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Plants
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‘Omics’ and ‘Multi-Omics’ Insights into Plant Responses to Abiotic Stresses
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‘Omics’ and ‘Multi-Omics’ Insights into Plant Responses to Abiotic Stresses

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Response to Abiotic Stress and Climate Change".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 5543

Special Issue Editors

Dr. Rudo Ngara

E-Mail Website
Guest Editor
Department of Plant Sciences, University of the Free State, Qwaqwa Campus, Phuthaditjhaba P. Bag X13, South Africa
Interests: plant responses to abiotic stresses; drought; heat; combined drought and heat; ABA signalling; “omics” technologies; secretomics; secreted proteins; plant extracellular matrix
Dr. Yuri Shavrukov

E-Mail Website
Guest Editor
College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA 5042, Australia
Interests: plant genetics and genomics; molecular markers; plant genotyping; abiotic stress tolerance; drought, salinity, and dehydration; gene identification and expression analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are excited to announce our Special Issue, and we hope that you will be interested in this pertinent topic.

Plants are often exposed to abiotic stresses, such as drought, salinity, heat, cold, freezing, nutrient deficiency, and heavy metal toxicity, which limit their growth and development. In the case of crops, yields may be reduced, resulting in insufficient food supply for the growing population. In addition, these stresses may occur concomitantly under field conditions, resulting in diverse effects on plant growth. While stress combinations such as drought and ozone may result in potentially positive interactions, others, including drought and heat or salinity with nutrient deficiency, may cause more extensive plant cell damage and more significant yield reductions than the individual stresses. Furthermore, the frequency and magnitude of stresses, such as drought and heat, will likely increase with global warming. Consequently, there is growing interest among researchers in understanding the complex responses of plants to individual and combinations of abiotic stresses. A range of “omics” technologies are also improving our insights into stress-responsive changes in the transcriptome, proteome, and metabolome of plants, while the sequencing of entire plant genomes is providing resources to guide crop-improvement strategies. Other research groups are working on validating the roles of these “omics-derived data” in stress adaptation using various methodologies, including transgenic plants, seed priming, and the exogenous application of growth-promoting compounds. Therefore, this Special Issue welcomes submissions that broaden our insights into plant responses to individual abiotic stresses and their combinations using various “omics” approaches, including the functional validation of these data.

Dr. Rudo Ngara
Dr. Yuri Shavrukov
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • abiotic stress
  • plant stress responses
  • “omics” profiling and validation
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • gene expression
  • transgenic plant biology

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Published Papers (6 papers)

