Abstract
Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.
Highlights
Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa
The Gulf region holds the oldest evidence of date palm exploitation, with seeds dating to 7100 BP excavated in site remains in Dalma Island, Abu Dhabi and Kuwait[15,16,17]
Seventeen of the cultivars are from Africa (North Africa, Egypt and Sudan), 36 from the Middle East and nine from South Asia (Pakistan; Supplementary Table 1), with the largest sample of 17 varieties in our data set originating from Iraq
Summary
Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. We identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop. The date palm (Phoenix dactylifera L.) is a dioecious, perennial diploid (2n 1⁄4 36) tree in the Arecaceae family and is the most important fruit-bearing crop in arid regions of the Middle East and North Africa[8,9,10]. Alternate hypotheses propose a domestication centre of date palm in North Africa[18], this crop appears B3,000 years later in the archaeological records of this region[19]
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