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Plants
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Multi-Omics Approaches for Plant Responses to Abiotic and Biotic Stresses
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Multi-Omics Approaches for Plant Responses to Abiotic and Biotic 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: closed (20 January 2025) | Viewed by 14154

Special Issue Editors

Dr. Pandiyan Muthuramalingam

E-Mail Website
Guest Editor
Division of Horticultural Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
Interests: plant stress physiology; bioinformatics; plant genetic engineering; plant biotechnology; multi-omics; abiotic stress; systems pharmacology
Special Issues, Collections and Topics in MDPI journals
Dr. Hyunsuk Shin

E-Mail Website
Guest Editor
Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
Interests: abiotic stress; pomology; ecophysiology; fruit trees; cold stress; abiotic stress; multi-omics; horticultural plants
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Manikandan Ramesh

E-Mail Website
Guest Editor
Department of Biotechnology, Alagappa University, Karaikudi 630003, India
Interests: abiotic stress; plant stress biology; plant biotechnology; plant tissue culture, genetic transformation, bioinformatics; molecular biology; multi-omics; crop plants; medicinal plants

Special Issue Information

Dear Colleagues,

Abiotic and biotic stresses are the primary environmental stressors that negatively impact overall plant growth, survival, and productivity. This is a comprehensive research topic on which many studies have been carried out worldwide to unravel the molecular and physiological cross-talk under various abiotic and biotic stress conditions. Regardless of all these efforts, the diverse adaptive mechanisms of plants under stressful environments are still major roadblocks. Thus, new high-throughput technologies and mitigation strategies are prerequisites for producing stress-tolerant plants with improved agronomical traits.

In recent years, emerging multi-omics, bioinformatics, and AI tools have been used to uncover novel molecular mechanisms underlying plant tolerance to various abiotic and biotic stress mechanisms. Therefore, this Special Issue aims to integrate various high-throughput sequencing datasets, multi-omics (genomics, epigenomics, transcriptomics, proteomics, hormonomics, metabolomics, interactomics, and phenomics) approaches, AI and bioinformatics tools, and other related topics, such as biotechnology, genetic transformation, systems biology, and breeding, to develop new progress in explaining the molecular-level aspects of stress-resistant plant production.

This Special Issue aims to unite the plant research community by publishing research findings and comprehensive reviews on strategies for enhancing stress avoidance and/or tolerance to abiotic and biotic stresses.

Dr. Pandiyan Muthuramalingam
Dr. Hyunsuk Shin
Prof. Dr. Manikandan Ramesh
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

  • biotic stress
  • bioinformatics
  • artificial intelligence
  • biotechnology
  • transcription factors
  • breeding
  • crop plants
  • horticultural plants
  • multi-omics
  • genomics
  • epigenomics
  • transcriptomics
  • proteomics
  • metabolomics
  • hormonomics
  • interactomics
  • phenomics
  • genetic diversity
  • systems biology
  • gene expression

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Published Papers (4 papers)

