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Biology
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Molecular Mechanisms of Plant Stress Adaptation
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Molecular Mechanisms of Plant Stress Adaptation

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 4801

Special Issue Editor

Dr. Wenqiang Li

E-Mail Website
Guest Editor
College of Life Science, Northwest A & F University, Yangling 712100, China
Interests: plant functional genomics; plant stress biology; molecular mechanisms of plant response to abiotic stresses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the face of ever-changing environmental conditions, plants have evolved remarkable molecular mechanisms to cope with various stressors. The field of molecular mechanisms of plant stress explores the intricate processes by which plants sense, signal, and respond to adverse conditions. Understanding these molecular mechanisms is crucial for developing strategies to enhance plant resilience, improve crop productivity, and ensure global food security in the face of climate change and other environmental challenges.

It is my pleasure to present this Special Issue on Molecular Mechanisms of Plant Stress Adaptation in this esteemed journal. There are a number of research articles in this issue that delve into the molecular processes underlying plant stress adaptation. This area of plant biology will provide us with a better understanding of how plants respond to different environmental stresses, allowing us to develop new strategies for increasing crop resilience and productivity.

The aim of this Special Issue, "Molecular Mechanisms of Plant Stress Adaptation", is to elucidate the molecular mechanisms and signaling networks involved in plant stress adaptation. This Special Issue covers a wide range of topics, including hormonal regulation, genetic factors, epigenetic modifications, reactive oxygen species signaling, nutrient sensing, and metabolic adaptations in plants under stress. This issue aims to advance our understanding and foster innovative strategies for improving crop resilience and productivity by exploring the molecular mechanisms underlying plant stress adaptation. In order to contribute to understanding molecular mechanisms underlying plant stress adaptation, researchers around the world were invited to submit original research articles, reviews, and perspectives.

Dr. Wenqiang Li
Guest Editor

Manuscript Submission Information

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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. Biology is an international peer-reviewed open access monthly 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

  • plant adaptation
  • environmental stress
  • molecular mechanism
  • genetic improvement
  • stress tolerance

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Published Papers (4 papers)

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Research

Jump to: Review

17 pages, 3655 KiB  
Article
The Mechanism of the Development and Maintenance of Sexual Dimorphism in the Dioecious Mulberry Plant (Morus alba)
by Yisu Shi, Michael Ackah, Frank Kwarteng Amoako, Mengdi Zhao, Grace C. van der Puije and Weiguo Zhao
Biology 2024, 13(8), 622; https://doi.org/10.3390/biology13080622 - 15 Aug 2024
Viewed by 735
Abstract
Intersexual differentiation is crucial for the speciation and maintenance of dioecious plants, but the underlying mechanisms, including the genes involved, are still poorly understood. Here, we focused on a typical dioicous plant Morus alba, to explore the molecular footprints relevant to sex [...] Read more.
Intersexual differentiation is crucial for the speciation and maintenance of dioecious plants, but the underlying mechanisms, including the genes involved, are still poorly understood. Here, we focused on a typical dioicous plant Morus alba, to explore the molecular footprints relevant to sex evolution by revealing the differentially expressed genes (DEGs) between two sexes and the testing signals of selection for these DEGs. From the results, we found a total of 1543 DEGs. Interestingly, 333 and 66 genes expression were detected only in male and female inflorescences, respectively. Using comparative transcriptomics, the expression of 841 genes were found to be significantly higher in male than in female inflorescences and were mainly enriched in defense-related pathways including the biosynthesis of phenylpropanoids, cutin, suberine and waxes. Meanwhile, the expression of 702 genes was female-biased and largely enriched in pathways related to growth and development, such as carbohydrate metabolism, auxin signaling and cellular responses. In addition, 16.7% and 17.6% signals of selection were significantly detected in female- and male-biased genes, respectively, suggesting their non-negligible role in evolution. Our findings expanded the understanding of the molecular basis of intersexual differentiation and contribute to further research on sex evolution in dioecious plants. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Adaptation)
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Figure 1

