Population Genomics of Date Palms

We present the first comprehensive catalogue of ~7 million single nucleotide polymorphisms (SNPs) in date palms (Phoenix dactylifera) based on whole genome re-sequencing of a worldwide 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 (PAV) 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 (VIR) gene associated with fruit color variation. This whole genome re-sequencing analysis documents patterns of post-domestication diversification and provides a key genomic resource in this economically important perennial tree crop.