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Multi-Omics Analysis of Plant under Abiotic Stress
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Multi-Omics Analysis of Plant under Abiotic Stress

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 8607

Special Issue Editors

Prof. Dr. Jingkui Tian

E-Mail Website
Guest Editor
Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou 310022, China
Interests: secondary metabolism; medicinal plants; plant proteomics; ultraviolet stress
Dr. Wei Zhu

E-Mail Website
Guest Editor
Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou 310022, China
Interests: plant metabolomics; medicinal plants; plant proteomics; synthetic biology

Special Issue Information

Dear Colleagues,

Abiotic stress such as drought, flooding, heat, cold, ultraviolet radiation, salinity etc, is the common adverse environmental factors to affect the plants’ growth or the crop productivity. However, the nature is marvelous, plants have evolved a variety of defense system against those stresses. Understanding the tolerance mechanism in plants will be significant for plant breeding, improving crop productivity, and even the biosynthesis of medicinal metabolites, which are closely related to our life. Recently, omics techniques such as proteomics, metabolomics, transcriptomics, phenomics, genomics etc., have been powerful tools to elucidate the growth, senescence, yield, and the responses to abiotic stress in plants at the different levels, especially for the combination of multi-omics approach. This Special Issue of Plants will highlight the significance and applications of omics or multi-omics techniques to gain new insights into plant molecular response to various abiotic stressors and their interactions with plants.

Prof. Dr. Jingkui Tian
Dr. Wei Zhu
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
  • plants
  • multi-omics
  • response mechanism

Published Papers (5 papers)

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Research

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20 pages, 11110 KiB  
Article
A Comprehensive Analysis of the Peanut SQUAMOSA Promoter Binding Protein-like Gene Family and How AhSPL5 Enhances Salt Tolerance in Transgenic Arabidopsis
by Xiaohui Sun, Lili Zhang, Weihua Xu, Jianpeng Zheng, Meiling Yan, Ming Zhao, Xinyu Wang and Yan Yin
Plants 2024, 13(8), 1057; https://doi.org/10.3390/plants13081057 - 09 Apr 2024
Viewed by 437
Abstract
SPL (SQUAMOSA promoter binding protein-like), as one family of plant transcription factors, plays an important function in plant growth and development and in response to environmental stresses. Despite SPL gene families having been identified in various plant species, the understanding of this gene [...] Read more.
SPL (SQUAMOSA promoter binding protein-like), as one family of plant transcription factors, plays an important function in plant growth and development and in response to environmental stresses. Despite SPL gene families having been identified in various plant species, the understanding of this gene family in peanuts remains insufficient. In this study, thirty-eight genes (AhSPL1-AhSPL38) were identified and classified into seven groups based on a phylogenetic analysis. In addition, a thorough analysis indicated that the AhSPL genes experienced segmental duplications. The analysis of the gene structure and protein motif patterns revealed similarities in the structure of exons and introns, as well as the organization of the motifs within the same group, thereby providing additional support to the conclusions drawn from the phylogenetic analysis. The analysis of the regulatory elements and RNA-seq data suggested that the AhSPL genes might be widely involved in peanut growth and development, as well as in response to environmental stresses. Furthermore, the expression of some AhSPL genes, including AhSPL5, AhSPL16, AhSPL25, and AhSPL36, were induced by drought and salt stresses. Notably, the expression of the AhSPL genes might potentially be regulated by regulatory factors with distinct functionalities, such as transcription factors ERF, WRKY, MYB, and Dof, and microRNAs, like ahy-miR156. Notably, the overexpression of AhSPL5 can enhance salt tolerance in transgenic Arabidopsis by enhancing its ROS-scavenging capability and positively regulating the expression of stress-responsive genes. These results provide insight into the evolutionary origin of plant SPL genes and how they enhance plant tolerance to salt stress. Full article
(This article belongs to the Special Issue Multi-Omics Analysis of Plant under Abiotic Stress)
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24 pages, 5722 KiB  
Article
Algal Bio-Stimulants Enhance Salt Tolerance in Common Bean: Dissecting Morphological, Physiological, and Genetic Mechanisms for Stress Adaptation
by Hoda H. Senousy, Yousef Alhaj Hamoud, Abdelghafar M. Abu-Elsaoud, Omar Mahmoud Al zoubi, Nessreen F. Abdelbaky, Muhammad Zia-ur-Rehman, Muhammad Usman and Mona H. Soliman
Plants 2023, 12(21), 3714; https://doi.org/10.3390/plants12213714 - 29 Oct 2023
Viewed by 1427
Abstract
Salinity adversely affects the plant’s morphological characteristics, but the utilization of aqueous algal extracts (AE) ameliorates this negative impact. In this study, the application of AE derived from Chlorella vulgaris and Dunaliella salina strains effectively reversed the decline in biomass allocation and water [...] Read more.
Salinity adversely affects the plant’s morphological characteristics, but the utilization of aqueous algal extracts (AE) ameliorates this negative impact. In this study, the application of AE derived from Chlorella vulgaris and Dunaliella salina strains effectively reversed the decline in biomass allocation and water relations, both in normal and salt-stressed conditions. The simultaneous application of both extracts in salt-affected soil notably enhanced key parameters, such as chlorophyll content (15%), carotene content (1%), photosynthesis (25%), stomatal conductance (7%), and transpiration rate (23%), surpassing those observed in the application of both AE in salt-affected as compared to salinity stress control. Moreover, the AE treatments effectively mitigated lipid peroxidation and electrolyte leakage induced by salinity stress. The application of AE led to an increase in GB (6%) and the total concentration of free amino acids (47%) by comparing with salt-affected control. Additionally, salinity stress resulted in an elevation of antioxidant enzyme activities, including superoxide dismutase, ascorbate peroxidase, catalase, and glutathione reductase. Notably, the AE treatments significantly boosted the activity of these antioxidant enzymes under salinity conditions. Furthermore, salinity reduced mineral contents, but the application of AE effectively counteracted this decline, leading to increased mineral levels. In conclusion, the application of aqueous algal extracts, specifically those obtained from Chlorella vulgaris and Dunaliella salina strains, demonstrated significant efficacy in alleviating salinity-induced stress in Phaseolus vulgaris plants. Full article
(This article belongs to the Special Issue Multi-Omics Analysis of Plant under Abiotic Stress)
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14 pages, 5191 KiB  
Article
Integrative Omic Analysis Reveals the Dynamic Change in Phenylpropanoid Metabolism in Morus alba under Different Stress
by Yaohan Li, Shengzhi Liu, Di Zhang, Amin Liu, Wei Zhu, Jianbin Zhang and Bingxian Yang
Plants 2023, 12(18), 3265; https://doi.org/10.3390/plants12183265 - 14 Sep 2023
Cited by 1 | Viewed by 910
Abstract
Morus alba is used as a traditional Chinese medicine due to its various biological activities. Phenylpropanoid metabolism is one of the most important pathways in Morus alba to produce secondary metabolites and response to stress. From the general phenylpropanoid pathway, there are two [...] Read more.
Morus alba is used as a traditional Chinese medicine due to its various biological activities. Phenylpropanoid metabolism is one of the most important pathways in Morus alba to produce secondary metabolites and response to stress. From the general phenylpropanoid pathway, there are two metabolic branches in M. alba, including flavonoid and lignin biosynthesis, which also play roles in response to stress. However, the dynamic changes between flavonoid and lignin biosynthesis under Botrytis cinerea infection and UV-B stress in M. alba were unclear. To explore the different regulation mode of flavonoid and lignin biosynthesis in M. alba leaves’ response to biotic and abiotic stress, a combined proteomic and metabolomic study of M. alba leaves under UV-B stress and B. cinerea infection was performed. The results showed that most of the proteins involved in the lignin and flavonoid biosynthesis pathway were increased under either UV-B stress or B. cinerea infection in M. alba. This was also confirmed by enzyme assays and metabolomics analysis. Additionally, the abundance of proteins involved in the biosynthesis of jasmonic acid was increased after B. cinerea infection. This suggests that both flavonoid and lignin biosynthesis participate in the responses to abiotic and biotic stress in M. alba, but they might be regulated by different hormone signaling. Full article
(This article belongs to the Special Issue Multi-Omics Analysis of Plant under Abiotic Stress)
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Review

