Abstract
BACKGROUND: Magnesium is an essential macronutrient for tobacco (Nicotiana tabacum L.) growth, as it participates in chlorophyll synthesis, photosynthesis, and enzyme activation. However, the molecular mechanisms underlying tobacco’s dynamic response to varying magnesium concentrations remain unclear. This study combined physiological, transcriptomic, and metabolomic analyses to explore the adaptive strategies of tobacco seedlings under complete magnesium deficiency (CK), deficient, optimal (T3, 4 mmol/L), excess, and toxic magnesium conditions. RESULTS: Magnesium deficiency/excess induced oxidative stress and inhibited growth, while T3 promoted agronomic traits. Transcriptomics of the CK and T3 treatment groups showed: 7 days (5,450 DEGs, 51.6% up/48.4% down), 15 days (15,582 DEGs, 49.9% up/50.1% down), 30 days (11,574 DEGs, 44.9% up/55.1% down). Genes highly sensitive to magnesium concentration included LOC107825700, LOC107808263, and LOC107759348 (consistently upregulated under optimal magnesium) and LOC107795938, LOC107785922 (significantly downregulated under magnesium deficiency). KEGG enrichment analysis showed that these DEGs were mainly enriched in photosynthesis, tricarboxylic acid (TCA) cycle, sucrose-galactose metabolism, amino acid biosynthesis, and nucleotide metabolism pathways. Metabolomic of the CK and T3 treatment groups results confirmed that optimal magnesium upregulated key metabolites such as fructose 6-phosphate, galactose, α-ketoglutaric acid, and guanosine, while suppressing purine and 2-aminopurine accumulation. Additionally, sucrose synthase (LOC107828804), arginine decarboxylase (LOC107773487), and nucleotide metabolism-related genes (LOC107773465) were identified as core regulatory genes for magnesium response. CONCLUSIONS: This study reveals that tobacco adapts to magnesium concentration changes through synergistic regulation of “photosynthesis-TCA cycle-sucrose-amino acid-nucleotide” metabolic networks. The identified magnesium-sensitive genes and key pathways provide a theoretical basis for breeding magnesium-deficiency-tolerant tobacco varieties and optimizing magnesium fertilizer application in tobacco production. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08138-0.