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Plant Stress Biology
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Plant Stress Biology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 August 2026 | Viewed by 6367

Special Issue Editor

Dr. Rui Li

E-Mail Website
Guest Editor
College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
Interests: plant metabolism; abiotic stresses; biotic stresses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are delighted to invite researchers to contribute to the Special Issue on “Plant Stress Biology”. This initiative seeks to advance our understanding of how plants perceive, respond to, and recover from diverse environmental and biotic stresses, which are escalating due to climate change, land degradation, and pathogen evolution.

Plant stress biology is a critical frontier in ensuring food security and ecological sustainability. This issue will highlight cutting-edge research on abiotic stresses (e.g., drought, salinity, extreme temperatures, heavy metals) and biotic challenges (e.g., pathogens, pests, invasive species), with a focus on molecular, physiological, and ecological mechanisms. Submissions may explore topics such as stress-signaling networks, epigenetic regulation, genome editing (e.g., CRISPR-based resilience engineering), microbiome interactions, and innovative phenotyping technologies. We particularly welcome studies integrating multi-omics approaches or synthetic biology to decode plant stress responses.

Join us in shaping a resilient future—submit your groundbreaking work and collaborate to turn stress biology insights into transformative tools for agriculture and ecosystems worldwide.

Dr. Rui Li
Guest Editor

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 250 words) can be sent to the Editorial Office for assessment.

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
  • stress response mechanisms
  • oxidative stress
  • phytohormones signaling
  • stress tolerance

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Published Papers (7 papers)

