scholarly journals Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview

Metabolites ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 445
Author(s):  
Morena M. Tinte ◽  
Kekeletso H. Chele ◽  
Justin J. J. van der Hooft ◽  
Fidele Tugizimana
Keyword(s):  
Machine Learning ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Industrial Revolution ◽  
Chemical Space ◽  
Big Data Analytics ◽  
Plant Responses ◽  
Next Generation ◽  
Computational Tools

Plants are constantly challenged by changing environmental conditions that include abiotic stresses. These are limiting their development and productivity and are subsequently threatening our food security, especially when considering the pressure of the increasing global population. Thus, there is an urgent need for the next generation of crops with high productivity and resilience to climate change. The dawn of a new era characterized by the emergence of fourth industrial revolution (4IR) technologies has redefined the ideological boundaries of research and applications in plant sciences. Recent technological advances and machine learning (ML)-based computational tools and omics data analysis approaches are allowing scientists to derive comprehensive metabolic descriptions and models for the target plant species under specific conditions. Such accurate metabolic descriptions are imperatively essential for devising a roadmap for the next generation of crops that are resilient to environmental deterioration. By synthesizing the recent literature and collating data on metabolomics studies on plant responses to abiotic stresses, in the context of the 4IR era, we point out the opportunities and challenges offered by omics science, analytical intelligence, computational tools and big data analytics. Specifically, we highlight technological advancements in (plant) metabolomics workflows and the use of machine learning and computational tools to decipher the dynamics in the chemical space that define plant responses to abiotic stress conditions.

Protein Phosphatase Type 2C Functions in Phytohormone-Dependent Pathways and in Plant Responses to Abiotic Stresses

2021 ◽  
Vol 22 ◽  
Author(s):  
Nguyen Nguyen Chuong ◽  
Xuan Lan Thi Hoang ◽  
Duong Hoang Trong Nghia ◽  
Thai Ngoc Trang Dai ◽  
Van-Anh Le Thi ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Abiotic Stress ◽  
Signaling Pathway ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Protein Phosphatases ◽  
Stress Factors ◽  
Plant Responses ◽  
Aba Signaling ◽  
In Planta

: Plants, as sessile organisms, are susceptible to a myriad of stress factors, especially abiotic stresses. Over the course of evolution, they have developed multiple mechanisms to sense and transduce environmental stimuli for appropriate responses. Among those, phosphorylation and dephosphorylation, regulated by protein kinases and protein phosphatases, respectively, are considered as crucial signal transduction mechanisms. Regarding the latter group, protein phosphatases type 2C (PP2Cs) represent the largest division of PPs. In addition, discovery of regulatory functions of PP2Cs in abscisic acid (ABA)-signaling pathway, the major signal transduction pathway in abiotic stress responses, indicates significant importance of PP2C members in plant adaptation to adverse environmental factors. In this review, current understanding of the roles of PP2Cs in different phytohormone-dependent pathways related to abiotic stress is summarized, highlighting the crosstalk between the ABA-signaling pathway with other hormonal pathways via certain ABA-related PP2Cs. We also updated progress of in planta characterization studies of PP2Cs under abiotic stress conditions, providing knowledge of PP2C manipulation in developing abiotic stress-tolerant crops.

scholarly journals The Role of Stress-Responsive Transcription Factors in Modulating Abiotic Stress Tolerance in Plants

Agronomy ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 788 ◽  
Author(s):  
Youngdae Yoon ◽  
Deok Hyun Seo ◽  
Hoyoon Shin ◽  
Hui Jin Kim ◽  
Chul Min Kim ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Crop Production ◽  
Global Climate ◽  
Abiotic Stress Tolerance ◽  
Plant Responses ◽  
Plant Tolerance

