Transcriptomics combined physiology reveal the key pathway responses in Setaria italica L. growth exposure to different Mo concentrations

Molybdenum (Mo), an essential micronutrient for plant physiology, impacts plant growth by regulating physiological activities, modulating gene expression, and altering metabolite content. However, the molecular mechanisms underlying plant responses to Mo remain poorly characterized. Consequently, we utilized extensive physiological and biochemical assays, along with molecular investigations, to decipher the response pathways of Setaria italica to varying levels of Mo. Using physiological profiling as a foundation, RNA-seq characterized the transcriptome of foxtail millet exposed to varying Mo levels, uncovering crucial pathways such as phenylpropanoid synthesis, starch metabolism, hormone signaling, and flavonoid/carotenoid metabolism. Results showed that there were more differentially expressed genes (DEGs) at 8 mg L ^− 1 Mo compared to other concentrations, indicating that foxtail millet responded rapidly at this threshold. Compared to the 8 mg L ^− 1 treatment, the 15 mg L ^− 1 treatment inhibited starch and sucrose metabolism while enhancing phenylpropanoid and flavonoid biosynthesis. High Mo levels up-regulated key carotenoid biosynthesis genes ( NCED4 , NCED5 , ZSD ) and modulated hormone signaling, optimizing starch-sucrose regulation and boosting stress resilience in foxtail millet. In conclusion, these results indicate that optimal Mo concentrations enhance plant growth through metabolic coordination, whereas supraoptimal exposure induces metabolic dysregulation characterized by: carbon and nitrogen cycle imbalance, antioxidant system impairment, and ultimately growth suppression, thereby delineating key regulatory nodes response to Mo in foxtail millet.