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Research

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18 pages, 21018 KB  
Article
Genome-Wide Association Study (GWAS) for Freezing and De-Acclimation Tolerance in Polish Winter Barley
by Ipsa Bani, Santosh Hadagali and Magdalena Wójcik-Jagła
Int. J. Mol. Sci. 2026, 27(6), 2759; https://doi.org/10.3390/ijms27062759 - 18 Mar 2026
Viewed by 396
Abstract
Winter survival in barley depends on freezing tolerance and de-acclimation tolerance, yet their genetic determinants under increasingly unstable winters remain poorly understood. Here, 188 Polish barley accessions were evaluated over two consecutive growing seasons (2021–2022) using genome-wide association studies (GWAS) with a mixed-linear [...] Read more.
Winter survival in barley depends on freezing tolerance and de-acclimation tolerance, yet their genetic determinants under increasingly unstable winters remain poorly understood. Here, 188 Polish barley accessions were evaluated over two consecutive growing seasons (2021–2022) using genome-wide association studies (GWAS) with a mixed-linear model (MLM) and high-density single nucleotide polymorphism (SNP) and diversity arrays technology sequencing (DArTseq) markers. Freezing and de-acclimation tolerance were quantified by 16 chlorophyll fluorescence parameters and post-freezing survival rates in plants subjected to 21 days of cold acclimation (4 °C/2 °C, day/night) and 7 days of de-acclimation (12 °C/5 °C, day/night). The results showed that freezing and de-acclimation tolerance are related but genetically distinct. The cold-acclimated (CA) state exhibited significant marker–trait associations on chromosomes 2H and 6H, whereas the de-acclimated (DA) state displayed a broader, more complex genetic architecture, particularly on chromosomes 2H and 7H. Fv/Fm showed the strongest associations for both SNP and DArTseq markers in both states. PI(csm), followed by PI(cs0) and PI(total), showed high SNP associations in the DA state, indicating a strong relationship between photosynthetic performance and freezing tolerance after de-acclimation. Notably, the DArTseq marker 11400277 on chromosome 7H showed multiple marker–trait associations across both states. These findings provide a genomic basis for marker-assisted selection of climate-resilient winter barley cultivars. Full article
(This article belongs to the Special Issue Plant Stress Biology)
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16 pages, 3732 KB  
Article
Comprehensive Transcriptomic Analysis of the Molecular Mechanisms Conferring Resistance to Rice Blast in the Elite Restorer Line Fuhui2165
by Shuijin Zhang, Yinyin Mao, Yonghe Hong, Feiyan Zheng, Ronghua Hu, Shihang Tu, Fantao Zhang and Peng Zhou
Int. J. Mol. Sci. 2025, 26(20), 10164; https://doi.org/10.3390/ijms262010164 - 19 Oct 2025
Viewed by 883
Abstract
Rice blast, caused by Magnaporthe oryzae (M. oryzae), severely threatens global rice production with substantial yield losses, endangering food security and driving demand for resistant varieties. Fuhui2165 (FH2165), an elite restorer line with stable blast resistance, superior agronomic traits, and high [...] Read more.
Rice blast, caused by Magnaporthe oryzae (M. oryzae), severely threatens global rice production with substantial yield losses, endangering food security and driving demand for resistant varieties. Fuhui2165 (FH2165), an elite restorer line with stable blast resistance, superior agronomic traits, and high grain quality, is valuable for hybrid breeding, but its resistance mechanisms remain unclear. In this study, we investigated the rice blast resistance and underlying mechanisms in FH2165 and its parental lines (Huahangsimiao/HHSM, Minghui86/MH86, and Shuhui527/SH527) using transcriptome sequencing analysis. Phenotypic analysis revealed that FH2165 and HHSM exhibited stronger resistance compared to MH86 and SH527. Differential expression analysis identified 3886, 2513, 3390, and 4678 differentially expressed genes (DEGs) in FH2165, HHSM, MH86, and SH527, respectively. Gene Ontology (GO) enrichment analysis highlighted DEGs associated with chloroplasts, plastids, thylakoids, and related cellular components. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified significant enrichment in pathways such as carbon metabolism, amino acid biosynthesis, and photosynthesis. This suggested that defense strategies could involve energy reprogramming and the synthesis of secondary metabolites. Additionally, the DEGs co-expressed specifically in FH2165 and HHSM were enriched in functions related to RNA processing, GTP binding, and L-ascorbic acid binding, with purine metabolism playing a role in the regulation of energy and signaling. These findings elucidated the critical metabolic and signaling networks that underlie the blast resistance of FH2165 and offered potential targets for breeding high-yield, disease-resistant hybrid rice varieties. Full article
(This article belongs to the Special Issue Plant Stress Biology)
