Abiotic stress constrains plant growth and productivity worldwide. To survive adverse environmental conditions, plants deploy sophisticated adaptive strategies involving transcriptional reprogramming and metabolic remodeling. Over the past decade, advancements in high-throughput sequencing and mass spectrometry have propelled transcriptomics and metabolomics as pivotal post-genomic disciplines, offering unprecedented opportunities to dissect molecular mechanisms underlying stress responses. This review synthesizes current progress in applying these omics technologies to investigate plant adaptations to key abiotic stresses (thermal, saline, water deficit/excess, and heavy metal stresses). We systematically evaluate the technical strengths and limitations of transcriptomic and metabolomic platforms, highlight recent breakthroughs in stress-responsive gene identification and metabolic pathway elucidation, and discuss emerging challenges in integrative data analysis. By bridging genotype–phenotype relationships through multi-omics approaches, this study aims to deepen our mechanistic understanding of plant stress resilience and inform the design of stress-resilient crops for sustainable agriculture.

Weighted gene co-expression network analysis (WGCNA) is a research method in systematic biology. It is widely used to identify gene modules related to target traits in multi-sample transcriptome data. In order to further explore the molecular mechanism of maize response to low-temperature stress at the seedling stage, B144 (cold stress tolerant) and Q319 (cold stress sensitive) provided by the Maize Research Institute of Heilongjiang Academy of Agricultural Sciences were used as experimental materials, and both inbred lines were treated with 5 °C for 0 h, 12 h, and 24 h, with the untreated material as a control. Eighteen leaf samples were used for transcriptome sequencing, with three biological replicates. Based on the above transcriptome data, co-expression networks of weighted genes associated with low-temperature-tolerance traits were constructed by WGCNA. Twelve gene modules significantly related to low-temperature tolerance at the seedling stage were obtained, and a number of hub genes involved in low-temperature stress regulation pathways were discovered from the four modules with the highest correlation with target traits. These results provide clues for further study on the molecular genetic mechanisms of low-temperature tolerance in maize at the seedling stage.

Glucose-6-phosphate dehydrogenase (G6PDH) is a key enzyme in the pentose phosphate pathway responsible for the generation of nicotinamide adenine dinucleotide phosphate (NADPH), thereby playing a central role in facilitating cellular responses to stress and maintaining redox homeostasis. This study aimed to characterize five G6PDH gene family members in maize. The classification of these ZmG6PDHs into plastidic and cytosolic isoforms was enabled by phylogenetic and transit peptide predictive analyses and confirmed by subcellular localization imaging analyses using maize mesophyll protoplasts. These ZmG6PDH genes exhibited distinctive expression patterns across tissues and developmental stages. Exposure to stressors, including cold, osmotic stress, salinity, and alkaline conditions, also significantly affected the expression and activity of the ZmG6PDHs, with particularly high expression of a cytosolic isoform (ZmG6PDH1) in response to cold stress and closely correlated with G6PDH enzymatic activity, suggesting that it may play a central role in shaping responses to cold conditions. CRISPR/Cas9-mediated knockout of ZmG6PDH1 on the B73 background led to enhanced cold stress sensitivity. Significant changes in the redox status of the NADPH, ascorbic acid (ASA), and glutathione (GSH) pools were observed after exposure of the zmg6pdh1 mutants to cold stress, with this disrupted redox balance contributing to increased production of reactive oxygen species and resultant cellular damage and death. Overall, these results highlight the importance of cytosolic ZmG6PDH1 in supporting maize resistance to cold stress, at least in part by producing NADPH that can be used by the ASA-GSH cycle to mitigate cold-induced oxidative damage.