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20 pages, 2451 KiB  
Article
The Proteomic and Peptidomic Response of Wheat (Triticum aestivum L.) to Drought Stress
by Regina Azarkina, Arina Makeeva, Anna Mamaeva, Sergey Kovalchuk, Daria Ganaeva, Igor Tikhonovich and Igor Fesenko
Plants 2025, 14(14), 2168; https://doi.org/10.3390/plants14142168 - 14 Jul 2025
Viewed by 388
Abstract
Drought conditions impact plants at the morphological, physiological, and molecular levels. Plant tolerance to drought conditions is frequently associated with maintaining proteome stability, highlighting the significance of proteomic analysis in understanding the mechanisms underlying plant resilience. Here, we performed proteomic and peptidomic analysis [...] Read more.
Drought conditions impact plants at the morphological, physiological, and molecular levels. Plant tolerance to drought conditions is frequently associated with maintaining proteome stability, highlighting the significance of proteomic analysis in understanding the mechanisms underlying plant resilience. Here, we performed proteomic and peptidomic analysis of spring wheat (Triticum aestivum L.) under drought stress conditions. Using isobaric tags for relative and absolute quantitation (iTRAQ), we identified 497 and 157 differentially abundant protein (DAP) groups in leaves and roots, respectively. The upregulated DAP groups in leaves were primarily involved in stress responses, such as oxidative stress and heat response, whereas those in roots were associated with responses to water deprivation and sulfur compound metabolic processes. The analysis of the extracellular root peptidome revealed 2294 native peptides, including members of small secreted peptide (SSP) families. In the peptidomes of stress-induced plants, we identified 16 SSPs as well as peptides derived from proteins involved in cell wall catabolism, intercellular signaling, and stress response. These peptides represent potential candidates as regulators of drought responses. Our results help us to understand adaptation mechanisms and develop new agricultural technologies to increase productivity. Full article
(This article belongs to the Special Issue ‘Omics’ and ‘Multi-Omics’ Insights into Plant Responses to Abiotic Stresses)
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36 pages, 6380 KiB  
Article
Metabolic Responses of Amaranthus caudatus Roots and Leaves to Zinc Stress
by Natalia Osmolovskaya, Tatiana Bilova, Anastasia Gurina, Anastasia Orlova, Viet D. Vu, Stanislav Sukhikh, Tatiana Zhilkina, Nadezhda Frolova, Elena Tarakhovskaya, Anastasia Kamionskaya and Andrej Frolov
Plants 2025, 14(14), 2119; https://doi.org/10.3390/plants14142119 - 9 Jul 2025
Viewed by 405
Abstract
In recent decades, heavy metal pollution has become a significant environmental stress factor. Plants are characterized by high biochemical plasticity and can adjust their metabolism to ensure survival under a changing environment. Here we report, to our knowledge, the first gas chromatography-mass spectrometry [...] Read more.
In recent decades, heavy metal pollution has become a significant environmental stress factor. Plants are characterized by high biochemical plasticity and can adjust their metabolism to ensure survival under a changing environment. Here we report, to our knowledge, the first gas chromatography-mass spectrometry (GC-MS)-based metabolomics study of Zn-induced stress responses in Amaranthus caudatus plants. The study was performed with root and leaf aqueous methanolic extracts after their lyophilization and sequential derivatization with methoxylamine hydrochloride and N-methyl-N-(trimethylsilyl)trifluoroacetamide. In total, 419 derivatives were detected in the samples, and 144 of them could be putatively annotated. The metabolic shifts in seven-week-old A. caudatus plants in response to a seven-day treatment with 300 µmol/L ZnSO4·7H2O in nutrient solution were organ-specific and more pronounced in roots. Most of the responsive metabolites were up-regulated and dominated by sugars and sugar acids. The revealed effects could be attributed to the involvement of these metabolites in osmotic regulation, antioxidant protection and Zn2+ complexation. A 59-fold up-regulation of gluconic acid in roots distinctly indicated enhanced glucose oxidation due to oxidative stress upon the Zn treatment. Gluconic acid might be further employed in Zn2+ complexation. Pronounced Zn-induced up-regulation of salicylic acid in roots and shoots suggested a key role of this hormone in stress signaling and activation of Zn stress tolerance mechanisms. Overall, our study provides the first insight into the general trends of Zn-induced biochemical rearrangements and main adaptive metabolic shifts in A. caudatus. Full article
(This article belongs to the Special Issue ‘Omics’ and ‘Multi-Omics’ Insights into Plant Responses to Abiotic Stresses)
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23 pages, 12391 KiB  
