Abstract
Consumer-driven demand for premium foxtail millet necessitates systematic identification of quality-determining metabolites. This investigation employed integrated metabolomic and transcriptomic analyses to compare two contrasting cultivars - the elite variety Jingu 21 (JG21) and traditional landrace Niumaobai (NMB) - during two critical grain-filling stages. 552 metabolites were identified in both cultivars, with 144 showing differential abundance. Comparative analysis of early (S2) to late (S4) grain-filling stage revealed 108 co-regulated metabolites alongside 78 JG21-exclusive and 72 NMB-specific metabolites, exhibiting differential accumulation patterns likely governing quality divergence. Differential metabolites were predominantly enriched in flavonoid and phenylpropanoid pathways between cultivars, suggesting potential roles in modulating color, nutritional quality, and grain texture. Co-expression network predictions revealed cultivar-specific regulatory associations, with 10 candidate genes potentially governing six pigmentation/nutrition-related flavonoid metabolites, while another four genes showed tentative correlations with five lignin pathway intermediates that may contribute to grain texture variations between JG21 and NMB cultivars. These findings provide mechanistic insights into metabolic determinants of millet quality while establishing a framework for targeted breeding strategies to enhance both nutritional value and sensory characteristics in foxtail millet.