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Abiotic Stress in Plants: Molecular Genetics and Genomics
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Abiotic Stress in Plants: Molecular Genetics and Genomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 June 2024) | Viewed by 6970

Special Issue Editor

Prof. Dr. Fei Gao

E-Mail Website
Guest Editor
College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
Interests: resource plant molecular biology; plant stress tolerance mechanisms; functional research on plant non-coding RNAs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Environmental stresses such as drought and low temperatures can have serious adverse effects on plant growth and development and crop yield. Global warming and climate change will further exacerbate the negative impact of adverse environments on plants, highlighting the necessity and importance of molecular mechanisms for plant abiotic stress response and tolerance. With the increasing maturity of high-throughput DNA sequencing technology and the development of various genetic modification methods, including CRISPR-Cas9, more and more molecular genetics and genomics technologies are being applied to the field of plant abiotic stress research, improving our understanding of the response mechanisms of various non-model plants to environmental stress.

The purpose of this Special Issue is to deeply analyze the response and adaptation mechanisms of plants to environmental stress by applying multiple types of omics methods, including genomics, transcriptomics, proteomics, and metabolomics, individually or in combination. The combination of bioinformatics and experimental validation is encouraged to analyze the abiotic stress response of plants.

Prof. Dr. Fei Gao
Guest Editor

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Keywords

  • abiotic stress
  • horticulture
  • gene family
  • transcriptomics
  • omics
  • medicinal plants

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Published Papers (5 papers)