Figure 1
<p>Physical appearance of collected adult <span class="html-italic">Morus alba</span> catkins. (<b>a</b>) Female catkins with protruding pistillate flowers. (<b>b</b>) Male catkins with protruding staminate flowers.</p> Full article ">Figure 2
<p>Comparisons of gene expression between male and female flower buds of <span class="html-italic">M. alba</span>. (<b>a</b>) Shared differentially expressed genes between male and female flower buds. (<b>b</b>) Gene expression comparison between male and female flower buds. (<b>c</b>) Volcano plot on sex-biased genes that were expressed significantly different in male and female flower buds.</p> Full article ">Figure 3
<p>Sex-biased gene expression in <span class="html-italic">M. alba</span>. (<b>a</b>) The proportion and range of DEGs and unbiased genes in <span class="html-italic">M. alba</span> catkins. (<b>b</b>) The upper-half shows the comparison of male and female catkin differentially expression genes (DEGs) at different sex bias fold change thresholds for all evaluated catkin male-biased and female-biased genes. The numbers in the brackets represent the number of DEGs in each catkin category. The lower-half shows the average male and female catkin expression of all genes at different sex bias fold change thresholds for all the evaluated catkin male-biased and female-biased genes. Significant differences between male and female expression based on Wilcoxon rank sum tests are denoted by asterisk at alpha level (<span class="html-italic">p</span> &lt; 0.0001). The sex-biased genes mentioned here include sex-limited genes. BT and Y20 are the male and female catkins.</p> Full article ">Figure 4
<p>Functional analysis of the DEGs in <span class="html-italic">M. alba</span> male and female catkins. (<b>a</b>) GO enrichment terms of male-biased expression genes. (<b>b</b>) GO enrichment terms of female-biased expression genes. (<b>c</b>) KEGG-enriched differential expression genes of male-biased expression genes. (<b>d</b>) KEGG-enriched differential expression genes of female-biased expression genes. BP; biological process. CC; cellular component. MF; molecular function.</p> Full article ">Figure 5
<p>A heat map analysis of the DEGs in <span class="html-italic">M. alba</span> male and female catkins. (<b>a</b>) A heat map diagram of the DEGs between male and female flower buds of <span class="html-italic">M. alba</span> in the phytohormone signaling pathways: abscisic acid (i), jasmonic acid (ii), salicylic acid (iii), cytokinin (iv), and auxin (v). (<b>b</b>) The transcription factor (TF) families differentially expressed in male-biased genes. (<b>c</b>) The TF families differentially expressed in male-biased and female-biased genes. The color scale represents the log<sub>10</sub>-transformed FPKM value. The sex-biased genes mentioned here include sex-limited genes. The male-biased genes are upregulated and female-biased genes are downregulated based on the figure legend.</p> Full article ">Figure 6
<p>RT-qPCR validation of differentially expressed genes between male and female <span class="html-italic">M. alba</span> flower buds, including 9 male-biased genes and 1 male-limited gene (<b>a</b>) and 9 female-biased genes and 1 female-limited gene (<b>b</b>). (<b>c</b>) Comparation of gene expression results of qPCR and RNA-seq. A1; stamen-specific protein FIL1 (male-limited gene). A2; probable aminotransferase TAT2. A3 pollen-specific leucine-rich repeat extension-like protein3. A4; pollen-receptor-like kinase1. A5; vesicle-associated. A6; protein eceriferum 12C. A7; PHD finger protein male sterility1. A8; plant UBX domain-containing protein 2. A9; endoglucanase 2C. A10; transcription factor DYT1. B1; auxin-responsive protein IAA32. B2; auxin transporter-like protein 2 (female-limited gene). B3 auxin-induced protein AUX22. B4: auxin efflux carrier component 3. B5; auxin-responsive protein IAA4. B6; alcohol dehydrogenase-like 2C. B7; protein PIN-LIKES 3. B8; auxin response factor 42C. B9; nudix hydrolase 2C. B10; transcriptional regulator SUPERMAN. Error bars represent mean ± SD of three replicates of relative expression of each gene. Bars with different letters indicate significant differences between expression levels for each gene (<span class="html-italic">p</span> ≤ 0.05) based on Duncan’s multiple range test.</p> Full article ">Figure 7