Abiotic stresses, such as drought, high temperature, and salinity, affect plant growth and productivity. Furthermore, global climate change may increase the frequency and severity of abiotic stresses, suggesting that development of varieties with improved stress tolerance is critical for future sustainable crop production. Improving stress tolerance requires a detailed understanding of the hormone signaling and transcriptional pathways involved in stress responses. Abscisic acid (ABA) and jasmonic acid (JA) are key stress-response hormones in plants, and some stress-responsive transcription factors such as ABFs and MYCs function as direct components of ABA and JA signaling, playing a pivotal role in plant tolerance to abiotic stress. In addition, extensive studies have identified other stress-responsive transcription factors belonging to the NAC, AP2/ERF, MYB, and WRKY families that mediate plant response and tolerance to abiotic stress. These suggest that transcriptional regulation of stress-responsive genes is an essential step to determine the mechanisms underlying plant stress responses and tolerance to abiotic stress, and that these transcription factors may be important targets for development of crops with enhanced abiotic stress tolerance. In this review, we briefly describe the mechanisms underlying plant abiotic stress responses, focusing on ABA and JA metabolism and signaling pathways. We then summarize the diverse array of transcription factors involved in plant responses to abiotic stress, while noting their potential applications for improvement of stress tolerance.

scholarly journals Progressive Genomic Approaches to Explore Drought- and Salt-Induced Oxidative Stress Responses in Plants under Changing Climate

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1910
Author(s):  
Masum Billah ◽  
Shirin Aktar ◽  
Marian Brestic ◽  
Marek Zivcak ◽  
Abul Bashar Mohammad Khaldun ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Crop Production ◽  
Ecological Factors ◽  
Crop Productivity ◽  
Stress Conditions ◽  
Plant Responses ◽  
World Population ◽  
Breeding Programs

Drought and salinity are the major environmental abiotic stresses that negatively impact crop development and yield. To improve yields under abiotic stress conditions, drought- and salinity-tolerant crops are key to support world crop production and mitigate the demand of the growing world population. Nevertheless, plant responses to abiotic stresses are highly complex and controlled by networks of genetic and ecological factors that are the main targets of crop breeding programs. Several genomics strategies are employed to improve crop productivity under abiotic stress conditions, but traditional techniques are not sufficient to prevent stress-related losses in productivity. Within the last decade, modern genomics studies have advanced our capabilities of improving crop genetics, especially those traits relevant to abiotic stress management. This review provided updated and comprehensive knowledge concerning all possible combinations of advanced genomics tools and the gene regulatory network of reactive oxygen species homeostasis for the appropriate planning of future breeding programs, which will assist sustainable crop production under salinity and drought conditions.

scholarly journals Small DNA Methylation, Big Player in Plant Abiotic Stress Responses and Memory

2020 ◽  
Vol 11 ◽  
Author(s):  
Junzhong Liu ◽  
Zuhua He
Keyword(s):  
Dna Methylation ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Genome Stability ◽  
Plant Stress ◽  
Epigenetic Inheritance ◽  
Future Research ◽  
Epigenetic Mark ◽  
Plant Responses

DNA methylation is a conserved epigenetic mark that plays important roles in maintaining genome stability and regulating gene expression. As sessile organisms, plants have evolved sophisticated regulatory systems to endure or respond to diverse adverse abiotic environmental challenges, i.e., abiotic stresses, such as extreme temperatures (cold and heat), drought and salinity. Plant stress responses are often accompanied by changes in chromatin modifications at diverse responsive loci, such as 5-methylcytosine (5mC) and N6-methyladenine (6mA) DNA methylation. Some abiotic stress responses are memorized for several hours or days through mitotic cell divisions and quickly reset to baseline levels after normal conditions are restored, which is referred to as somatic memory. In some cases, stress-induced chromatin marks are meiotically heritable and can impart the memory of stress exposure from parent plants to at least the next stress-free offspring generation through the mechanisms of transgenerational epigenetic inheritance, which may offer the descendants the potential to be adaptive for better fitness. In this review, we briefly summarize recent achievements regarding the establishment, maintenance and reset of DNA methylation, and highlight the diverse roles of DNA methylation in plant responses to abiotic stresses. Further, we discuss the potential role of DNA methylation in abiotic stress-induced somatic memory and transgenerational inheritance. Future research directions are proposed to develop stress-tolerant engineered crops to reduce the negative effects of abiotic stresses.

scholarly journals Jasmonic Acid in Plant Abiotic Stress Tolerance and Interaction with Abscisic Acid

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1886
Author(s):  
Hui Jin Kim ◽  
Subhin Seomun ◽  
Youngdae Yoon ◽  
Geupil Jang
Keyword(s):  
Abscisic Acid ◽  
Abiotic Stress ◽  
Jasmonic Acid ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Crucial Role ◽  
Abiotic Stress Tolerance ◽  
Plant Responses ◽  
Plant Abiotic Stress