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Research

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15 pages, 4465 KiB  
Article
A Global Identification of Protein Disulfide Isomerases from ‘duli’ Pear (Pyrus betulaefolia) and Their Expression Profiles under Salt Stress
by Hao Zhang, Yuyue Zhang, Kexin Cui, Chang Liu, Mengya Chen, Yufan Fu, Zhenjie Li, Hui Ma, Haixia Zhang, Baoxiu Qi and Jianfeng Xu
Genes 2024, 15(8), 968; https://doi.org/10.3390/genes15080968 - 23 Jul 2024
Viewed by 617
Abstract
Protein disulfide isomerases (PDIs) and PDI-like proteins catalyze the oxidation and reduction in protein disulfide bonds, inhibit aggregation of misfolded proteins, and participate in isomerization and abiotic stress responses. The wild type ‘duli’ pear (Pyrus betulaefolia) is an important rootstock commonly [...] Read more.
Protein disulfide isomerases (PDIs) and PDI-like proteins catalyze the oxidation and reduction in protein disulfide bonds, inhibit aggregation of misfolded proteins, and participate in isomerization and abiotic stress responses. The wild type ‘duli’ pear (Pyrus betulaefolia) is an important rootstock commonly used for commercial pear tree grafting in northern China. In this study, we identified 24 PDI genes, named PbPDIs, from the genome of ‘duli’ pear. With 12 homologous gene pairs, these 24 PbPDIs distribute on 12 of its 17 chromosomes. Phylogenetic analysis placed the 24 PbPDIs into four clades and eleven groups. Collinearity analysis of the PDIs between P. betulaefolia, Arabidopsis thaliana, and Oryza sativa revealed that the PbPDIs of ‘duli’ pear show a strong collinear relationship with those from Arabidopsis, a dicot; but a weak collinear relationship with those from rice, a monocot. Quantitative RT-PCR analysis showed that most of the PbPDIs were upregulated by salt stress. Identification and expression analysis of ‘duli’ pear PbPDIs under salt stress conditions could provide useful information for further research in order to generate salt-resistant rootstock for pear grafting in the future. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Molecular Genetics and Genomics)
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24 pages, 2421 KiB  
Article
Concordant Gene Expression and Alternative Splicing Regulation under Abiotic Stresses in Arabidopsis
by Aala A. Abulfaraj and Sahar A. Alshareef
Genes 2024, 15(6), 675; https://doi.org/10.3390/genes15060675 - 23 May 2024
Cited by 1 | Viewed by 1198
Abstract
The current investigation endeavors to identify differentially expressed alternatively spliced (DAS) genes that exhibit concordant expression with splicing factors (SFs) under diverse multifactorial abiotic stress combinations in Arabidopsis seedlings. SFs serve as the post-transcriptional mechanism governing the spatiotemporal dynamics of gene expression. The [...] Read more.
The current investigation endeavors to identify differentially expressed alternatively spliced (DAS) genes that exhibit concordant expression with splicing factors (SFs) under diverse multifactorial abiotic stress combinations in Arabidopsis seedlings. SFs serve as the post-transcriptional mechanism governing the spatiotemporal dynamics of gene expression. The different stresses encompass variations in salt concentration, heat, intensive light, and their combinations. Clusters demonstrating consistent expression profiles were surveyed to pinpoint DAS/SF gene pairs exhibiting concordant expression. Through rigorous selection criteria, which incorporate alignment with documented gene functionalities and expression patterns observed in this study, four members of the serine/arginine-rich (SR) gene family were delineated as SFs concordantly expressed with six DAS genes. These regulated SF genes encompass cactin, SR1-like, SR30, and SC35-like. The identified concordantly expressed DAS genes encode diverse proteins such as the 26.5 kDa heat shock protein, chaperone protein DnaJ, potassium channel GORK, calcium-binding EF hand family protein, DEAD-box RNA helicase, and 1-aminocyclopropane-1-carboxylate synthase 6. Among the concordantly expressed DAS/SF gene pairs, SR30/DEAD-box RNA helicase, and SC35-like/1-aminocyclopropane-1-carboxylate synthase 6 emerge as promising candidates, necessitating further examinations to ascertain whether these SFs orchestrate splicing of the respective DAS genes. This study contributes to a deeper comprehension of the varied responses of the splicing machinery to abiotic stresses. Leveraging these DAS/SF associations shows promise for elucidating avenues for augmenting breeding programs aimed at fortifying cultivated plants against heat and intensive light stresses. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Molecular Genetics and Genomics)
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19 pages, 3509 KiB  
Article
Overexpression of NtGPX8a Improved Cadmium Accumulation and Tolerance in Tobacco (Nicotiana tabacum L.)
by Xiang Peng, Tengfei Ma, Kejin Song, Xue Ji, Lien Xiang, Nan Chen, Ronglei Zu, Wenyi Xu, Shunqin Zhu and Wanhong Liu
Genes 2024, 15(3), 366; https://doi.org/10.3390/genes15030366 - 15 Mar 2024
Cited by 1 | Viewed by 1415
Abstract
Cadmium (Cd)-induced oxidative stress detrimentally affects hyperaccumulator growth, thereby diminishing the efficacy of phytoremediation technology aimed at Cd pollution abatement. In the domain of plant antioxidant mechanisms, the role of glutathione peroxidase (GPX) in conferring Cd tolerance to tobacco (Nicotiana tabacum) [...] Read more.
Cadmium (Cd)-induced oxidative stress detrimentally affects hyperaccumulator growth, thereby diminishing the efficacy of phytoremediation technology aimed at Cd pollution abatement. In the domain of plant antioxidant mechanisms, the role of glutathione peroxidase (GPX) in conferring Cd tolerance to tobacco (Nicotiana tabacum) remained unclear. Our investigation employed genome-wide analysis to identify 14 NtGPX genes in tobacco, revealing their organization into seven subgroups characterized by analogous conserved domain patterns. Notably, qPCR analysis highlighted NtGPX8a as markedly responsive to Cd2+ stress. Subsequent exploration through yeast two-hybridization unveiled NtGPX8a’s utilization of thioredoxins AtTrxZ and AtTrxm2 as electron donors, and without interaction with AtTrx5. Introduction of NtGPX8a into Escherichia coli significantly ameliorated Cd-induced adverse effects on bacterial growth. Transgenic tobacco overexpressing NtGPX8a demonstrated significantly augmented activities of GPX, SOD, POD, and CAT under Cd2+ stress compared to the wild type (WT). Conversely, these transgenic plants exhibited markedly reduced levels of MDA, H2O2, and proline. Intriguingly, the expression of NtGPX8a in both E. coli and transgenic tobacco led to increased Cd accumulation, confirming its dual role in enhancing Cd tolerance and accumulation. Consequently, NtGPX8a emerges as a promising candidate gene for engineering transgenic hyperaccumulators endowed with robust tolerance for Cd-contaminated phytoremediation. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Molecular Genetics and Genomics)
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16 pages, 3812 KiB  
Article
Genome-Wide Identification of Vascular Plant One-Zinc-Finger Gene Family in Six Cucurbitaceae Species and the Role of CmoVOZ2 in Salt and Drought Stress Tolerance
by Minyan Xu, Zhi Zhang, Yuhuan Jiao, Yaling Tu and Xin Zhang
Genes 2024, 15(3), 307; https://doi.org/10.3390/genes15030307 - 27 Feb 2024
Viewed by 1468
Abstract
As a plant-specific transcription factor, the vascular plant one-zinc-finger (VOZ) plays a crucial role in regulating various biological processes. In this study, a total of 17 VOZ genes in the Cucurbitaceae family were investigated using various bioinformatics methods. The 17 VOZ genes in [...] Read more.
As a plant-specific transcription factor, the vascular plant one-zinc-finger (VOZ) plays a crucial role in regulating various biological processes. In this study, a total of 17 VOZ genes in the Cucurbitaceae family were investigated using various bioinformatics methods. The 17 VOZ genes in Cucurbitaceae are distributed across 16 chromosomes. Based on the affinity of VOZ proteins to AtVOZ proteins, these 17 proteins were categorized into two groups: group I encompassed eight VOZ members, while group II comprised nine VOZ members. The expression profiles of CmoVOZs under various hormonal and abiotic stresses indicated that these genes were induced differentially by JA, ABA, GA, salt, and drought stress. Subsequently, CmoVOZ1 and CmoVOZ2 were found to be transcriptionally active, with the CmoVOZ2 protein being located mainly in the nucleus. Further experiments revealed that yeast cells expressing CmoVOZ2 gene showed increased tolerance to salt stress and drought stress. These results suggest that the VOZ gene family is not only important for plant growth and development but also that this mechanism may be universal across yeast and plants. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Molecular Genetics and Genomics)
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Review