<p>(<b>a</b>) Distribution of dN/dS for genes biased in expression in female and (green) or male (blue) in <span class="html-italic">M. alba</span>, compared with genes randomly chosen from unbiased genes. Center line represents median value of dN/dS distribution. (<b>b</b>–<b>e</b>) Relevant biological processes and possible functions involved in male and female DEGs subjected to positive selection. <span class="html-italic">ADH</span>; genes encoding alcohol dehydrogenase; <span class="html-italic">CER1</span>; ECERIFERUM1 gene predicted to encode enzyme involved in alkane biosynthesis; <span class="html-italic">TAT</span>; genes encoding tyrosine aminotransferase. Genes in red dashed boxes are male-biased genes, and genes in green dashed boxes are female-biased genes. Corresponding gene ID is in lower-left corner.</p> Full article ">
23 pages, 5828 KiB  
Article
Exogenous Glycinebetaine Regulates the Contrasting Responses in Leaf Physiochemical Attributes and Growth of Maize under Drought and Flooding Stresses
by Guo-Yun Wang, Shakeel Ahmad, Bing-Wei Wang, Li-Bo Shi, Yong Wang, Cheng-Qiao Shi and Xun-Bo Zhou
Biology 2024, 13(6), 360; https://doi.org/10.3390/biology13060360 - 21 May 2024
Viewed by 963
Abstract
Flooding and drought are the two most devastating natural hazards limiting maize production. Exogenous glycinebetaine (GB), an osmotic adjustment agent, has been extensively used but there is limited research on its role in mitigating the negative effects of different abiotic stresses. This study [...] Read more.
Flooding and drought are the two most devastating natural hazards limiting maize production. Exogenous glycinebetaine (GB), an osmotic adjustment agent, has been extensively used but there is limited research on its role in mitigating the negative effects of different abiotic stresses. This study aims to identify the different roles of GB in regulating the diverse defense regulation of maize against drought and flooding. Hybrids of Yindieyu 9 and Heyu 397 grown in pots in a ventilated greenhouse were subjected to flooding (2–3 cm standing layer) and drought (40–45% field capacity) at the three-leaf stage for 8 d. The effects of different concentrations of foliar GB (0, 0.5, 1.0, 5.0, and 10.0 mM) on the physiochemical attributes and growth of maize were tested. Greater drought than flooding tolerance in both varieties to combat oxidative stress was associated with higher antioxidant activities and proline content. While flooding decreased superoxide dismutase and guaiacol peroxidase (POD) activities and proline content compared to normal water, they all declined with stress duration, leading to a larger reactive oxygen species compared to drought. It was POD under drought stress and ascorbate peroxidase under flooding stress that played crucial roles in tolerating water stress. Foliar GB further enhanced antioxidant ability and contributed more effects to POD to eliminate more hydrogen peroxide than the superoxide anion, promoting growth, especially for leaves under water stress. Furthermore, exogenous GB made a greater increment in Heyu 397 than Yindieyu 9, as well as flooding compared to drought. Overall, a GB concentration of 5.0 mM, with a non-toxic effect on well-watered maize, was determined to be optimal for the effective mitigation of water-stress damage to the physiochemical characteristics and growth of maize. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Adaptation)
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Graphical abstract