Article
Genus-Wide Pan-Genome Analysis of Oryza Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics
by Fu Shi, Li Li, Mingjie Chen, Junli Chang, Min Tu, Guangyuan He, Yin Li and Guangxiao Yang
Plants 2025, 14(10), 1542; https://doi.org/10.3390/plants14101542 - 20 May 2025
Viewed by 527
Abstract
The Oryza genus serves not only as a gene pool for rice improvement but also as a model system for plant evolutionary research. Calcium-dependent protein kinases (CPKs) function as both effectors and sensors in calcium signaling and play versatile roles in plant development [...] Read more.
The Oryza genus serves not only as a gene pool for rice improvement but also as a model system for plant evolutionary research. Calcium-dependent protein kinases (CPKs) function as both effectors and sensors in calcium signaling and play versatile roles in plant development and stress responses. Four kinase families, namely CPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PPCK-related kinases (PEPRKs), and calcium- and calmodulin-dependent kinases (CCaMKs), are frequently called CPK-related kinases. This study utilized evolutionary genomics approaches and provided the pan-genome repertoires of CPKs and their related kinases in 34 Oryza genomes by leveraging the rich genomics resources of the Orzya genus. Gene duplication analysis revealed that distinct duplication types contributed to expanding CPKs and their related kinases in wild rice. We depicted the protein domain architectures of CPKs and their related kinases, highlighting the complexity of EF-hand motifs in CPKs and CCaMKs. Transcriptome analysis determined that alternative splicing was a mechanism contributing to the diversity in the domain architectures of CPKs and CCaMKs. We also generated the expression atlas of CPKs and their related kinases in multiple species of Oryza genus, emphasizing divergent homoeolog expression patterns across tissues and species in allotetraploid wild rice. Collectively, our Oryza-wide analysis of CPKs and their related kinases revealed their evolutionary trajectories and highlighted their diversified domain architectures and expression dynamics, providing gene resources of wild relatives for rice improvement. Full article
(This article belongs to the Special Issue ‘Omics’ and ‘Multi-Omics’ Insights into Plant Responses to Abiotic Stresses)
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17 pages, 3106 KiB  
Article
Integrative Transcriptomics and Metabolomics Reveal the Key Metabolic Pathways in Endophyte-Infected Rice Seedlings Resistance to Na2CO3 Stress
by Xinnan Wang, Yanan Li, Hefei Sun, Lihong Zhang and Xuemei Li
Plants 2025, 14(10), 1524; https://doi.org/10.3390/plants14101524 - 19 May 2025
Viewed by 554
Abstract
Soil saline-alkalization is a key factor affecting rice growth and physiological metabolism, which leads to reduced yields. Endophyte EF0801 significantly promoted growth and improved its saline-alkali resistance. We investigated growth parameters and physiological indices of endophyte EF0801-infected and control rice seedlings under sodium [...] Read more.
Soil saline-alkalization is a key factor affecting rice growth and physiological metabolism, which leads to reduced yields. Endophyte EF0801 significantly promoted growth and improved its saline-alkali resistance. We investigated growth parameters and physiological indices of endophyte EF0801-infected and control rice seedlings under sodium carbonate (Na2CO3) stress. The results showed that endophyte-infected rice seedlings showed plant height increase by 1.25-fold, root length shortening by 0.79-fold, sucrose synthase (SS), sucrose phosphosynthase (SPS), hexokinase (HXK), and α-glucosidase (α-GC) activities increased by 0.15-fold, 0.29-fold, 0.06-fold, and 1.45-fold, respectively, and β-glucosidase (β-GC) activity decreased by 0.12-fold. Utilizing gas chromatography and mass spectrometry (GC-MS) technology and RNA sequencing (RNA-seq) technology, we identified 419 differentially expressed genes (DEGs) and 37 differentially accumulated metabolites (DAMs). Comprehensive enrichment analysis of DAMs and DEGs showed that 6 DEGs and 6 DAMs were strongly correlated with the mitigating effects of endophytes on rice leaves under Na2CO3 treatment, highlighting the co-enrichment in starch and sucrose metabolism, as well as alanine, aspartate, and glutamate metabolism. The gene encoding HXK was found to be upregulated in endophyte-infected rice seedlings under Na2CO3 stress. HXK plays a key role in the conversion of fructose and glucose to fructose 6-phosphate (F-6-P) and glucose 6-phosphate (G-6-P), which are important intermediates in cellular energy metabolism and glycolytic pathways, providing energy and biosynthesis of precursor substances. Our findings provide a potential perspective for unraveling the molecular response of endophyte-mediated saline-alkali resistance in rice leaves and a theoretical rationale for exploring the mechanisms of growth-promoting effects by endophytes. Full article