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29 pages, 21040 KB  
Article
The DIR Gene Family in Watermelon: Evolution, Stress Expression Profiles, and Functional Exploration of ClDIR8
by Kaijing Zhang, Zhu Wang, Huiyu Tian, Jiong Gao, Rongjing Cui, Yingjie Shu, Qiangqiang Ding, Li Jia and Congsheng Yan
Int. J. Mol. Sci. 2025, 26(16), 7730; https://doi.org/10.3390/ijms26167730 - 10 Aug 2025
Viewed by 1230
Abstract
Dirigent proteins (DIR) are involved in lignan biosynthesis, stress responses, and disease resistance in plants. However, systematic characterization of the DIR gene family in watermelon (Citrullus lanatus) remains limited. Here, we identified 22 ClDIR genes in watermelon using bioinformatics methods, designated [...] Read more.
Dirigent proteins (DIR) are involved in lignan biosynthesis, stress responses, and disease resistance in plants. However, systematic characterization of the DIR gene family in watermelon (Citrullus lanatus) remains limited. Here, we identified 22 ClDIR genes in watermelon using bioinformatics methods, designated ClDIR1 to ClDIR22, which were unevenly distributed across eight chromosomes and classified into three subfamilies (DIR-a, DIR-b/d, DIR-e) based on phylogenetic analysis, with DIR-b/d being the largest. Synteny analysis revealed that tandem duplication primarily drove ClDIR family expansion, and collinear relationships with Arabidopsis, rice, and cucurbit species indicated evolutionary conservation. Cis-acting element analysis showed abundant stress- and hormone-responsive elements in ClDIR promoters, suggesting roles in stress regulation. Tissue-specific expression analysis demonstrated distinct patterns, with most genes highly expressed in roots. Expression profiling under 16 abiotic and biotic stresses showed 18 ClDIR genes responded to stress, with ClDIR8 differentially expressed across all conditions. qRT-PCR validation of six key genes (ClDIR5, ClDIR8, ClDIR9, ClDIR12, ClDIR16, ClDIR22) confirmed their expression patterns under high-temperature, drought, salt, and low-temperature stresses, showing a high degree of consistency with transcriptome data. Subcellular localization indicated ClDIR8 is peroxisome-localized. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays validated two ClDIR8-interacting proteins, Cla97C02G049920 (encoding peroxidase) and Cla97C08G152180 (encoding catalase). These findings provide insights into ClDIR genes in watermelon, highlighting ClDIR8 as a key stress-responsive candidate for further functional studies and breeding. Full article
(This article belongs to the Special Issue Plant Stress Biology)
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19 pages, 4354 KB  
Article
Genomic Insights into ARR Genes: Key Role in Cotton Leaf Abscission Formation
by Hongyan Shi, Zhenyu Wang, Yuzhi Zhang, Gongye Cheng, Peijun Huang, Li Yang, Songjuan Tan, Xiaoyu Cao, Xiaoyu Pei, Yu Liang, Yu Gao, Xiang Ren, Quanjia Chen and Xiongfeng Ma
Int. J. Mol. Sci. 2025, 26(15), 7161; https://doi.org/10.3390/ijms26157161 - 24 Jul 2025
Cited by 1 | Viewed by 1190
Abstract
The cytokinin response regulator (ARR) gene is essential for cytokinin signal transduction, which plays a crucial role in plant growth and development. However, the functional mechanism of ARR genes in cotton leaf abscission remains incompletely understood. In this study, a total [...] Read more.
The cytokinin response regulator (ARR) gene is essential for cytokinin signal transduction, which plays a crucial role in plant growth and development. However, the functional mechanism of ARR genes in cotton leaf abscission remains incompletely understood. In this study, a total of 86 ARR genes were identified within the genome of Gossypium hirsutum. These genes were categorized into four distinct groups based on their phylogenetic characteristics, supported by analyses of gene structures and conserved protein motifs. The GhARR genes exhibited an uneven distribution across 25 chromosomes, with three pairs of tandem duplication events observed. Both segmental and tandem duplication events significantly contributed to the expansion of the ARR gene family. Furthermore, numerous putative cis-elements were identified in the promoter regions, with hormone and stress-related elements being common among all 86 GhARRs. Transcriptome expression profiling screening results demonstrated that GhARRs may play a mediating role in cotton’s response to TDZ (thidiazuron). The functional validation of GhARR16, GhARR43, and GhARR85 using virus-induced gene silencing (VIGS) technology demonstrated that the silencing of these genes led to pronounced leaf wilting and chlorosis in plants, accompanied by a substantial decrease in petiole fracture force. Overall, our study represents a comprehensive analysis of the G. hirsutum ARR gene family, revealing their potential roles in leaf abscission regulation. Full article
(This article belongs to the Special Issue Plant Stress Biology)
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Review

