Integrated transcriptomic and metabolomic analysis of a mutant reveals the potential mechanism of endosperm content increase in sweet-waxy double recessive maize

The shrunken kernel phenotype in double recessive sweet-waxy maize (sh2sh2wxwx), caused by impaired starch biosynthesis, severely limits its commercial value. Methods: To explore mechanisms for overcoming this limitation, we characterized a novel mutant, M4-6, derived from EMS mutagenesis, which exhibits significantly increased kernel weight. An integrated transcriptomic and metabolomic analysis was performed on 20-day-after-pollination endosperms of M4-6 and its wild-type (WT) counterpart. Results: The mutant displayed a 41.4% increase in dry grain weight, accompanied by elevated levels of soluble sugars (43.4%), sucrose (21.2%), and a marked enhancement in ADP-glucose pyrophosphorylase (AGPase) content (85.3%) and activity (45.2%). Transcriptome analysis revealed 2,055 differentially expressed genes, predominantly enriched in carbon metabolism, amino acid degradation (e.g., valine, leucine, and isoleucine), and transport (e.g., ABC transporters) pathways. Metabolomic profiling identified 68 differential metabolites, indicating enhanced turnover of carbon compounds, with depletion of intermediates like succinic acid and serine alongside accumulation of metabolites such as β-alanine and tartaric acid. Integrated analysis suggested that the mutant orchestrates a metabolic shift characterized by a state of heightened carbon flux and interconversion, driven by augmented AGPase activity and transcriptional reprogramming of starch and sucrose metabolism. Conclusions: Our study reveals that the M4-6 mutant achieves improved kernel filling through a multifaceted reprogramming of central metabolism, providing a theoretical basis and candidate pathways for potentially overcoming the post-harvest shriveling defect and improving kernel quality of sweet-waxy maize.