Ecological and genetic regulation of nutritional composition, pasting properties and metabolomic profiles in foxtail millet

The chemical composition and functional properties of foxtail millet is jointly regulated by genetic and ecological factors. In this study, field trials and UPLC-ESI-MS-based widely-targeted metabolomics were combined to evaluate the nutritional quality, pasting properties, and metabolomic profiles of three cultivars grown in three distinct ecological regions. Nutritional composition was mainly influenced by altitude, effective accumulated temperature, and available potassium, whereas pasting properties were mainly influenced by precipitation and altitude. Metabolomic analysis identified lipids, flavonoids, and alkaloids as the predominant classes, with significant variations observed across different regions. High-altitude conditions promoted the accumulation of L-malic acid (an organic acid) and flavonoid glycosides, supported by enhanced carbon and linoleic acid metabolism. In contrast, low-altitude regions favored phenolamine alkaloids and amino acid derivatives. Cultivar-specific metabolic patterns were also identified. The traditional cultivar accumulated alkaloids and phenolic acids with potential health-promoting properties, whereas the modern cultivar was characterized by a distinct abundance of flavonoids with strong antioxidant activity. These results clarify the metabolic foundation of foxtail millet quality and provide a strategy for cultivar selection and breeding to enhance its value for functional food applications.