Comparative Multi-Omics Insights into Flowering-Associated Sucrose Accumulation in Contrasting Sugarcane Cultivars

Flowering often perturbs carbon allocation in sugarcane, yet its transcriptomic–metabolomic basis remains unclear. We profiled two contrasting cultivars, Gui Tang 16-3285 (sugar increases during flowering) and Gui Tang 44 (sugar decreases), sampling apical tissues at five stages (Non-spikelet-bearing stage (NSB), Early booting stage (ESB), Late booting stage (LSB), Tasseling stage (TS), and Flowering stage (FS)). RNA-seq and untargeted LC–MS revealed a strong stage/genotype structure (PCA) with high reproducibility. Pairwise contrasts (FS vs. earlier stages) and time series clustering (Mfuzz) showed extensive, stage-resolved reprogramming with small cross-cultivar overlaps. GO/KEGG indicated that GT16 is enriched for central carbon processes and glucose response, whereas GT44 favors cell-wall remodeling (xylan/xyloglucan), amino/nucleotide sugar, and phenylpropanoid pathways. Integrated analysis identified opposing temporal features across omics layers: in GT16, late-rising metabolites—including sedoheptulose—were consistent with enhanced pentose phosphate/Calvin coupling that regenerates fructose-6-phosphate for sucrose biosynthesis; in GT44, early activation of wall and secondary sinks, together with trehalose/(trehalose-6-phosphate) T6P signatures, paralleled declining soluble sugars. Across cultivars we resolved 11 and 18 genes in reciprocal opposite-trend sets (most with clear temporal order) and eight vs. five metabolites with mirrored dynamics, nominating actionable biomarkers (e.g., sedoheptulose/S7P) and regulatory nodes. These results provide a mechanistic framework linking flowering stage to carbon partitioning and suggest practical levers—timing growth moderation/ripeners, prioritizing sucrose phosphate synthase/Sucrose Phosphate Phosphatase, tempering wall flux, to sustain sucrose during reproductive development and inform breeding for high-sugar, flowering-resilient ideotypes.