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Plant Responses to Biotic and Abiotic Stresses

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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 December 2025 | Viewed by 9137

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Prof. Dr. Shu Yuan

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College of Resources, Sichuan Agricultural University, Chengdu 611130, China
Interests: plant nutritional signaling and responses; redox homeostasis in plant cells; nitrate reductase biochemistry; ethylene signaling; circadian clock; photosynthetic and respiratory adapations to nutritional stresses
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Special Issue Information

Dear Colleagues,

This Special Issue explores the intricate relationships within plant genomics and genetics, secondary metabolism, plant pharmacology, developmental biology, physiology, and pathology, particularly in the context of responses to biotic and abiotic stresses. It also highlights important areas such as plant growth signaling, gene editing technologies, environmental remediation, molecular nutrition, and functional activity. Additionally, the impact of microorganisms and pathogens on plants is a critical aspect of biotic stress, influencing plant health and development through various mechanisms, including pathogen infection, changes in secondary metabolites, regulation of phytohormones, and modulation of gene expression.

Papers submitted to this Special Issue should present innovative research findings, new regulatory models, and the latest insights related to plant signaling, development, or stress responses. The focus will be on the identification of new genes, enzymes, or metabolites, the discovery of novel signaling pathways, the interactions among phytohormones, and the characterization of gene regulation networks that contribute to plant growth specificity, alongside the interplay between environmental stressors, microbial interactions, and biochemical responses.

Prof. Dr. Shu Yuan
Guest Editor

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Keywords

plant enzymes and metabolites
abiotic stress
stress response
phytohormones
secondary metabolism
gene regulation network
developmental and environmental adaptation
microbial interactions
biotic stress
pathogen response

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Published Papers (11 papers)

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Research

14 pages, 11718 KiB

Open AccessArticle

Identification of R2R3-MYB Gene Family and Functional Analysis of Responses of S22 Subfamily to Abiotic Stresses in Dandelion (Taraxacum mongolicum Hand.-Mazz.)

by Liangruinan Lu, Songle Fan, Bi Qin, Jingang Wang, Lifeng Wang and Shizhong Liu

Int. J. Mol. Sci. 2025, 26(7), 3422; https://doi.org/10.3390/ijms26073422 - 5 Apr 2025

Viewed by 332

Abstract

Dandelions possess a wide range of medicinal properties and demonstrate remarkable adaptability and tolerance to salinity and alkalinity. MYB genes in plants are implicated in growth, differentiation, metabolism, and responses to both biotic and abiotic stresses. The function of MYB genes in dandelions, particularly the R2R3-MYB gene family, requires further investigation. In this study, we identified a total of 130 members of the dandelion R2R3-MYB gene family at the genome-wide level, all of which were mapped to eight dandelion chromosomes. MEME analysis revealed that TmR2R3-MYB proteins contain three conserved motifs. Phylogenetic analysis categorized all TmR2R3-MYBs into 29 subfamilies. Transcriptomic studies in different tissues indicated that TmR2R3-MYBs exhibit distinct expression patterns in different tissues, indicating their diverse functions in dandelions. Notably, TmMYB44 from the S22 subfamily displayed the highest expression level in roots. Additionally, six representative TmR2R3-MYBs were selected from the S22 subfamily for expression profiling under salinity and alkalinity treatments. The results demonstrated that the TmR2R3-MYBs from the S22 subfamily are involved in the response to salinity and alkalinity stress. These findings provide a basis for further exploration of the functions of TmR2R3-MYBs in abiotic stress tolerance. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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18 pages, 16933 KiB

Open AccessArticle

Functions of Tomato (Solanum lycopersicum L.) Signal Transducer and Activator of Transcription (STAT) in Seed Germination and Low-Temperature Stress Response

by Yidan Zhang, Jiahui Zhao, Jingyuan Li, Yanting Li, Libo Jiang and Na Wang

Int. J. Mol. Sci. 2025, 26(7), 3338; https://doi.org/10.3390/ijms26073338 - 3 Apr 2025

