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.

Genomic in situ hybridization using total genomic DNA extracted from the C genome diploid species Avena eriantha (2n = 2x = 14, genome CpCp) was used to identify monosomics (2n = 6x − 1 = 41) of the constituent genomes of the hexaploid cultivated oat A. sativa L. cv. Sun II (2n = 6x = 42, genomes AACCDD). The results demonstrate 3 AD/C and 6 C/AD chromosome translocations, indicate that five of the missing monosomics are derived from the C genome, and show that there are duplicates within the partial monosomic series. Chromosome polymorphisms between some monosomic lines are also demonstrated.

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