Integrated comparative transcriptomics and WGCNA reveal the core transcriptional network and hub genes regulating...

Sucrose accumulation is a key agronomic trait of sugarcane, a primary sucrose-producing crop. However, the molecular mechanisms underlying the performance differences between high- and low-sucrose genotypes remain unclear. In this study, two high-sucrose genotypes (YZ08-1609, YZ05-51) and one low-sucrose genotype (CP79-318) were used as materials to systematically analyze the dynamic transcriptional differences between high- and low-sucrose genotypes.

Phenotypic analysis indicated that the high-sucrose genotypes exhibited the characteristic of "early accumulation." The rapid sucrose accumulation period (S1-S2) in high-sucrose genotypes preceded that in the low-sucrose genotype (S2-S3). Comparative transcriptome analysis revealed that the two high-sucrose genotypes commonly exhibited a conserved regulatory pattern of "enhancing influx while reducing efflux," characterized by the coordinated upregulation of the starch and sugar metabolism pathway and the coordinated downregulation of the phenylpropanoid biosynthesis pathway. WGCNA identified 17 co-expression modules. Among them, modules highly significantly positively correlated with sugar-related traits were significantly enriched in pathways such as translation, peptide biosynthetic process, and ribosome, whereas the negatively correlated modules (ME.darkorange, ME.darkseagreen3) were significantly enriched in pathways such as glycolysis and phenylpropanoid biosynthesis. Further analysis identified multiple key hub genes, including ribosomal protein genes (such as RPS3A, RPL6C) and key enzyme genes in the phenylpropanoid biosynthesis pathway (such as PAL1, CAD).

This study identified a core, conserved transcriptional regulatory network in high-sucrose sugarcane genotypes through integrated comparative transcriptomics and WGCNA analyses. This network is associated with efficient sucrose accumulation, and appears to reflect a pattern characterized by enhanced biosynthesis capacity, optimized allocation of carbon sources to sucrose, and restricted diversion to lignin. The research results not only deepen the understanding of the regulatory mechanisms of carbon metabolism in sugarcane but also provide important candidate gene resources for the molecular breeding of high-sucrose traits.