The phytohormone jasmonic acid (JA), a cyclopentane fatty acid, mediates plant responses to abiotic stresses. Abiotic stresses rapidly and dynamically affect JA metabolism and JA responses by upregulating the expression of genes involved in JA biosynthesis and signaling, indicating that JA has a crucial role in plant abiotic stress responses. The crucial role of JA has been demonstrated in many previous studies showing that JA response regulates various plant defense systems, such as removal of reactive oxygen species and accumulation of osmoprotectants. Furthermore, increasing evidence shows that plant tolerance to abiotic stresses is linked to the JA response, suggesting that abiotic stress tolerance can be improved by modulating JA responses. In this review, we briefly describe the JA biosynthetic and signaling pathways and summarize recent studies showing an essential role of JA in plant responses and tolerance to a variety of abiotic stresses, such as drought, cold, salt, and heavy metal stress. Additionally, we discuss JA crosstalk with another key stress hormone, abscisic acid, in plant abiotic stress responses.

scholarly journals WRKY Proteins: Signaling and Regulation of Expression during Abiotic Stress Responses

2015 ◽  
Vol 2015 ◽  
pp. 1-17 ◽  
Author(s):  
Aditya Banerjee ◽  
Aryadeep Roychoudhury
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Biotic Stress ◽  
Abiotic Stresses ◽  
Abiotic Stress Tolerance ◽  
Plant Signaling ◽  
Biological Functions ◽  
Abiotic And Biotic Stress ◽  
Regulation Of Expression ◽  
Wrky Proteins

WRKY proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. However, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. WRKY proteins act as major transcription factors, either as positive or negative regulators. Specific WRKY factors which help in the expression of a cluster of stress-responsive genes are being targeted and genetically modified to induce improved abiotic stress tolerance in plants. The knowledge regarding the signaling cascade leading to the activation of the WRKY proteins, their interaction with other proteins of the signaling pathway, and the downstream genes activated by them are altogether vital for justified targeting of theWRKYgenes. WRKY proteins have also been considered to generate tolerance against multiple abiotic stresses with possible roles in mediating a cross talk between abiotic and biotic stress responses. In this review, we have reckoned the diverse signaling pattern and biological functions of WRKY proteins throughout the plant kingdom along with the growing prospects in this field of research.

scholarly journals Identification of conserved and novel miRNAs responsive to heat stress in flowering Chinese cabbage using high-throughput sequencing

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Waqas Ahmed ◽  
Yanshi Xia ◽  
Hua Zhang ◽  
Ronghua Li ◽  
Guihua Bai ◽  
...  
Keyword(s):  
Heat Stress ◽  
Abiotic Stress ◽  
High Throughput ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
High Throughput Sequencing ◽  
Differential Expression Analysis ◽  
Plant Responses ◽  
Limited Information ◽  
Flowering Chinese Cabbage

Abstract Plant microRNAs (miRNAs) are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development. Heat stress is a critical abiotic stress that reduces the yield and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, limited information is available on whether miRNAs are involved in the regulation of heat stress in B. campestris. A high-throughput sequencing approach was used to identify novel and conserved heat-responsive miRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0 h, 1 h, 6 h and 12 h after a 38 °C heat-stress treatment. The analysis identified 41 conserved miRNAs (belonging to 19 MIR families), of which MIR156, MIR159, MIR168, MIR171 and MIR1885 had the most abundant molecules. Prediction and evaluation of novel miRNAs using the unannotated reads resulted in 18 candidate miRNAs. Differential expression analysis showed that most of the identified miRNAs were downregulated in heat-treated groups. To better understand functional importance, bioinformatic analysis predicted 432 unique putative target miRNAs involved in cells, cell parts, catalytic activity, cellular processes and abiotic stress responses. Furthermore, the Kyoto Encyclopedia of Genes and Genomes maps of flowering Chinese cabbage identified the significant role of miRNAs in stress adaptation and stress tolerance, and in several mitogen-activated protein kinases signaling pathways including cell death. This work presents a comprehensive study of the miRNAs for understanding the regulatory mechanisms and their participation in the heat stress of flowering Chinese cabbage.

scholarly journals Conserved miR396b-GRF Regulation Is Involved in Abiotic Stress Responses in Pitaya (Hylocereus polyrhizus)

