Integration of phytohormones, miRNAs and transcriptome sequencing in cucumber fruit development under high-temperature stress

Continuous heat stress resulted in abnormal cucumber fruit development. Mult-omics analyses of heat-sensitive cucumber line '75-2' across four developmental stages under HT/NT conditions, revealed miRNA-mediated morphogenesis mechanisms. Integrated phenotyping identified IPA, ZT, JA, and GA3 as key regulators of cell proliferation/expansion. We identified 8,171 DEGs and 147 DE-miRNAs, with GO/KEGG enrichment analyses implicating hormone biosynthesis/response and secondary metabolism pathways as core hormone regulators. Cross-dataset integration refined 815 DEGs and 18 DE-miRNAs targeting nine phytohormone pathways. Specifically: (1) a CsmiR166-mediated network involving its HD-ZIP III target and JA biosynthesis genes LOX/ACX6 suggests its miRNA likely coordinates heat adaptation by modulating JA biosynthesis during fruit development; (2) CsmiR398 exhibits negative correlation with GXR and NDUFS9. Cooperative regulation of ubiquitin-conjugating enzyme E2 by CsmiR482 further disrupts GA3 biosynthesis, driving heat-induced fruit malformation. These findings elucidate novel epigenetic mechanisms of miRNA-mediated fruit morphogenesis under thermal stress.