Soil salinization is currently one of the main abiotic stresses that restrict plant growth. Plant endophytic bacteria can alleviate abiotic stress. The aim of the current study was to isolate, characterize, and assess the plant growth-promoting and saline and alkaline stress-alleviating traits of Peribacillus simplex M1 (P. simplex M1) isolates from maize. One endophytic bacterial isolate, named P. simplex M1, was selected from the roots of maize grown in saline–alkali soil. The P. simplex M1 genome sequence analysis of the bacteria with a length of 5.8 Mbp includes about 700 genes that promote growth and 16 antioxidant activity genes that alleviate saline and alkaline stress. P. simplex M1 can grow below 400 mM NaHCO₃ on the LB culture medium; The isolate displayed multiple plant growth-stimulating features, such as nitrogen fixation, produced indole-3-acetic acid (IAA), and siderophore production. This isolate had a positive effect on the resistance to salt of maize in addition to the growth. P. simplex M1 significantly promoted seed germination by enhancing seed vigor in maize whether under normal growth or NaHCO₃ stress conditions. The seeds with NaHCO₃ treatment exhibited higher reactive oxygen species (ROS) levels than the maize in P. simplex M1 inoculant on maize. P. simplex M1 can colonize the roots of maize. The P. simplex M1 inoculant plant increased chlorophyll in leaves, stimulated root and leaf growth, increased the number of lateral roots and root dry weight, increased the length and width of the blades, and dry weight of the blades. The application of inoculants can significantly reduce the content of malondialdehyde (MDA) and increase the activity of plant antioxidant enzymes (Catalase (CAT), Superoxide Dismutase (SOD), and Peroxidase (POD)), which may thereby improve maize resistance to saline and alkaline stress. Conclusion: P. simplex M1 isolate belongs to plant growth-promoting bacteria by having high nitrogen concentration, indoleacetic acid (IAA), and siderophore, and reducing the content of ROS through the antioxidant system to alleviate salt alkali stress. This study presents the potential application of P. simplex M1 as a biological inoculant to promote plant growth and mitigate the saline and alkaline effects of maize and other crops.

The C2H2 zinc finger protein is one of the most common zinc finger proteins, widely exists in eukaryotes, and plays an important role in plant growth and development, as well as in salt, low-temperature, and drought stress and other abiotic stress responses. In this study, C2H2 members were identified and analyzed from the low-temperature tolerant transcriptome sequencing data of maize seedlings. The chromosome position, physical and chemical properties, evolution analysis, gene structure, conservative motifs, promoter cis elements and collinearity relationships of gene the family members were analyzed using bioinformatics, and the expression of the ZmC2H2 gene family under cold stress was analyzed by fluorescent quantitative PCR. The results showed that 150 members of the C2H2 zinc finger protein family were identified, and their protein lengths ranged from 102 to 1223 bp. The maximum molecular weight of the ZmC2H2s was 135,196.34, and the minimum was 10,823.86. The isoelectric point of the ZmC2H2s was between 33.21 and 94.1, and the aliphatic index was 42.07–87.62. The promoter cis element analysis showed that the ZmC2H2 family contains many light-response elements, plant hormone-response elements, and stress-response elements. The analysis of the transcriptome data showed that most of the ZmC2H2 genes responded to cold stress, and most of the ZmC2H2 genes were highly expressed in cold-tolerant materials and lowly expressed in cold-sensitive materials. The real-time quantitative PCR (qRT-PCR) analysis showed that ZmC2H2-69, ZmC2H2-130, and ZmC2H2-76 were significantly upregulated, and that ZmC2H2-149, ZmC2H2-33, and ZmC2H2-38 were significantly downregulated. It is hypothesized that these genes, which function in different metabolic pathways, may play a key role in the maize cold response. These genes could be further studied as candidate genes. This study provides a theoretical reference for further study on the function analysis of the maize C2H2 gene family.

Maize (Zea mays L.) is sensitive to a minor decrease in temperature at early growth stages, resulting in deteriorated growth at later stages. Although there are significant variations in maize germplasm in response to cold stress, the metabolic responses as stress tolerance mechanisms are largely unknown. Therefore, this study aimed at providing insight into the metabolic responses under cold stress at the early growth stages of maize. Two inbred lines, tolerant (B144) and susceptible (Q319), were subjected to cold stress at the seedling stage, and their corresponding metabolic profiles were explored. The study identified differentially accumulated metabolites in both cultivars in response to induced cold stress with nine core conserved cold-responsive metabolites. Guanosine 3′,5′-cyclic monophosphate was detected as a potential biomarker metabolite to differentiate cold tolerant and sensitive maize genotypes. Furthermore, Quercetin-3-O-(2″′-p-coumaroyl)sophoroside-7-O-glucoside, Phloretin, Phloretin-2′-O-glucoside, Naringenin-7-O-Rutinoside, L-Lysine, L-phenylalanine, L-Glutamine, Sinapyl alcohol, and Feruloyltartaric acid were regulated explicitly in B144 and could be important cold-tolerance metabolites. These results increase our understanding of cold-mediated metabolic responses in maize that can be further utilized to enhance cold tolerance in this significant crop.