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30 pages, 2292 KB  
Review
From Lab to Field: CRISPRing Major Cultivated Solanaceae for Crop Improvement
by Martina Ferrero, Alberto Acquadro and Andrea Moglia
Int. J. Mol. Sci. 2026, 27(5), 2238; https://doi.org/10.3390/ijms27052238 - 27 Feb 2026
Viewed by 834
Abstract
The Solanaceae family includes some of the most economically and agronomically important crops, such as tomato, potato, pepper and eggplant. Recently, CRISPR/Cas-based genome editing has emerged as a powerful tool for functional genomics and crop improvement, enabling precise and efficient genetic modifications. This [...] Read more.
The Solanaceae family includes some of the most economically and agronomically important crops, such as tomato, potato, pepper and eggplant. Recently, CRISPR/Cas-based genome editing has emerged as a powerful tool for functional genomics and crop improvement, enabling precise and efficient genetic modifications. This review provides an overview of CRISPR/Cas-mediated genome editing technologies and their applications in the major cultivated Solanaceae crops. The use of CRISPR/Cas9 systems for targeted gene knockout and knock-in approaches is described, together with advances in precision editing strategies such as base editing and prime editing, which allow precise nucleotide substitutions and small sequence changes. The expanding CRISPR toolbox is further explored through alternative Cas proteins, such as Cas12a and Cas13 with distinct targeting features and potential applications. Emerging delivery strategies, including ribonucleoprotein-mediated editing in protoplasts, virus-induced gene editing (VIGE), de novo induction of meristems and genome editing by grafting, represent promising approaches to generate transgene-free edited plants. In addition, the current status of field trials involving genome-edited Solanaceae crops in Europe is outlined, considering the regulatory landscape and legislative requirements for their release in the environment. Despite regulatory constraints, some genome-edited crops have reached the market, highlighting their potential to contribute to sustainable agriculture and crop improvement. Full article
(This article belongs to the Special Issue Plant Stress Biology)
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17 pages, 643 KB  
Review
The Hrd1-Mediated ERAD Pathway in Plants: Conserved Principles and Plant-Specific Innovations
by Jiarui Wu, Peiqi Huang and Jianming Li
Int. J. Mol. Sci. 2026, 27(4), 1801; https://doi.org/10.3390/ijms27041801 - 13 Feb 2026
Viewed by 694
Abstract
Endoplasmic reticulum-mediated protein quality control (ERQC) safeguards secretory pathway proteostasis by recognizing, retaining, repairing, and removing misfolded proteins, and is therefore essential for plant growth, development, and stress tolerance. This system relies on ER-associated degradation (ERAD), in which irreparably misfolded proteins are first [...] Read more.
Endoplasmic reticulum-mediated protein quality control (ERQC) safeguards secretory pathway proteostasis by recognizing, retaining, repairing, and removing misfolded proteins, and is therefore essential for plant growth, development, and stress tolerance. This system relies on ER-associated degradation (ERAD), in which irreparably misfolded proteins are first recognized in the ER, then exported across the ER membrane to the cytosol, where they are ubiquitinated by ER membrane-anchored ubiquitin ligases, and subsequently degraded by the cytosolic proteasome. Studies in yeast and mammals have defined several conserved ERAD branches, including a multiprotein ERAD complex centered on the polytopic ER membrane E3 ligase HMG-CoA reductase degradation protein 1 (Hrd1), which integrates substrate recognition, membrane retrotranslocation, ubiquitin conjugation, and cytosolic extraction. Recent advances in Arabidopsis show that plants retain the core Hrd1 ERAD architecture while incorporating additional regulatory elements that adapt this machinery to plant-specific physiological demands. Genetic and biochemical analyses of misfolded receptor kinases and engineered substrates have uncovered conserved and plant-specific components of the plant Hrd1 complex, revealing how the plant ERAD pathway integrates ERQC with hormone signaling, stress adaptation, immune responses, and growth regulation. This review synthesizes recent advances in plant ERAD research and highlights key conceptual and mechanistic questions that remain to be resolved. Full article
(This article belongs to the Special Issue Plant Stress Biology)
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11 pages, 1117 KB  
Review
Coding Transcript-Derived Small Interfering RNAs: Their Biogenesis and Molecular Function in Arabidopsis
by Xintong Xu, Nier Chen, Xinwen Qing, Xiaoli Peng, Xiangze Chen, Beixin Mo and Yongbing Ren
Int. J. Mol. Sci. 2026, 27(4), 1701; https://doi.org/10.3390/ijms27041701 - 10 Feb 2026
Viewed by 456
Abstract
Coding transcripts-derived small interfering RNAs (ct-siRNAs) have emerged as a special class of endogenous siRNAs and have been implicated in the regulation of gene expression in plants, particularly under conditions where RNA metabolic pathways are perturbed. When the RNA quality control (RQC) system [...] Read more.
Coding transcripts-derived small interfering RNAs (ct-siRNAs) have emerged as a special class of endogenous siRNAs and have been implicated in the regulation of gene expression in plants, particularly under conditions where RNA metabolic pathways are perturbed. When the RNA quality control (RQC) system is impaired, the aberrant mRNA fragments were converted to double stranded forms by RNA-directed RNA polymerase 6 (RDR6) with the assistance of Suppressor of Gene Silencing 3 (SGS3) and subsequently processed by DICER-LIKE proteins into 21-nt and 22-nt ct-siRNAs. The accumulation of ct-siRNAs and the resulting suppression of their cognate genes are usually associated with altered plant growth and stress response. In this review, we summarize our current understanding of the ct-siRNAs, particularly their biogenesis under different RNA metabolic defective conditions. Comparative analysis of these genetic contexts indicates that ct-siRNAs act through translation inhibition and/or mRNA cleavage, with regulatory outcomes influenced by siRNA length and genetic background. We further summarize the biological consequence of ct-siRNA accumulation, which are frequently associated with impaired plant growth and stress adaptation. Finally, we discuss current controversies on ct-siRNAs research and highlight key unsolved questions for future investigation. Collectively, this review highlights ct-siRNAs as a link between impaired RNA metabolisms and post-transcriptional gene silencing, with context-dependent effects on plant growth and stress responses. Full article
(This article belongs to the Special Issue Plant Stress Biology)
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