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25 pages, 1608 KiB  
Review
Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications
by Mukhtar Iderawumi Abdulraheem, Yani Xiong, Abiodun Yusuff Moshood, Gregorio Cadenas-Pliego, Hao Zhang and Jiandong Hu
Plants 2024, 13(2), 163; https://doi.org/10.3390/plants13020163 - 07 Jan 2024
Cited by 2 | Viewed by 2741
Abstract
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to [...] Read more.
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5–10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement. Full article
(This article belongs to the Special Issue Multi-Omics Analysis of Plant under Abiotic Stress)
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22 pages, 1881 KiB  
Review
Exploring the Potential of Multiomics and Other Integrative Approaches for Improving Waterlogging Tolerance in Plants
by Anshika Tyagi, Sajad Ali, Suvin Park and Hanhong Bae
Plants 2023, 12(7), 1544; https://doi.org/10.3390/plants12071544 - 03 Apr 2023
Cited by 7 | Viewed by 2226
Abstract
Soil flooding has emerged as a serious threat to modern agriculture due to the rapid global warming and climate change, resulting in catastrophic crop damage and yield losses. The most detrimental effects of waterlogging in plants are hypoxia, decreased nutrient uptake, photosynthesis inhibition, [...] Read more.
Soil flooding has emerged as a serious threat to modern agriculture due to the rapid global warming and climate change, resulting in catastrophic crop damage and yield losses. The most detrimental effects of waterlogging in plants are hypoxia, decreased nutrient uptake, photosynthesis inhibition, energy crisis, and microbiome alterations, all of which result in plant death. Although significant advancement has been made in mitigating waterlogging stress, it remains largely enigmatic how plants perceive flood signals and translate them for their adaptive responses at a molecular level. With the advent of multiomics, there has been significant progress in understanding and decoding the intricacy of how plants respond to different stressors which have paved the way towards the development of climate-resistant smart crops. In this review, we have provided the overview of the effect of waterlogging in plants, signaling (calcium, reactive oxygen species, nitric oxide, hormones), and adaptive responses. Secondly, we discussed an insight into past, present, and future prospects of waterlogging tolerance focusing on conventional breeding, transgenic, multiomics, and gene-editing approaches. In addition, we have also highlighted the importance of panomics for developing waterlogging-tolerant cultivars. Furthermore, we have discussed the role of high-throughput phenotyping in the screening of complex waterlogging-tolerant traits. Finally, we addressed the current challenges and future perspectives of waterlogging signal perception and transduction in plants, which warrants future investigation. Full article
(This article belongs to the Special Issue Multi-Omics Analysis of Plant under Abiotic Stress)
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