2019 ◽  
Vol 20 (10) ◽  
pp. 2501 ◽  
Author(s):  
A-Li Li ◽  
Zhuang Wen ◽  
Kun Yang ◽  
Xiao-Peng Wen
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Binding Site ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Molecular Mechanisms ◽  
Evolutionary Relationship ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
Hylocereus Polyrhizus

MicroRNA396 (miR396) is a conserved microRNA family that targets growth-regulating factors (GRFs), which play significant roles in plant growth and stress responses. Available evidence justifies the idea that miR396-targeted GRFs have important functions in many plant species; however, no genome-wide analysis of the pitaya (Hylocereus polyrhizus) miR396 gene has yet been reported. Further, its biological functions remain elusive. To uncover the regulatory roles of miR396 and its targets, the hairpin sequence of pitaya miR396b and the open reading frame (ORF) of its target, HpGRF6, were isolated from pitaya. Phylogenetic analysis showed that the precursor miR396b (MIR396b) gene of plants might be clustered into three major groups, and, generally, a more recent evolutionary relationship in the intra-family has been demonstrated. The sequence analysis indicated that the binding site of hpo-miR396b in HpGRF6 is located at the conserved motif which codes the conserved “RSRKPVE” amino acid in the Trp–Arg–Cys (WRC) region. In addition, degradome sequencing analysis confirmed that four GRFs (GRF1, c56908.graph_c0; GRF4, c52862.graph_c0; GRF6, c39378.graph_c0 and GRF9, c54658.graph_c0) are hpo-miR396b targets that are regulated by specific cleavage at the binding site between the 10th and 11th nucleotides from the 5′ terminus of hpo-miR396b. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that hpo-miR396b is down-regulated when confronted with drought stress (15% polyethylene glycol, PEG), and its expression fluctuates under other abiotic stresses, i.e., low temperature (4 ± 1 °C), high temperature (42 ± 1 °C), NaCl (100 mM), and abscisic acid (ABA; 0.38 mM). Conversely, the expression of HpGRF6 showed the opposite trend to exposure to these abiotic stresses. Taken together, hpo-miR396b plays a regulatory role in the control of HpGRF6, which might influence the abiotic stress response of pitaya. This is the first documentation of this role in pitaya and improves the understanding of the molecular mechanisms underlying the tolerance to drought stress in this fruit.

scholarly journals Signal Integration by Cyclin-Dependent Kinase 8 (CDK8) Module and Other Mediator Subunits in Biotic and Abiotic Stress Responses

2020 ◽  
Vol 22 (1) ◽  
pp. 354
Author(s):  
Leelyn Chong ◽  
Xiaoning Shi ◽  
Yingfang Zhu
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Current Knowledge ◽  
Signal Integration ◽  
Cyclin Dependent Kinase ◽  
Biotic And Abiotic Stress ◽  
Biotic And Abiotic Stresses ◽  
Adverse Conditions ◽  
Plant Transcriptome

Environmental stresses have driven plants to develop various mechanisms to acclimate in adverse conditions. Extensive studies have demonstrated that a significant reprogramming occurs in the plant transcriptome in response to biotic and abiotic stresses. The highly conserved and large multi-subunit transcriptional co-activator of eukaryotes, known as the Mediator, has been reported to play a substantial role in the regulation of important genes that help plants respond to environmental perturbances. CDK8 module is a relatively new component of the Mediator complex that has been shown to contribute to plants’ defense, development, and stress responses. Previous studies reported that CDK8 module predominantly acts as a transcriptional repressor in eukaryotic cells by reversibly associating with core Mediator. However, growing evidence has demonstrated that depending on the type of biotic and abiotic stress, the CDK8 module may perform a contrasting regulatory role. This review will summarize the current knowledge of CDK8 module as well as other previously documented Mediator subunits in plant cell signaling under stress conditions.

scholarly journals Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects

2021 ◽  
Vol 22 (2) ◽  
pp. 682
Author(s):  
Hymavathi Salava ◽  
Sravankumar Thula ◽  
Vijee Mohan ◽  
Rahul Kumar ◽  
Fatemeh Maghuly
Keyword(s):  
Abiotic Stress ◽  
Stress Tolerance ◽  
Genome Editing ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Nutritional Quality ◽  
Insertional Mutagenesis ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Crop Plants

Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed.

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