MicroRNA-mediated regulation of cucumber (Cucumis sativus L.) fruit curvature

Curved cucumber fruits are classified as a malformation, significantly compromising their commercial value. However, research on cucumber curvature remains limited, and there are no existing reports addressing post-transcriptional regulation mediated by microRNA. In this study, histological and endogenous hormone analyses revealed different distributions of auxin, brassinosteroid, and cytokinin between the concave and convex sides of curved fruits. This asymmetry in hormone distribution led to uneven growth. The growth was driven by parenchyma cells division on the second day post anthesis, and by cell enlargement on the tenth day. Messenger RNA and small RNA sequencing were conducted using two representative germplasm selected from a resources survey. Differentially expressed genes were mainly enriched in plant hormone signal transduction and phenylpropanoid biosynthesis pathways. Weighted gene co-expression network analysis identified 45 core genes associated with fruit curvature across five modules. Small RNA sequencing detected 156 differentially expressed microRNAs and 950 target genes. Among these, 107 microRNA-target pairs exhibited inverse expression patterns. Cleavage site analysis confirmed direct regulatory interactions between key microRNAs and their target. Additionally, expression correlation analysis demonstrated that certain microRNA target transcription factors were co-expressed with differentially expressed genes and core genes. Collectively, the study elucidates a regulatory network in which microRNAs directly targeted-or indirectly modulate (via transcription factors)-genes involved in hormone signal transduction and cell wall biosynthesis, thereby contributing to curved fruit development. These findings provide novel insights into the molecular mechanisms underlying cucumber curvature and asymmetric growth in plants. They also offer a potential strategy for genetically improving straight-fruit traits in cucumber and other horticultural crops.