Ancient Population Structure in Phoenix dactylifera Revealed By Genome-Wide Genotyping of Geographically Diverse Date Palm Cultivars

The date palm was one of the earliest cultivated fruit trees and is intimately tied to the history of human migration. With no true known wild ancestor little is known about the genetic origins and the effect of human cultivation on the date palm. Recent genome projects have just begun to provide the foundation for detailed genetic analysis of the date palm. We applied a modified version of genotyping-by-sequencing to geographically diverse samples of date palm cultivars. For the first time we have generated genome-wide genotypes for between 13,000 and 65,000 SNPs in 70 female cultivars of date palm. Here we confirm that date palm cultivars show at minimum two major genetic backgrounds originating in North Africa and the Arabian Gulf. Cultivars at the boundaries of the two major regions show admixture and may ultimately reveal a third site of domestication. We observe more frequent allele fixation on the recently described X chromosome than on autosomes. We also identify regions of the genome with high levels of geographically segregating SNPs and functionally analyze genes in these regions. Our data supports the recent observations that date palm cultivars show at least two major genetic backgrounds. The data contradicts earlier theories of a single domestication event in the Arabian Gulf. These studies will lead to a clearer understanding of history of human civilization and help design more effective genotype-phenotype studies in the date palm.

Funding for this research was provided by Qatar Foundation’s National Priorities Research Program – Exceptional Award (NPRP-EP) NPRPX-014-4-001