Sodium carbonate (Na₂CO₃) presents a huge challenge to plants by the combined damaging effects of Na⁺, high pH, and CO₃²⁻. Little is known about the cellular responses to Na₂CO₃ stress. In this study, the transcriptome of maize (Zea mays L. cv. B73) roots exposed to Na₂CO₃ stress for 5 h was compared with those of NaCl and NaOH stresses. The expression of 8,319 genes, representing over a quarter of the total number of genes in the maize genome, was altered by Na₂CO₃ stress, and the downregulated genes (5,232) outnumbered the upregulated genes (3,087). The effects of Na₂CO₃ differed from those of NaCl and NaOH, primarily by downregulating different categories of genes. Pathways commonly altered by Na₂CO₃, NaCl, and NaOH were enriched in phenylpropanoid biosynthesis, oxidation of unsaturated fatty acids, ATP-binding cassette (ABC) transporters, as well as the metabolism of secondary metabolites. Genes for brassinosteroid biosynthesis were specifically upregulated by Na₂CO₃, while genes involved in ascorbate and aldarate metabolism, protein processing in the endoplasmic reticulum and by N-glycosylation, fatty acid biosynthesis, and the circadian rhythm were downregulated. This work provides the first holistic picture of early transcriptomic adaptation to Na₂CO₃ stress, and highlights potential molecular pathways that could be manipulated to improve tolerance in maize.

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