Comparative analysis of starch structure and multi-omics profiles reveals candidate pathways associated with a novel...

A novel soft-waxy maize, characterized by soft texture and slow retrogradation after cooking, was identified in this study. To investigate the structural and molecular features associated with this distinct trait, we conducted a comprehensive comparative study integrating analyses of starch physicochemical properties, molecular structure, transcriptomics and metabolomics. Soft-waxy maize starch showed a lower amylose content, reduced swelling power, distinct pasting characteristics (including a higher peak viscosity time and lower system viscosities), and higher gelatinization temperatures compared to waxy maize starch. Molecular structure characterization indicated a higher Mw and Mn, lower polydispersity, and an altered amylopectin chain-length profile, with increased proportions of B1 chains and decreased proportions of A and B2 chains. Transcriptome profiling identified differential expression of key starch biosynthesis genes, with SSIIIb-2 emerging as a candidate gene potentially contributing to the observed structural variations. Integrated metabolomic and transcriptomic profiling revealed shifts in metabolic pathways that may be associated with the observed textural and palatability traits. These results provide a multi-scale characterization of a new type of maize with unique sensory profile, which offer a foundation for developing comprehensive evaluation methods and suggests potential targets for breeding waxy maize with enhanced palatability.