(This article belongs to the Special Issue ‘Omics’ and ‘Multi-Omics’ Insights into Plant Responses to Abiotic Stresses)
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19 pages, 5560 KiB  
Article
Genome-Wide Identification, Classification, Expression Analysis, and Screening of Drought and Heat Resistance-Related Candidates of the Rboh Gene Family in Wheat
by Miyuan Cao, Yue Zhang, Xiaoxiao Zou, Huangping Yin, Yan Yin, Zeqi Li, Wenjun Xiao, Shucan Liu, Yongliang Li and Xinhong Guo
Plants 2024, 13(23), 3377; https://doi.org/10.3390/plants13233377 - 30 Nov 2024
Viewed by 1167
Abstract
Plant respiratory burst oxidase homologs (Rbohs) are key enzymes that produce reactive oxygen species (ROS), which serve as signaling molecules regulating plant growth and stress responses. In this study, 39 TaRboh genes (TaRboh01–TaRboh39) were identified. These genes were distributed [...] Read more.
Plant respiratory burst oxidase homologs (Rbohs) are key enzymes that produce reactive oxygen species (ROS), which serve as signaling molecules regulating plant growth and stress responses. In this study, 39 TaRboh genes (TaRboh01–TaRboh39) were identified. These genes were distributed unevenly among the wheat genome’s fourteen chromosomes, with the exception of homoeologous group 2 and 7 and chromosomes 4A, as well as one unidentified linkage group (Un). TaRbohs were classified into ten distinct clades, each sharing similar motif compositions and gene structures. The promoter regions of TaRbohs contained cis-elements related to hormones, growth and development, and stresses. Furthermore, five TaRboh genes (TaRboh26, TaRboh27, TaRboh31, TaRboh32, and TaRboh34) exhibited strong evolutionary conservation. Additionally, a Ka/Ks analysis confirmed that purifying selection was the predominant force driving the evolution of these genes. Expression profiling and qPCR results further indicated differential expression patterns of TaRboh genes between heat and drought stresses. TaRboh11, TaRboh20, TaRboh22, TaRboh24, TaRboh29, and TaRboh34 were significantly upregulated under multiple stress conditions, whereas TaRboh30 was only elevated in response to drought stress. Collectively, our findings provide a systematic analysis of the wheat Rboh gene family and establish a theoretical framework for our future research on the role of Rboh genes in response to heat and drought stress. Full article
(This article belongs to the Special Issue ‘Omics’ and ‘Multi-Omics’ Insights into Plant Responses to Abiotic Stresses)
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9 pages, 233 KiB  
Opinion
Polyethylene Glycol (PEG) Application Triggers Plant Dehydration but Does Not Accurately Simulate Drought
by Gulnar Kylyshbayeva, Nazira Bishimbayeva, Sativaldy Jatayev, Serik Eliby and Yuri Shavrukov
Plants 2025, 14(1), 92; https://doi.org/10.3390/plants14010092 - 31 Dec 2024
Cited by 1 | Viewed by 1698
Abstract
Polyethylene glycol (PEG), especially at high molecular weights, is highly soluble in water, and these solutions have reduced water potential. It is convenient to use PEG in hydroponics (liquid nutrient solution) for experiments with plants. However, some authors have been found to describe [...] Read more.
Polyethylene glycol (PEG), especially at high molecular weights, is highly soluble in water, and these solutions have reduced water potential. It is convenient to use PEG in hydroponics (liquid nutrient solution) for experiments with plants. However, some authors have been found to describe the application of PEG to plants incorrectly, such as drought, dehydration, osmotic, or water stresses, which can mislead readers. The presented opinion paper shows our arguments for a terminology in such experiments that is strictly limited to ‘PEG-induced’ or ‘simulated’ or ‘mimicked’ dehydration, and osmotic or water stresses, with the best option being ‘PEG-induced dehydration’. The most popular term, ‘drought’, is inappropriate to be used for hydroponics at all, with or without PEG. Traditionally, drought stress study was related to only plants in soil or other substrates mixed with soil. Based on 139 published papers, the examples presented in our opinion paper can demonstrate differences in gene expression between plants grown in containers with soil and under PEG-induced stress in hydroponics. Researchers can carry out any type of experiments suitable for the purposes of their study. However, clear and correct description of experiments and careful interpretation of the results are strongly required, especially with PEG, to avoid incorrect information. In all cases, at the final stage, results of experiments in controlled conditions have to be verified in field trials with naturally occurring drought. Full article
(This article belongs to the Special Issue ‘Omics’ and ‘Multi-Omics’ Insights into Plant Responses to Abiotic Stresses)
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