Multi-omics-based molecular mechanism underlying differences in edible quality of foxtail millet grains

Background Foxtail millet ( Setaria italica L.) is an important minor cereal crop in arid and semi-arid regions, but the molecular mechanisms underlying its edible quality differences remain unclear. In this study, 12 foxtail millet varieties were subjected to systematic edible quality evaluation, and comparative transcriptomics and untargeted metabolomics were integrated to elucidate the molecular basis of quality differences between high-quality and low-quality varieties. Results Edible quality evaluation indicated that flavor, grain color, and palatability were the key indicators distinguishing high-quality from low-quality varieties. Transcriptomic analysis identified a total of 667 differentially expressed genes, with up-regulated genes significantly enriched in phenylpropanoid biosynthesis, flavonoid/anthocyanin biosynthesis, and terpenoid metabolism pathways, while down-regulated genes were enriched in defense response and plant-pathogen interaction pathways. Nineteen key genes were identified, including those encoding flavanone 3-dioxygenase (F3H), dihydroflavonol 4-reductase (DFR), and anthocyanin 3-O-glucosyltransferase (3GT). Metabolomic analysis detected 455 differential metabolites, of which 50 were significantly differential metabolites. Integrated analysis constructed a molecular network, revealing that high-quality varieties promoted significant accumulation of homoplantaginin, delphinidin, kaempferide, myristicin, and (-)-trans-carveol by activating flavonoid/anthocyanin synthesis and terpenoid metabolism pathways. Meanwhile, they suppressed defense response and pectin synthesis pathways, reducing the content of bitter metabolites such as ingenol and cichorioside B and optimizing cell wall structure, thereby synergistically improving edible quality. Conclusions This study systematically elucidated the molecular basis of edible quality differences in foxtail millet from a multi-omics perspective, providing a theoretical basis and candidate genes for the genetic improvement of quality traits in foxtail millet.