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20 pages, 1699 KiB  
Review
The Euphrates Poplar Responses to Abiotic Stress and Its Unique Traits in Dry Regions of China (Xinjiang and Inner Mongolia): What Should We Know?
by Boniface Ndayambaza, Jianhua Si, Yanfang Deng, Bing Jia, Xiaohui He, Dongmeng Zhou, Chunlin Wang, Xinglin Zhu, Zijin Liu, Jie Qin, Boyang Wang and Xue Bai
Genes 2023, 14(12), 2213; https://doi.org/10.3390/genes14122213 - 14 Dec 2023
Cited by 1 | Viewed by 1699
Abstract
At the moment, drought, salinity, and low-temperature stress are ubiquitous environmental issues. In arid regions including Xinjiang and Inner Mongolia and other areas worldwide, the area of tree plantations appears to be rising, triggering tree growth. Water is a vital resource in the [...] Read more.
At the moment, drought, salinity, and low-temperature stress are ubiquitous environmental issues. In arid regions including Xinjiang and Inner Mongolia and other areas worldwide, the area of tree plantations appears to be rising, triggering tree growth. Water is a vital resource in the agricultural systems of countries impacted by aridity and salinity. Worldwide efforts to reduce quantitative yield losses on Populus euphratica by adapting tree plant production to unfavorable environmental conditions have been made in response to the responsiveness of the increasing control of water stress. Although there has been much advancement in identifying the genes that resist abiotic stresses, little is known about how plants such as P. euphratica deal with numerous abiotic stresses. P. euphratica is a varied riparian plant that can tolerate drought, salinity, low temperatures, and climate change, and has a variety of water stress adaptability abilities. To conduct this review, we gathered all available information throughout the Web of Science, the Chinese National Knowledge Infrastructure, and the National Center for Biotechnology Information on the impact of abiotic stress on the molecular mechanism and evolution of gene families at the transcription level. The data demonstrated that P. euphratica might gradually adapt its stomatal aperture, photosynthesis, antioxidant activities, xylem architecture, and hydraulic conductivity to endure extreme drought and salt stress. Our analyses will give readers an understanding of how to manage a gene family in desert trees and the influence of abiotic stresses on the productivity of tree plants. They will also give readers the knowledge necessary to improve biotechnology-based tree plant stress tolerance for sustaining yield and quality trees in China’s arid regions. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Molecular Genetics and Genomics)
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