Integration of phytohormones, miRNAs and transcriptome sequencing in cucumber fruit development under...

The molecular mechanisms by which heat stress compromises cucumber yield and quality, particularly the epigenetic regulatory networks, remain largely unknown. Here, we show that miRNAs act as key epigenetic mediators that integrating environmental and hormonal signals to coordinate stress adaptation with fruit development. Using a heat-sensitive cucumber line, we performed a multi-omics analysis, including fruit phenotyping, hormone profiling, and transcriptome and sRNA sequencing across development under heat stress. Our results reveal that heat stress induces regional imbalances in endogenous hormones, especially JA and GA₃, among the medial, proximal, and distal regions of the fruit. Integrated analysis RNA-seq and sRNA-seq data from four developmental stages under normal and high-temperature conditions, we identified 92 DE-miRNAs and 8171 DEGs. Notably, 11 consistently down-regulated DE-miRNAs formed 65 miRNA-mRNA pairs with 24 DEGs (Cor > 0.7, P < 0.01). These regulatory modules participate in maintaining JA and GA₃ homeostasis and signaling, thereby contributing to fruit thermal adaptation and morphogenesis under heat stress. Our findings uncover a potential miRNA-hormone regulatory network that orchestrates fruit adaptation and morphogenesis under heat stress, providing a foundation for understanding stress-induced fruit deformity and offers potential targets for breeding thermotolerant cucumber varieties.