Progress in Transcriptomics and Metabolomics in Plant Responses to Abiotic Stresses
Abstract
1. Introduction
2. Transcriptomics
2.1. Comparative Analysis of Transcriptomic Research Technologies
2.2. Application of Transcriptomics in Plant Stress Resistance Research
3. Metabolomics
3.1. Characteristics of Metabolomic Research Techniques
3.2. Application of Metabolomics in Plant Stress Resistance
4. Studies on Transcriptomics and Metabolomics of Plant Responses to Different Abiotic Stresses
4.1. Studies on Transcriptomics and Metabolomics of Plant Responses to Temperature Stress
4.1.1. Heat Stress
4.1.2. Cold Stress
4.2. Transcriptomic and Metabolomic Studies of Plant Responses to Water Stress
4.2.1. Drought Stress
4.2.2. Waterlogging Stress
4.3. Research on Transcriptomics and Metabolomics of Plant Responses to Heavy Metal Stress
4.4. Research on Transcriptomics and Metabolomics of Plant Response to Salt Stress
4.5. Emerging Insights into Other Abiotic Stressors
5. Perspectives and Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Technology | Theory | Advantage | Limitation | Examples |
---|---|---|---|---|
Microassay [26] | Hybrid | 1. Fast speed 2. Low cost 3. Simple sample preparation 4. Flexible analysis range | 1. The sensitivity for detecting low-expression genes is insufficient 2. The sensitivity of hybridization technology is limited 3. The prerequisite work requires a high level of foundation 4. It is difficult to detect abnormal transcription products | Microarray technology was used for the expression analysis of genes in Arabidopsis thaliana responding to salt stress, and salt-tolerant-related genes were screened by fluorescence signal differences [27]. |
EST [28] | Sanger | 1. Detection range is wide 2. Accuracy is high 3. Improves the efficiency of gene isolation | 1. The sequencing read length is short 2. The error rate is high 3. The sequencing throughput is low | Multiple gene fragments encoding protease inhibitors were identified through EST technology, providing a molecular basis for insect-resistant breeding [29]. |
SAGE [30] | Sanger | 1. High-throughput detection 2. Can quantitatively evaluate gene expression levels 3. Gain a comprehensive understanding of gene expression regulation mechanisms | 1. High cost 2. Complex data processing 3. Relying on known gene databases, there are certain limitations in identifying unknown genes | The significant upregulation of ABA synthesis-related genes was discovered using SAGE technology, revealing the critical role of ABA in drought responses [31]. |
MPSS [32] | Sanger | 1. High throughput 2. Quantitatively display the expression of genes within cells | 1. High cost 2. Complex operation 3. Difficulties in bioinformatics processing | In yeast transcriptome research, MPSS (Massively Parallel Signature Sequencing) technology is used for genome-wide quantitative analysis of gene expression [33]. |
RNA sequencing [34] | High-throughput sequencing | 1. High throughput 2. High accuracy 3. Wide detection range 4. Low cost | 1. The sample preparation is cumbersome 2. It cannot reveal the heterogeneity of expression among single cells 3. The bioinformatics analysis tools are limited | RNA-sequencing analysis revealed that the expression patterns of genes associated with translation, membrane, and oxidoreductase activity pathways were altered under drought stress [35]. |
scRNA-seq [36] | High-throughput sequencing | 1. High accuracy and specificity 2. Clarify cell function and localization | 1. High requirements for sample quality 2. High cost 3. Difficulties in data analysis/interpretation | Single-cell analysis of Arabidopsis root tips reveals specific transcriptional responses of epidermal and cortical cells under salt stress [37]. |
Gene | Crops | Abiotic Stress | Gene Function | References |
---|---|---|---|---|
OsWRKY87 | Rice | Drought, salt stress | OsWRKY87 functions as a transcriptional activator | [42] |
OsSEH1 | Rice | Cold stress | OsSEH1 regulates the expression and metabolite accumulation of genes related to phenylpropanoid and flavonoid biosynthesis, mediating ABA expression levels in response to cold stress | [43] |
OsCSLD4 | Rice | Salt stress | OsCSLD4, a cell wall polysaccharide synthase, responds to salt stress through ABA-induced osmotic stress | [44] |
OsNAC5 | Rice | Drought stress, cold stress | It enhances stress tolerance by upregulating the expression of the OsLEA3 gene | [45] |
ZmHsf01 | Maize | Heat stress | Plays an important role in heat shock signal transduction and downstream gene expression | [46] |
ZmNAC3 | Maize | Cold stress, salt stress | ZmNAC3 encodes a nuclear-targeted protein with a highly conserved NAC domain at its N-terminus | [47] |
ZmICE1 | Maize | Cold stress | ZmICE1 regulates the expression of the DREB1 gene, inhibits the expression of ZmAS, and reduces Glu/Asn biosynthesis, thus alleviating the production of reactive oxygen species | [48] |
TdSHN1 | Wheat | Heavy metal stress | Enhances cadmium tolerance by increasing the activity of superoxide dismutase and catalase | [49] |
ZmCAO1 | Maize | Waterlogging stress | Mutation of ZmCAO1 leads to the downregulation of key photosynthetic genes, increased reactive oxygen species, and sensitivity to waterlogging | [50] |
