Multi-omics reveals growth differences and regulatory mechanisms in different source-sink types of sugar beet

Sugar beet ( Beta vulgaris L.) is an important sugar crop, with its taproot serving as the sugar-storing organ. A higher root-shoot (R/S) ratio indicates a higher sugar yield. To uncover the molecular basis underlying the contrasting R/S ratios of two genotypes, KWS1197 and SX1517, we integrated physiological, transcriptomic, proteomic, and metabolomic analyses. The KWS1197 genotype exhibited higher chlorophyll content, net photosynthetic rate, and biomass accumulation, indicating a stronger source capacity supporting taproot sink development. Transcriptome profiling revealed that, the expression levels of genes involved in raffinose catabolism, starch and sucrose metabolism, and secondary metabolite biosynthesis were higher in KWS1197 leaf cells, whereas in root cells of KWS1197, genes associated with cell wall biosynthesis, metabolite transport, and hormone signaling pathways exhibited higher expression levels, suggesting coordinated transcriptional regulation of both source and sink functions. Proteomic analysis further indicated active regulation of signal transduction, redox homeostasis, and carbon-nitrogen metabolism in leaves, and enhanced proteolysis and antioxidant defense in roots. Metabolomic data supported these findings: KWS1197 leaves accumulated more carbohydrate metabolic intermediates, promoting sustained carbon assimilation and export, whereas roots showed increased phenylpropanoid and flavonoid metabolites, contributing to cell wall strengthening and storage-root expansion. Additionally, elevated auxin biosynthesis and signaling in both tissues of KWS1197 suggest hormonal control in directing assimilate allocation and R/S ratio formation. Collectively, these results demonstrate that KWS1197 achieves a genotype-specific source-sink balance through enhanced photosynthetic carbon acquisition, efficient assimilate transport, and reinforced sink development, leading to a higher R/S ratio. This study provides insights into source–sink regulation and offers a molecular foundation for improving sugar beet yield.