Abstract
BACKGROUND: Hollow heart is a common physiological disorder in cucumber (Cucumis sativus L.) characterized by internal fruit cavities that are not visible externally, severely compromising fruit quality and marketability. Although previous studies have implicated both genetic and environmental factors, the molecular regulatory mechanisms, particularly the role of long non-coding RNAs (lncRNAs), remain largely uncharacterized. RESULTS: In this study, we conducted an integrated histological and transcriptomic analysis to elucidate the regulatory basis of the hollow heart trait using two cucumber sister lines: H6 (hollow fruit) and H7 (non-hollow fruit). Histological observations revealed that the hollow heart trait emerges approximately two days after anthesis (DAA), marked by the progressive separation of dual cell layers in the carpel transport channels. RNA-seq analysis identified 16,176 differentially expressed mRNAs (DEmRNAs) and 594 differentially expressed lncRNAs (DElncRNAs) between H6 and H7. From these, seven core DElncRNAs and 28 co-expressed DEmRNAs were implicated in a regulatory network enriched in plant hormone signal transduction and phenylpropanoid biosynthesis pathways. Several key genes involved in lignin biosynthesis, auxin transport, and UDP-glycosyltransferase activity were predicted as targets of these DElncRNAs. Notably, exogenous application of plant hormones, particularly cytokinins and gibberellins, substantially reduced the formation of hollowness in H6, supporting the functional relevance of the identified regulatory components. CONCLUSIONS: This study offers insights into the regulatory role of lncRNAs in hollow fruit development in cucumber. The elucidated lncRNA-mRNA putative regulatory network, along with its association with hormone signaling and lignin biosynthesis pathways, identifies candidate targets for future genetic and biotechnological strategies aimed at improving fruit quality. These findings provide valuable insights for future molecular breeding efforts to reduce hollow heart incidence.