Targeted metabolomic and transcriptomic analyses provide insights into flavonoid biosynthesis in the grain of foxtail millet

Background Foxtail millet ( Setaria italica L.), a traditional Chinese crop, is valued for its considerable abundance of compounds with health benefits (e.g., flavonoids). Despite the nutritional significance of flavonoids, their biosynthetic pathways in foxtail millet remain poorly characterized. In this study, we integrated targeted metabolomic and transcriptomic analyses to systematically elucidate the flavonoid biosynthesis pathway and identify genes encoding key regulators. Results Quantitative profiling of a foxtail millet recombinant inbred line (RIL) population revealed differences in the grain flavonoid content, with flavonoid levels 5-fold higher in the high-flavonoid (HF) group than in the low-flavonoid (LF) group. Targeted metabolomic and transcriptomic analyses revealed key regulatory networks controlling flavonoid biosynthesis in foxtail millet. A comparative transcriptomic analysis detected significant differences in the expression profiles of flavonoid biosynthesis-related genes between the HF and LF groups. According to a targeted metabolomic analysis, the concentrations of 10 distinct flavonoids were significantly higher in the HF group than in the LF group. Integrated analyses indicated that genes encoding shikimate O-hydroxycinnamoyl transferase ( HCT ), phenylalanine ammonia-lyase ( PAL ), and phenylalanine/tyrosine ammonia-lyase ( PTAL ) are crucial for the observed differences in the flavonoid contents of the HF and LF groups. Conclusions These findings provide insights into the genetic regulation of flavonoid metabolism in foxtail millet. Furthermore, this study identified candidate genes that may be useful molecular targets for breeding foxtail millet varieties with optimal nutritional quality.