Technology | Targets | Advantage | Limitation | Examples |
---|---|---|---|---|
liNMR | Most compounds in metabolites | 1. Small sample size required 2. No sample preprocessing required 3. Accurate provision of metabolite structure information | 1. Low detection sensitivity and resolution 2. Difficult to detect low-abundance metabolites 3. High requirements for sample preparation | Plant holistic metabolic profiling, metabolic flux analysis, in situ/non-destructive metabolic studies [59,60]. |
1GC-MS | Volatile, gasifiable, or small molecules | 1. High-resolution and sensitivity 2. Ability to identify metabolite structures 3. Easy qualitative analysis of metabolites | 1. Unable to separate macromolecules 2. Cannot analyze thermally unstable and non-gasifiable substances 3. Complex and time-consuming derivatization preprocessing procedures | Plant primary metabolite analysis, volatile organic compound analysis, fatty acid profiling [61,62]. |
LC-MS | High boiling point, non-volatile, non-derivatizable macromolecules | 1. High detection sensitivity 2. Fast analysis speed 3. Ability to separate metabolites with similar structures | 1. Limited database size 2. Limited types of metabolites analyzed 3. Not all metabolites can be accommodated by the same column material | Plant secondary metabolite analysis, lipidomics—phospholipids, glycolipids, phytohormone quantification [63,64]. |
CE-MS | Trace, complex samples | 1. High detection sensitivity 2. Fast analysis speed 3. Small sample size required 4. Wide coverage of metabolites | 1. High requirements for equipment and devices 2. Small sample size, poor reproducibility of separation 3. Narrow linear range for quantitative analysis 4. Limited quantitative analysis due to narrow linear range | Highly polar/ionic compound analysis, analysis of minute samples (single-cell metabolomics) [65,66]. |
Abiotic Stress | Crops | Metabolite | Change | References |
---|---|---|---|---|
Heat stress | Maize | Tryptophan, Threonine, Histidine, Raffinose, Galactitol, Lactitol | Upregulated | [67] |
Heat stress | Wheat | N-based Amino Acids, ABA, IAA-conjugates | Upregulated | [68] |
Cold stress | Maize | Guanosine 30, 50-Cyclic Monophosphate, Sophoroside-7-O-Glucoside, L-Lysine, L-Phenylalanine, L-Glutamine, Shanenol, Feruloyl Tartaric Acid | Upregulated | [69] |
Cold stress | Maize | Trans-aconitate, Coumaroyl Hydroxycitrate, Geranyl Glucosyl Rhamnoside Rhamnoside, Caffeoylquinate, Ferroylquinate, (Iso)Vitexin, DIBOA-Glucoside | Upregulated | [70] |
Cold stress | Maize | Chlorophyll, Glucose-6-Phosphate Dehydrogenase, Sucrose-to-Starch Ratio | Upregulated | [71] |
Cold stress | Canola seed | Amino Acids, Organic Acids, Sugars | Upregulated | [72] |
Drought stress | Wheat | 1-Aminocyclopropane-1-Carboxylic Acid, Asn, 5-HT, GABA, Cystine, Deoxyuridine, Tryptamine, Putrescine | Upregulated | [73] |
Drought stress | Mulberry tree | Galactolipids, Phospholipids, Flavonoids, Cinnamic Acid, Amino Acids, Carbohydrates, Benzenoids, Organic Heterocyclic Compounds | Upregulated | [74] |
Drought stress | Barley | Amino Acids, Sugars, Abscisic Acid, Jasmonic Acid, Ferulic Acid | Upregulated | [75] |
Salt stress | Barley | Aminoacyl-tRNA Biosynthesis, Glycine, Serine, and Threonine Metabolism, Glyoxylate and Dicarboxylate Metabolism, Porphyrin and Chlorophyll Metabolism | Upregulated | [76] |
Salt stress | Wheat | Amino Acids and Derivatives, Flavonoid Compounds, Organic Acids and Derivatives, Nucleotides and Derivatives, Lipids | Upregulated | [77] |
Salt stress | Blueberry | Glycine, Malic Acid, Octadecanoic Acid, L-Threonic Acid | Upregulated | [78] |
Heavy metal stress | Rice | Lipids, Eicosanoids | Upregulated | [79] |
Heavy metal stress | Purple sweet potato | Glutathione, Tryptophan | Upregulated | [80] |
Heat stress | Maize | Chlorophyll a, Glutathione (GSH) | Downregulated | [81] |
Cold stress | Maize | Fructose-6-phosphate, Phosphatidylcholine | Downregulated | [82] |
Drought stress | Wheat | Citric Acid, Malic Acid | egulaDownrted | [83] |
Salt stress | Wheat | Riboflavin, Ascorbic Acid | Downregulated | [84] |
Heavy metal stress | Rice | Glutamine, Succinic Acid | Downregulated | [85] |
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Yu, T.; Ma, X.; Zhang, J.; Cao, S.; Li, W.; Yang, G.; He, C. Progress in Transcriptomics and Metabolomics in Plant Responses to Abiotic Stresses. Curr. Issues Mol. Biol. 2025, 47, 421. https://doi.org/10.3390/cimb47060421
Yu T, Ma X, Zhang J, Cao S, Li W, Yang G, He C. Progress in Transcriptomics and Metabolomics in Plant Responses to Abiotic Stresses. Current Issues in Molecular Biology. 2025; 47(6):421. https://doi.org/10.3390/cimb47060421
Chicago/Turabian StyleYu, Tao, Xuena Ma, Jianguo Zhang, Shiliang Cao, Wenyue Li, Gengbin Yang, and Changan He. 2025. "Progress in Transcriptomics and Metabolomics in Plant Responses to Abiotic Stresses" Current Issues in Molecular Biology 47, no. 6: 421. https://doi.org/10.3390/cimb47060421
APA StyleYu, T., Ma, X., Zhang, J., Cao, S., Li, W., Yang, G., & He, C. (2025). Progress in Transcriptomics and Metabolomics in Plant Responses to Abiotic Stresses. Current Issues in Molecular Biology, 47(6), 421. https://doi.org/10.3390/cimb47060421