Viewed by 255

Abstract

Tomato (Solanum lycopersicum L.) is one of the major vegetable crops worldwide. Research on the Janus kinase–signal transducer and activator of transcription (JAK–STAT) signaling pathway in tomatoes and other plant systems is extremely limited. In this study, the roles of STAT, a crucial element of the JAK–STAT signaling pathway in tomato seed germination and low-temperature stress responses are examined, employing gene family analysis and genetic transformation. The results indicate that the S. lycopersicum genome contains only one member of the STAT gene family, SlSTAT. Subcellular localization experiments reveal that SlSTAT is found in both the cytoplasm and nucleus, suggesting its potential involvement in biological functions within these cellular compartments. Among the 26 different tomato tissue/organs tested, SlSTAT exhibited higher expression levels in hypocotyl (8 days past germination; 8 DPG), and low expression of SlSTAT significantly reduced the germination rate and impacted biomass at 8 DPG. In addition, the SlSTAT gene was significantly downregulated during low-temperature treatment. Compared with the wild-type (WT) tomatoes, the SlSTAT-overexpressing plants showed more resistance to low-temperature conditions, whereas the downexpressing tomatoes exhibited increased sensitivity. The expressions of low-temperature marker genes (SlCBF1-3) and N⁶-methyladenosine (m⁶A)-modification-related genes (m⁶A writer, reader, and eraser genes) were detected to explore possible molecular mechanisms by which SlSTAT causes changes in tomato low-temperature stress resistance. The expression changes of SlCBF1-3 in transgenic plants do not merely follow a straightforward linear relationship with the changes in SlSTAT expression, suggesting a more complex molecular mechanism and a non-direct interaction between SlSTAT and the promoters of SlCBFs. On the other hand, SlSTAT also changes the expression levels of RNA m⁶A-modification-related genes, especially SlFIP37 (writer gene), SlYTP8/9 (reader genes), and SlALKBH8 (eraser gene), ultimately leading to changes in the levels of m⁶A modification. These research findings lay the groundwork for exploring functions of JAK–STAT pathway in tomato development and stress responses, expanding the scope of JAK–STAT signaling studies in plant systems. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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21 pages, 4709 KiB

Open AccessArticle

Genome-Wide Identification and Functional Characterization of the Dof Family in Dendrobium officinale

by Shoujie Li, Weiping Zhang, Can Si, Jing Chen, Yuhan Huang, Muyi Li, Hanzhi Liang, Jun Duan and Chunmei He

Int. J. Mol. Sci. 2025, 26(6), 2671; https://doi.org/10.3390/ijms26062671 - 16 Mar 2025

Viewed by 370

Abstract

The Dof gene family represents a class of plant-specific transcription factors that play crucial regulatory roles in various biological processes, including plant growth, development, and responses to abiotic stress. However, genome-wide identification and functional characterization of the Dof gene family remain unexplored in Dendrobium officinale. In this study, we performed a genome-wide identification and functional analysis of the DoDof gene family. A total of 28 Dof family members were identified and named DoDof1–28 based on genome annotation data. Phylogenetic analysis classified these genes into four major groups (A–D) and further subdivided them into nine subfamilies. Gene structure analysis revealed that most DoDofs lack introns, with no distinct specificity observed among different subfamilies and considerable diversity within the same subfamily. Sequence alignment analysis demonstrated that all DoDof proteins contain a conserved Dof domain consisting of 52 amino acids, which includes a C2-C2 zinc finger motif and a DNA-binding domain. MEME analysis revealed that the conserved motif composition exhibits a certain degree of conservation among DoDof proteins, but significant differences exist across subfamilies. Expression pattern analysis demonstrated that DoDofs have exhibited diverse expression profiles across different developmental stages, tissues, and under abiotic stresses (such as low temperature, salinity, and drought) in D. officinale, suggesting their potential roles in plant development and stress responses. Subcellular localization analysis indicated that DoDof15, DoDof22, and DoDof24 are localized exclusively in the nucleus. Yeast one-hybrid assays revealed that DoDof22 binds to the promoter of the ABA receptor DoPYL9, while DoDof15 and DoDof24 bind to the promoter of the bHLH transcription factor DobHLH68. These results suggest that DoDof proteins may regulate the growth, development, and stress response processes of D. officinale by binding to the promoters of target genes. This study provides critical insights into the functional roles of Dof transcription factors in Orchidaceae family and establishes a theoretical foundation for molecular breeding and stress resistance improvement in D. officinale. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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14 pages, 7571 KiB

Open AccessArticle

Sterol Regulatory Element-Binding Protein Sre1 Mediates the Development and Pathogenicity of the Grey Mould Fungus Botrytis cinerea

by Ye Yuan, Shengnan Cao, Jiao Sun, Jie Hou, Mingzhe Zhang, Qingming Qin and Guihua Li

Int. J. Mol. Sci. 2025, 26(3), 1365; https://doi.org/10.3390/ijms26031365 - 6 Feb 2025

