Gynoecy instability in cucumber ( L.) is due to unequal crossover at the copy number variation-dependent () locus.

Cucumber, is an important vegetable crop, and gynoecy has played a critical role in yield increase of hybrid cucumber production. Cucumber has a unique genetic system for gynoecious sex expression, which is determined by the copy number variation (CNV)-based, dominant, and dosage-dependent () locus. However, this gynoecy expression system seems unstable since monecious plants could often be found in -dependent gynoecious cucumber inbreds. We hypothesized that gynoecy instability (gynoecy loss) may be due to unequal crossing over (UCO) during meiosis among repeat units of the CNV. In this study, using high throughput genome resequencing, fiber-FISH and genomic qPCR analyses, we first confirmed and refined the structure of the locus, which was a CNV of a 30.2-kb tandem repeat. Gynoecious plants contained three genes: , , and , of which is a duplication of but with a recombinant distal promoter that may contribute to gynoecy sex expression. In two large populations from self-pollinated gynoecious inbred lines, 'gynoecy loss' mutants were identified with similar mutation rates (~0.12%). We show that these monecious mutants have lost . In addition, we identified gynoecious lines in natural populations that carry two copies of . We proposed a model to explain gynoecy instability in -dependent cucumbers, which is caused by UCO among units during meiosis. The findings present a convincing case that the phenotypic variation of an economically important trait is associated with the dynamic changes of copy numbers at the locus. This work also has important implications in cucumber breeding.