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Research

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15 pages, 11288 KiB  
Article
De Novo Transcriptome Assembly of Rice Bean (Vigna umbellata) and Characterization of WRKY Transcription Factors Response to Aluminum Stress
by Gunasekaran Ariharasutharsan, Manoharan Akilan, Manickam Dhasarathan, Manivel Amaravel, Sankaran Divya, Mariyappan Deivamani, Manickam Sudha, Muthaiyan Pandiyan, Adhimoolam Karthikeyan and Natesan Senthil
Plants 2024, 13(22), 3170; https://doi.org/10.3390/plants13223170 - 12 Nov 2024
Viewed by 1225
Abstract
Rice bean is an underutilized legume crop cultivated in Asia, and it is a good source of protein, minerals, and essential fatty acids for human consumption. Moreover, the leaves left over after harvesting rice bean seeds contain various biological constituents beneficial to humans [...] Read more.
Rice bean is an underutilized legume crop cultivated in Asia, and it is a good source of protein, minerals, and essential fatty acids for human consumption. Moreover, the leaves left over after harvesting rice bean seeds contain various biological constituents beneficial to humans and animals. In our study, we performed a de-novo transcriptome assembly of rice bean, characterized the WRKY transcription factors, and studied their response to aluminum stress. A total of 46.6 million clean reads, with a GC value of 43%, were generated via transcriptome sequencing. De novo assembly of the clean reads resulted in 90,933 transcripts and 74,926 unigenes, with minimum and maximum lengths of 301 bp and 24,052 bp, and N50 values of 1801 bp and 1710 bp, respectively. A total of 27,095 and 28,378 unigenes were annotated and subjected to GO and KEGG analyses. Among the unigenes, 15,593, 20,770, and 15,385 unigenes were identified in the domains of biological process, molecular function, and cellular component, respectively. A total of 16,132 unigenes were assigned to 188 pathways, including metabolic pathways (5500) and secondary metabolite biosynthesis (2858). Transcription factor analysis revealed 4860 unigenes from 98 different transcription factor families. For WRKY, a total of 95 unigenes were identified. Further analysis revealed the diverse response of WRKY transcription factors to aluminum stress. Collectively, the results of this study boost genomic resources and provide a baseline for further research on the role of WRKY transcription factors in aluminum tolerance in rice bean. Full article
(This article belongs to the Special Issue Multi-Omics Approaches for Plant Responses to Abiotic and Biotic Stresses)
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23 pages, 8408 KiB  
Article
Genome-Wide Identification and Analysis of Phospholipase C Gene Family Reveals Orthologs, Co-Expression Networks, and Expression Profiling Under Abiotic Stress in Sorghum bicolor
by Hongcheng Wang, Junxing Yu, Xingyu Zhang, Qian Zeng, Tuo Zeng, Lei Gu, Bin Zhu, Feng Yu and Xuye Du
Plants 2024, 13(21), 2976; https://doi.org/10.3390/plants13212976 - 24 Oct 2024
Viewed by 8278
Abstract
Phospholipase C (PLC) is an essential enzyme involved in lipid signaling pathways crucial for regulating plant growth and responding to environmental stress. In sorghum, 11 PLC genes have been identified, comprising 6 PI-PLCs and 5 NPCs. Through phylogenetic and interspecies collinearity analyses, [...] Read more.
Phospholipase C (PLC) is an essential enzyme involved in lipid signaling pathways crucial for regulating plant growth and responding to environmental stress. In sorghum, 11 PLC genes have been identified, comprising 6 PI-PLCs and 5 NPCs. Through phylogenetic and interspecies collinearity analyses, structural similarities between SbPLCs and ZmPLCs proteins have been observed, with a particularly strong collinearity between SbPLCs and OsPLCs. Promoter function analysis has shown that SbPLCs are significantly enriched under abiotic stress and hormonal stimuli, like ABA, jasmonic acid, drought, high temperature, and salt. Gene co-expression networks, constructed using a weighted gene co-expression network analysis (WGCNA), highlight distinct expression patterns of SbPLC1, SbPLC3a, and SbPLC4 in response to abiotic stress, providing further insights into the expression patterns and interactions of SbPLCs under various environmental stimuli. qRT-PCR results reveal variations in expression levels among most SbPLCs members under different stress conditions (drought, NaCl, NaHCO3), hormone treatments (ABA), and developmental stages, indicating both specific and overlapping expression patterns. This comprehensive analysis offers valuable insights into the roles of SbPLCs in sorghum, shedding light on their specific expression patterns, regulatory elements, and protein interactions across different environmental stimuli and developmental stages. Full article
(This article belongs to the Special Issue Multi-Omics Approaches for Plant Responses to Abiotic and Biotic Stresses)
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19 pages, 5544 KiB  
Article
Comprehensive Transcriptomic Analysis Reveals Defense-Related Genes and Pathways of Rice Plants in Response to Fall Armyworm (Spodoptera frugiperda) Infestation
by Xueyan Zhang, Xihao Wang and Tao Wang
Plants 2024, 13(20), 2879; https://doi.org/10.3390/plants13202879 - 15 Oct 2024
Cited by 2 | Viewed by 1594
Abstract
Rice (Oryza sativa L.) serves as a substitute for bread and is a staple food for half of the world’s population, but it is heavily affected by insect pests. The fall armyworm (Spodoptera frugiperda) is a highly destructive pest, threatening [...] Read more.
Rice (Oryza sativa L.) serves as a substitute for bread and is a staple food for half of the world’s population, but it is heavily affected by insect pests. The fall armyworm (Spodoptera frugiperda) is a highly destructive pest, threatening rice and other crops in tropical regions. Despite its significance, little is known about the molecular mechanisms underlying rice’s response to fall armyworm infestation. In this study, we used transcriptome analysis to explore the global changes in gene expression in rice leaves during a 1 h and 12 h fall armyworm feeding. The results reveal 2695 and 6264 differentially expressed genes (DEGs) at 1 and 12 h post-infestation, respectively. Gene Ontology (GO) and KEGG enrichment analyses provide insights into biological processes and pathways affected by fall armyworm feeding. Key genes associated with hormone regulation, defense metabolic pathways, and antioxidant and detoxification processes were upregulated, suggesting the involvement of jasmonic acid (JA) signaling, salicylic acid biosynthesis pathways, auxin response, and heat shock proteins in defense during 1 h and 12 h after fall armyworm infestation. Similarly, key genes involved in transcriptional regulation and defense mechanisms reveal the activation of calmodulins, transcription factors (TFs), and genes related to secondary metabolite biosynthesis. Additionally, MYB, WRKY, and ethylene-responsive factors (ERFs) are identified as crucial TF families in rice’s defense response. This study provides a comprehensive understanding of the molecular dynamics in rice responding to fall armyworm infestation, offering valuable insights for developing pest-resistant rice varieties and enhancing global food security. The identified genes and pathways provide an extensive array of genomic resources that can be used for further genetic investigation into rice herbivore resistance. This also suggests that rice plants may have evolved strategies against herbivorous insects. It also lays the groundwork for novel pest-resistance techniques for rice. Full article
(This article belongs to the Special Issue Multi-Omics Approaches for Plant Responses to Abiotic and Biotic Stresses)
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Review

