title: A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations in Phoenix dactylifera.
abstract: The date palm (Phoenix dactylifera L.) is one of the oldest cultivated trees and is intimately tied to the history of human civilization. There are hundreds of commercial cultivars with distinct fruit shapes, colors, and sizes growing mainly in arid lands from the west of North Africa to India. 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 the 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 identify genomic regions with high densities of geographically segregating SNPs and also observe higher levels of allele fixation on the recently described X-chromosome than on the autosomes. Our results fit a model with two centers of earliest cultivation including date palms autochthonous to North Africa. 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.
authors.affiliation: Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
authors.forename: Lisa S
authors.initials: LS
authors.lastname: Mathew
authors.affiliation: MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Seidel
authors.affiliation: Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
authors.forename: Binu
authors.initials: B
authors.lastname: George
authors.affiliation: Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
authors.forename: Sweety
authors.initials: S
authors.lastname: Mathew
authors.affiliation: MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
authors.forename: Manuel
authors.initials: M
authors.lastname: Spannagl
authors.affiliation: MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Haberer
authors.affiliation: Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
authors.forename: Maria F
authors.initials: MF
authors.lastname: Torres
authors.affiliation: Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
authors.forename: Eman K
authors.initials: EK
authors.lastname: Al-Dous
authors.affiliation: Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
authors.forename: Eman K
authors.initials: EK
authors.lastname: Al-Azwani
authors.affiliation: Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
authors.forename: Ilhem
authors.initials: I
authors.lastname: Diboun
authors.affiliation: USDA-ARS National Clonal Germplasm Repository for Citrus and Dates, University of California, Riverside, California 92507.
authors.forename: Robert R
authors.initials: RR
authors.lastname: Krueger
authors.affiliation: MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.affiliation: Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
authors.forename: Yasmin Ali
authors.initials: YA
authors.lastname: Mohamoud
authors.affiliation: MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar.
authors.forename: Karsten
authors.initials: K
authors.lastname: Suhre
authors.affiliation: Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar Weill Cornell Medical College in Qatar, Qatar Foundation, 24144 Doha, Qatar jom2042@qatar-med.cornell.edu.
authors.forename: Joel A
authors.initials: JA
authors.lastname: Malek
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D065749:Phoeniceae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA
keywords: date palm; domestication; genotyping-by-sequencing; plant sex chromosomes; population genetics