Genome-Wide Methylation and Transcriptomic Analyses Reveal Hormonal Crosstalk in Ethylene-Mediated Parthenocarpy of Zucchini

Abstract Parthenocarpy is a valuable trait for greenhouse squash production, but the molecular basis of fruit set without pollination or fertilization remains unclear. The ethylene-insensitive etr2b mutation confers parthenocarpic fruit development, indicating that ethylene acts as a negative regulator of fruit set. Here, we analyzed the hormonal profile, the transcriptomic and epigenetic changes occurring in unfertilized ovaries of both WT and etr2b at anthesis and 3 days post anthesis (DPA). At 3 DPA, WT ovaries aborted while those of the mutant showed parthenocarpic development, with no significant transcriptomic changes detected in etr2b ovaries between 0 and 3 DPA. The delayed flower opening observed in the mutant supports the idea that ethylene-mediated parthenocarpy in etr2b is a passive mechanism that maintains ovary growth when the regulatory decision at anthesis is not activated. By contrast, many transcriptomic changes between WT and etr2b fruits were found at 3 DPA. Downstream analysis of DEGs revealed the hormonal crosstalk underlying etr2b -induced parthenocarpy. Although global DNA methylation levels remained stable, analysis revealed a redistribution of methylation with specific genomic regions exhibiting methylation or demethylation in the mutant relative to WT. Among the 4748 DEGs associated with parthenocarpy, approximately 15% contained DMRs, evidencing epigenetic regulation mediated by the etr2b mutation. The accumulation of the ethylene precursor ACC, together with ABA promoted WT ovary abortion at 3 DPA through a jasmonate-independent pathway, whereas cytokinins, auxins, gibberellins, and brassinosteroids acted as positive regulators of etr2b parthenocarpy. Several genes have been identified as putative regulators of ethylene-insensitive parthenocarpic fruit development.