Objectives Maize seedlings employ a series of physiological and biochemical mechanisms to resist salt stress-induced damage. We investigated the metabolic pathways and major differential gene expressions of different salt-tolerant maize varieties in order to provide gene targets for maize breeding.

Methods A pot experiment was conducted using a 1∶1 mixture of vermiculite and perlite as the substrate. The test materials were Xianyu 335 (salt-sensitive type) and DK815 (salt-tolerant type). At the 6-leaf stage, maize seedlings were irrigated with nutrient solutions containing 0 mmol/L (CK) or 240 mmol/L NaCl (ST), and the 5th leaf samples were collected after one day of salt treatment. A portable photosynthesis system LI-6400XT was used to measure photosynthetic parameters. ELISA kits were used to determine the abscisic acid (ABA), auxin (IAA), gibberellin (GA), and jasmonic acid (JA) contents. The transcriptome sequencing analysis of the leaf samples was also performed to clearify the differentiable expression genes.

Results Compared with CK, salt stress significantly decreased the stomatal conductance (Gs), net photosynthetic rate (Pn) and transpiration rate (Tr) of Xianyu 335 and DK815, but did not decrease intercellular CO₂ concentration (Ci). Salt stress significantly decreased the contents of growth promoting hormones IAA and GA, and significantly increased the contents of stress response hormones ABA and JA. DK815 was examined smaller variations of photosynthetic parameters (Pn, Tr, Gs) and hormones (IAA, GA, JA) than Xianyu 335. Salt stress resulted 2500 and 2251 up-regulated genes and 2537 and 2466 down-regulated genes in Xianyu 335 and DK815, respectively. The differential genes of Xianyu 335 were mainly involved in ribosome biogenesis, protein synthesis, energy metabolism, amino acid metabolism, DNA repair, antioxidant and peroxisome pathways. While the differential genes of DK815 were associated with RNA modification, cell cycling, cell wall biogenesis, amino acid metabolism, nucleic acid metabolism, material transport, structural substance synthesis, and photosynthesis. Under salt stress, the starch and trehalose synthesis genes (glgC, glgA, WAXY, TPS, ostB) were down-regulated, and starch and cellulose degradation genes (AMY, malZ, bglB, EG) were up-regulated, the up-regulated range of starch and cellulose degradation genes in DK815 was significantly higher than that in Xianyu 335. In addition, the two cultivars also adapted to salt stress by regulating key genes of hormone signaling pathway (ARF, AUX/IAA, SAUR, ARR-A, PP2C, SnRK2). The up-regulation amplitude of SAUR, ARR-A, PP2C, SnRK2 genes in DK815 was significantly higher than that in Xianyu 335.

Conclusions Under salt stress, the upregulated genes in the sensitive variety Xianyu 335 are primarily enriched in cellular functions related to protein synthesis, such as ribosome biosynthesis, translation, and peptide metabolism. In contrast, the upregulated genes in the salt-tolerant variety DK815 are mainly enriched in processes associated with RNA metabolism and cellular structural adjustments, including RNA modification, cell cycle regulation, and cell wall biogenesis. Under salt stress, Xianyu 335 enhances the expression of genes related to energy production and DNA repair pathways while inhibiting the glutathione metabolism pathway. DK815, on the other hand, increases the expression of genes involved in amino acid metabolism and material transport pathways, while downregulating the expression of genes related to structural metabolism and photosynthesis. Genes such as glgC, glgA, WAXY, TPS, ostB, AMY, malZ, bglB, and EG in starch and sucrose metabolism pathways, as well as genes like ARF, AUX/IAA, SAUR, ARR-A, PP2C, and SnRK2 in hormone signaling pathways, participate in regulating salt tolerance in maize.