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33 pages, 2472 KiB  
Review
Multi-Omics Approaches Against Abiotic and Biotic Stress—A Review
by Venkatramanan Varadharajan, Radhika Rajendran, Pandiyan Muthuramalingam, Ashish Runthala, Venkatesh Madhesh, Gowtham Swaminathan, Pooja Murugan, Harini Srinivasan, Yeonju Park, Hyunsuk Shin and Manikandan Ramesh
Plants 2025, 14(6), 865; https://doi.org/10.3390/plants14060865 - 10 Mar 2025
Cited by 1 | Viewed by 1979
Abstract
Plants face an array of environmental stresses, including both abiotic and biotic stresses. These stresses significantly impact plant lifespan and reduce agricultural crop productivity. Abiotic stresses, such as ultraviolet (UV) radiation, high and low temperatures, salinity, drought, floods, heavy metal toxicity, etc., contribute [...] Read more.
Plants face an array of environmental stresses, including both abiotic and biotic stresses. These stresses significantly impact plant lifespan and reduce agricultural crop productivity. Abiotic stresses, such as ultraviolet (UV) radiation, high and low temperatures, salinity, drought, floods, heavy metal toxicity, etc., contribute to widespread crop losses globally. On the other hand, biotic stresses, such as those caused by insects, fungi, and weeds, further exacerbate these challenges. These stressors can hinder plant systems at various levels, including molecular, cellular, and development processes. To overcome these challenges, multi-omics computational approaches offer a significant tool for characterizing the plant’s biomolecular pool, which is crucial for maintaining homeostasis and signaling response to environmental changes. Integrating multiple layers of omics data, such as proteomics, metabolomics, ionomics, interactomics, and phenomics, simplifies the study of plant resistance mechanisms. This comprehensive approach enables the development of regulatory networks and pathway maps, identifying potential targets for improving resistance through genetic engineering or breeding strategies. This review highlights the valuable insights from integrating multi-omics approaches to unravel plant stress responses to both biotic and abiotic factors. By decoding gene regulation and transcriptional networks, these techniques reveal critical mechanisms underlying stress tolerance. Furthermore, the role of secondary metabolites in bio-based products in enhancing plant stress mitigation is discussed. Genome editing tools offer promising strategies for improving plant resilience, as evidenced by successful case studies combating various stressors. On the whole, this review extensively discusses an advanced multi-omics approach that aids in understanding the molecular basis of resistance and developing novel strategies to improve crops’ or organisms’ resilience to abiotic and biotic stresses. Full article
(This article belongs to the Special Issue Multi-Omics Approaches for Plant Responses to Abiotic and Biotic Stresses)
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