Graphical abstract
Full article ">Figure 1
<p>The change in soil water content (<b>A</b>) and the diagram of the time (<b>B</b>) for foliar glycinebetaine (GB) and sampling during the experiment. FC represents maximum field capacity; CK represents maize planted in normal field capacity; V2 and V3 are two-leaf stage and three-leaf stage for maize, respectively; B2d is 2 d before water stress (WS), and A1d, A3d, A4d, A5d, A7d, and A8d indicate 1, 3, 4, 5, 7, and 8 days after WS, respectively; SM is sampling and measuring for indicators.</p> Full article ">Figure 2
<p>The effects of glycinebetaine on the accumulations of hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) and superoxide anion (O<sub>2</sub><sup>−</sup>) after 4 d (A4d) and 8 d (A8d) of water stress. CK represents maize planted in normal field capacity; bars represent standard error (<span class="html-italic">n</span> = 3, biological replicates); different letters in a water treatment indicate the least significant differences as <span class="html-italic">p</span> value ≤ 0.05.</p> Full article ">Figure 3
<p>The effect of glycinebetaine on superoxide dismutase (SOD) activity after 4 d (<b>A</b>,<b>B</b>) and 8 d (<b>C</b>,<b>D</b>) of water stress. Data with standard error bars (<span class="html-italic">n</span> = 3, biological replicates) are presented; CK represents maize planted in normal field capacity; the 0, 0.5, 1.0, 5.0, and 10.0 mM are the different concentrations of glycinebetaine; *, **, *** mean significant <span class="html-italic">p</span> value ≤ 0.05, ≤0.01, ≤0.001, respectively, if no symbol is presented between treatments, meaning <span class="html-italic">p</span> value &gt; 0.05.</p> Full article ">Figure 4
<p>The effect of glycinebetaine on guaiacol peroxidase (POD) activity after 4 d (<b>A</b>,<b>B</b>) and 8 d (<b>C</b>,<b>D</b>) of water stress. Data with standard error bars (<span class="html-italic">n</span> = 3, biological replicates) are presented; CK represents maize planted in normal field capacity; the 0, 0.5, 1.0, 5.0, and 10.0 mM are the different concentrations of glycinebetaine; *, **, *** mean significant <span class="html-italic">p</span> value ≤ 0.05, ≤0.01, ≤0.001, respectively, if no symbol is presented between treatments, meaning <span class="html-italic">p</span> value &gt; 0.05.</p> Full article ">Figure 5
<p>The effect of glycinebetaine on ascorbate peroxidase (APX) activity after 4 d (<b>A</b>,<b>B</b>) and 8 d (<b>C</b>,<b>D</b>) of water stress. Data with standard error bars (<span class="html-italic">n</span> = 3, biological replicates) are presented; CK is maize planted in normal field capacity; 0, 0.5, 1.0, 5.0, and 10.0 mM are the different concentrations of glycinebetaine; *, **, *** mean significant <span class="html-italic">p</span> value ≤ 0.05, ≤0.01, ≤0.001, respectively, if no symbol is presented between treatments, meaning <span class="html-italic">p</span> value &gt; 0.05. Data.</p> Full article ">Figure 6
<p>The effect of glycinebetaine on maize morphology after 4 d (A4d) and 8 d (A8d) of water stress. CK represents maize planted in normal field capacity; the letters A and C are the variety Heyu 397, and B and D represent the variety Yindieyu 9; bars represent standard error (<span class="html-italic">n</span> = 3, biological replicates); different letters in a water treatment indicate the least significant differences as <span class="html-italic">p</span> value ≤ 0.05.</p> Full article ">Figure 7
<p>The effect of glycinebetaine on stem and leaf biomass accumulation after 4 d (<b>A</b>,<b>B</b>) and 8 d (<b>C</b>,<b>D</b>) of water stress. CK represents maize planted in normal field capacity; the 0, 0.5, 1.0, 5.0, and 10.0 mM are the different concentrations of glycinebetaine; vertical bars represent standard error (<span class="html-italic">n</span> = 3, biological replicates); different letters in a water treatment indicate the least significant differences as <span class="html-italic">p</span> value ≤ 0.05.</p> Full article ">Figure 8
<p>Correlation analyses of the inspected parameters of maize under CK (<b>a</b>), flooding (<b>b</b>), and drought (<b>c</b>) stresses in the influence of glycinebetaine. CK represents maize planted in normal field capacity; Correlation coefficient <span class="html-italic">r</span> with the least significant difference according to <span class="html-italic">p</span> value ≤ 0.05 (*, **, *** mean significant <span class="html-italic">p</span> value ≤ 0.05, ≤0.01, ≤0.001) is shown. H<sub>2</sub>O<sub>2</sub>, O<sub>2</sub><sup>−</sup>, SOD, POD, APX, LA, PH, SD, SDM, and LDM represent hydrogen peroxide, superoxide anion, superoxide dismutase, guaiacol peroxidase, ascorbate peroxidase, leaf area, plant height, stem diameter, stem dry matter, and leaf dry matter, respectively.</p> Full article ">

