Comprehensive physiological, transcriptomic, and metabolomic analysis of the response of Panicum miliaceum L. roots to alkaline stress

Abstract Alkaline stress disrupts transcriptional expression and causes metabolite accumulation, thus affecting plant growth. However, there are gaps in the response mechanism of plants to alkaline stress at the molecular dimension. Broomcorn millet ( Panicum miliaceum L.) is a pioneer plant for stress resistance also is a future smart food crop. To explore the physiological‐molecular response and adaptation mechanism of broomcorn millet root to alkaline stress, we conducted physiological, transcriptomic, and metabolomic analyses on roots of two broomcorn millet cultivars (alkaline‐sensitive S223 and alkaline‐tolerant T289) that were exposed to normal conditions (CK) and alkaline stress (AS) treatments (40 mM and a molar ratio of Na 2 CO 3 : NaHCO 3 = 1:9) for 7 days. Alkaline stress inhibited mineral uptake in broomcorn millet roots and enhanced the antioxidant enzyme activities, malondialdehyde, and soluble substances, resulting in changes in growth, biomass, and root structure. Correspondingly, differentially expressed genes induced by alkaline stress were prominently enriched in the plant hormone signal transduction, mitogen‐activated protein kinase (MAPK) signaling, phenylpropanoid biosynthesis, ATP binding cassette (ABC) transporters, and other biological pathways. Similar results were obtained from the differentially accumulated metabolites analysis. In addition, joint transcriptome and metabolome analysis indicated that genes of phenylpropanoid and flavonoid biosynthesis pathways were upregulated or downregulated in AS groups, however, the related metabolite accumulations were inhibited. This study integrates multiple methods to uncover the mechanisms of broomcorn millet response to alkaline stress. These findings suggest a new direction for phytoremediation of alkaline lands.