A genome-wide survey of date palm cultivars supports two independent domestication events in Phoenix dactylifera

Authors: MATTHEW, L - Weill Medical College - Cornell; SEIDEL, M - Helmholtz Centre; GEORGE, B - Weill Medical College - Cornell; MATTHEW, S - Weill Medical College - Cornell; SPANNAGL, M - Helmholtz Centre; HABERER, G - Helmholtz Centre; TORRES, M - Weill Medical College - Cornell; AL-DOUS, E - Weill Medical College - Cornell; AL-AZWANI, E - Weill Medical College - Cornell; DIBOUN, I - Weill Medical College - Cornell; Krueger, Robert; MAYER, K - Helmholtz Centre; MOHAMOUD, Y - Weill Medical College - Cornell; SHURE, K - Weill Medical College - Cornell; MALEK, J - Weill Medical College - Cornell

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/5/2015
Publication Date: 5/8/2015
Publication URL: http://handle.nal.usda.gov/10113/61680
Citation: Matthew, L.S., Seidel, M.A., George, B., Matthew, S., Spannagl, M., Haberer, G., Torres, M.F., Al-Dous, E.K., Al-Azwani, E.K., Diboun, I., Krueger, R., Mayer, K.F., Mohamoud, Y.A., Shure, K., Malek, J.A. 2015. A genome-wide survey of date palm cultivars supports two independent domestication events in Phoenix dactylifera. Genes Genomes Genetics. 5:1429-1438.

Interpretive Summary: The date palm and its fruit that offers high energy content, nutrition and portability is intimately tied to the history of human civilization and migration. Early archaeological evidence, historical records, and the presence of related Phoenix species growing in close proximity suggested that it was first cultivated in the Arabian Gulf basin. With a lack of clear wild ancestor, the location and effects of date palm domestication has been debated. We conduct the first genome-wide genetic survey of date palm cultivars from multiple geographic regions. Our results suggest there were at least two independent domestication events with one occurring in North Africa. Despite multiple empires that allowed free movement across the date palm cultivating regions, little genetic admixture is observed at the geographic extremes. These findings will adjust our views of the history of fruit tree domestication. Our results also shed light on the development of the sex chromosomes in the Phoenix species by showing high population variation along the X allele of the newly described sex chromosome in date palm. Analysis of polymorphisms that segregate with geographical region show enrichment of functional categories and lay the foundation for understanding selective pressure differences in the various geographical regions.

Technical Abstract: The date palm (Phoenix dactylifera L.) is one of the oldest cultivated trees and is a key fruit crop in many arid regions of the world. There are hundreds of commercial cultivars with distinct fruit shapes, colors and sizes growing mainly from the west of North Africa to India. However, the origin of date palm domestication is still uncertain and few studies have attempted to document genetic diversity across multiple regions. We conducted genotyping-by-sequencing on 70 female cultivar samples from across the date palm-growing regions, including four Phoenix species as outgroup. Here, for the first time we generate genome-wide genotyping data for 13,000 - 65,000 SNPs in a diverse set of date palm fruit and leaf samples. Our analysis provides the first genome-wide evidence confirming recent findings that the date palm cultivars segregate into two main regions of shared genetic background from North Africa and the Arabian Gulf. We show that the boundaries between these two geographical regions contain admixed date palms and that the genetic origin of new cultivars being bred can be distinguished despite conflicting geographical data. We identify genomic regions with high densities of geographically segregating SNPs and functionally analyze genes within the region. With sampling only from date-producing females, we also observe higher levels of allele fixation on the recently described X- chromosome than on the autosomes. In contrast to the popular theory of a single domestication event in the Arabian Gulf, our results fit a model with two domestication centers including date palms autochthonous to North Africa. Distinct genetic groups remain despite multiple empires allowing trade between these two regions for Millennia. These results adjust our understanding of human agriculture history and will provide the foundation for more directed functional studies and a better understanding of genetic diversity in date palm.