Multi-omics integration of transcriptome, miRNA, and metabolome uncovers molecular mechanisms of male flower development in cucumber line B10 (Cucumis sativus L.)

Abstract

Abstract Male flower development in cucumber ( Cucumis sativus L.) is a highly coordinated and genetically regulated process, yet the full complexity of its molecular underpinnings remains incompletely understood. In this study, we present a comprehensive, multi-omics analysis of male flower development in the cucumber line B10, integrating transcriptomic (RNA-seq), small RNA (miRNA) profiling, and metabolomic data across key tissues, including leaves, shoot apex, and floral buds at distinct developmental stages. Our analyses reveal dynamic gene expression changes and novel regulatory miRNAs, several of which have not previously been linked to male bud formation in cucumber. Functional enrichment analyses using GO and KEGG highlight critical pathways, including starch and sucrose metabolism, carbohydrate utilization, sporopollenin biosynthesis, and lignin catabolism. An integrative analysis combining miRNA–target interactions, transcriptomic shifts, and differential metabolite accumulation revealed coherent regulatory cascades linking transcription factors, carbohydrate metabolism, and cell wall dynamics. This study provides novel insights into the intricate genetic and metabolic networks shaping male flower morphogenesis and provides a valuable resource for advancing cucumber reproductive biology and crop improvement strategies.