivars, red labels indicate Western cultivars, and black labels are new in this study. All previously reported variants cluster in the present much larger study, and in exactly the same way, showing the robustness of this approach.

Fig 2. GPS locations of 55 date palm trees from which leaves have been collected in the State of Qatar.

Collection sites around the Eastern coast line are representative for municipalities in which date palm trees are grown. Few trees are found in the Western part of Qatar and in the desert region to the South. Map was created using U.S. Geological Survey (USGS) Topological Imagery as a base map in MATLAB (The Mathworks, Natick, USA).

Fig 3. A rooted hierarchical cluster tree showing the relationship between date palm cultivars and date palm trees from the state of Qatar.

The tree highlights the clustering of date palm trees from the State of Qatar with common date palm cultivars. The edge length represents the (1-Identity-by-state) distances. For clarity, Western cultivars (larger triangles) and outgroup (small triangles) are collapsed as no municipality samples cluster in one of them. Date palm trees collected in the State of Qatar are labeled in pink. The labels are colored based on their annotations reported in our previous work [22]. Green labels indicate cultivars that were annotated as Eastern cultivars, and black labels are new cultivars used in this study. The complete tree is presented in S1 Fig.