Review

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16 pages, 679 KiB  
Review
Integrated Review of Transcriptomic and Proteomic Studies to Understand Molecular Mechanisms of Rice’s Response to Environmental Stresses
by Naveed Aslam, Qinying Li, Sehrish Bashir, Liuzhen Yuan, Lei Qiao and Wenqiang Li
Biology 2024, 13(9), 659; https://doi.org/10.3390/biology13090659 - 25 Aug 2024
Viewed by 956
Abstract
Rice (Oryza sativa L.) is grown nearly worldwide and is a staple food for more than half of the world’s population. With the rise in extreme weather and climate events, there is an urgent need to decode the complex mechanisms of rice’s [...] Read more.
Rice (Oryza sativa L.) is grown nearly worldwide and is a staple food for more than half of the world’s population. With the rise in extreme weather and climate events, there is an urgent need to decode the complex mechanisms of rice’s response to environmental stress and to breed high-yield, high-quality and stress-resistant varieties. Over the past few decades, significant advancements in molecular biology have led to the widespread use of several omics methodologies to study all aspects of plant growth, development and environmental adaptation. Transcriptomics and proteomics have become the most popular techniques used to investigate plants’ stress-responsive mechanisms despite the complexity of the underlying molecular landscapes. This review offers a comprehensive and current summary of how transcriptomics and proteomics together reveal the molecular details of rice’s response to environmental stresses. It also provides a catalog of the current applications of omics in comprehending this imperative crop in relation to stress tolerance improvement and breeding. The evaluation of recent advances in CRISPR/Cas-based genome editing and the application of synthetic biology technologies highlights the possibility of expediting the development of rice cultivars that are resistant to stress and suited to various agroecological environments. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Adaptation)
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Figure 1

Figure 1
<p>A graphical route for transcriptomic and proteomic strategies to investigate rice’s responses to biotic and abiotic stresses.</p> Full article ">
16 pages, 971 KiB  
Review
The Molecular Mechanism of Cold-Stress Tolerance: Cold Responsive Genes and Their Mechanisms in Rice (Oryza sativa L.)
by Nida Shahzad, Hafiz Ghulam Nabi, Lei Qiao and Wenqiang Li
Biology 2024, 13(6), 442; https://doi.org/10.3390/biology13060442 - 17 Jun 2024
Viewed by 1504
Abstract
Rice (Oryza sativa L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate [...] Read more.
Rice (Oryza sativa L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate the physiological, biochemical, and molecular mechanisms of cold stress tolerance in rice. This review aims to provide a comprehensive overview of the recent developments and trends in this field. We summarized the previous advancements and methodologies used for identifying cold-responsive genes and the molecular mechanisms of cold tolerance in rice. Integration of new technologies has significantly improved studies in this era, facilitating the identification of essential genes, QTLs, and molecular modules in rice. These findings have accelerated the molecular breeding of cold-resistant rice varieties. In addition, functional genomics, including the investigation of natural variations in alleles and artificially developed mutants, is emerging as an exciting new approach to investigating cold tolerance. Looking ahead, it is imperative for scientists to evaluate the collective impacts of these novel genes to develop rice cultivars resilient to global climate change. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Adaptation)
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Figure 1

Figure 1
<p>Physiological responses during cold stress. It shows a detailed recognition of the paradox in plant responses to chilling stress. (<b>A</b>) Pathway shows the sensibility of plants during chilling stress. It initiates membrane damage that minimizes photosynthetic movement and subsequent electrolyte leakage, which ultimately leads to reduced growth and plant death. (<b>B</b>) This route illustrates the complex physiological alterations, including photosynthetic acclimation, changes in membrane structure, and accumulation of ROS and osmolytes in cold-tolerant plants, demonstrating their capacity to withstand low temperatures, and the side flow diagram shows the response of various genes during cold.</p> Full article ">Figure 2
<p>Flow chart diagram of signal transduction and membrane stability. Presents the coordinated molecular response of rice plants during cold stress. (<b>A</b>) Cascade is started by an immediate signal perception. (<b>B</b>) Signal transduction pathways quickly come into action, opening the door for (<b>C</b>) the participation of several transcriptional regulatory elements, and (<b>D</b>) the plant’s defense mechanism against cold stress is the result of the subsequent gene expression.</p> Full article ">
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