Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation
mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber
(Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of
cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated
with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with
cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the
Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node.
The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated breakinduced
replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for
exploring genes underlying key traits and for facilitating practical breeding in cucumber.