Viewed by 743

Abstract

The grey mould fungus Botrytis cinerea is a dangerous plant pathogen responsible for substantial agricultural losses worldwide. The pathogenic mechanisms still have many unclear aspects, and numerous new pathogenic genes remain to be identified. Here, we show that the sterol regulatory element-binding protein Sre1 plays an important role in the development and pathogenicity of B. cinerea. We identified a homologue of gene SRE1 in the B. cinerea genome and utilized a reverse genetics approach to create the knockout mutant Δsre1. Our results demonstrate that SRE1 is essential for conidiation, as Δsre1 produced only 3% of the conidia compared to the wild-type strain. Conversely, Δsre1 exhibited increased sclerotium production, indicating a negative regulatory role of SRE1 in sclerotium formation. Furthermore, ergosterol biosynthesis was significantly reduced in the Δsre1 mutant, correlating with increased sensitivity to low-oxygen conditions. Pathogenicity assays revealed that Δsre1 had significantly reduced virulence, although it maintained normal infection cushion formation and penetration capabilities. Additionally, SRE1 was found to be crucial for hypoxia adaptation, as Δsre1 showed abnormal germination and reduced growth under low-oxygen conditions. These findings suggest that SRE1 mediates the development and pathogenicity of B. cinerea by regulating lipid homeostasis and facilitating adaptation to host tissue environments. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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25 pages, 5575 KiB

Open AccessArticle

Genome-Wide Identification of GmPIF Family and Regulatory Pathway Analysis of GmPIF3g in Different Temperature Environments

by Xuefeng Liang, Caitong Zhao, Jiayang Cui, Zhihua Liu, Dezhi Han, Qingshan Chen, Mingliang Yang and Zhenfeng Jiang

Int. J. Mol. Sci. 2025, 26(2), 551; https://doi.org/10.3390/ijms26020551 - 10 Jan 2025

Viewed by 667

Abstract

Phytochrome-interacting factors (PIFs) play a crucial role in regulating plant growth and development. However, studies on soybean PIFs are limited. Here, we identified 22 GmPIF genes from the soybean genome and classified the GmPIF proteins into 13 subfamilies based on amino acid sequence homology, secondary and tertiary structures, protein structure, and conserved motifs. Genome-wide collinearity analysis revealed that fragment duplication events play a dominant role in expanding the GmPIF gene family. Cis-acting element analysis revealed that the GmPIF gene family is involved in light response, hormone response, biotic–abiotic stress response elements, and plant growth and development. Gene expression analysis in different temperature environments showed that the GmPIF family was found to be induced by phytohormone treatments, with a significant increase in the expression level of GmPIF3g. GmPIF3g plays a key role in the regulation of the entire network, and in addition, 30 proteins interacting with the GmPIF3g promoter were identified through the use of a novel biofilm interference technique. This technique showed that the transcription factor Dof (DNA binding with one finger) binds to the GmPIF3g promoter, and Y1H assays indicated that Dof regulates its expression by binding to the PIF promoter. These results provide a theoretical basis for further studies on the regulatory network of GmPIF genes to improve the structure of soybean plants under shade environments, as well as a new method for analyzing regulatory elements that interact with gene promoters. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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15 pages, 2860 KiB

Open AccessArticle

Systematic Analysis of Cotton RING E3 Ubiquitin Ligase Genes Reveals Their Potential Involvement in Salt Stress Tolerance

by Hao Li, Yizhen Chen, Mingchuan Fu, Liguo Wang, Renzhong Liu and Zhanji Liu

Int. J. Mol. Sci. 2025, 26(1), 359; https://doi.org/10.3390/ijms26010359 - 3 Jan 2025

Viewed by 710

Abstract

The Really Interesting New Gene (RING) E3 ubiquitin ligases represent the largest class of E3 ubiquitin ligases involved in protein degradation and play a pivotal role in plant growth, development, and environmental responses. Despite extensive studies in numerous plant species, the functions of RING E3 ligases in cotton remain largely unknown. In this study, we performed systematic identification, characterization, and expression analysis of RING genes in cotton. A total of 514, 509, and 914 RING genes were identified in Gossypium arboretum, G. raimondii, and G. hirsutum, respectively. Duplication analysis indicates that segmental duplication may be the primary mechanism responsible for the expansion of the cotton RING gene family. Moreover, the Ka/Ks analysis suggests that these duplicated genes have undergone purifying selection throughout the evolutionary history of cotton. Notably, 393 G. hirsutum RING genes exhibited differential expression in response to salt stress. The overexpression of the specific C3H2C3 RING gene, GhZFRG1, in Arabidopsis resulted in enhanced tolerance to salt stress. This study contributes to our understanding of the evolution of cotton RING ligases and paves the way for further functional analysis of the RING E3 ligase genes in cotton. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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18 pages, 3680 KiB

Open AccessArticle

γ-Aminobutyric Acid Alleviates Programmed Cell Death in Two Brassica Species Under Cadmium Stress

by Zhong-Wei Zhang, Tao-Tao Dang, Xin-Yue Yang, Lin-Bei Xie, Yang-Er Chen, Ming Yuan, Guang-Deng Chen, Jian Zeng and Shu Yuan

Int. J. Mol. Sci. 2025, 26(1), 129; https://doi.org/10.3390/ijms26010129 - 27 Dec 2024

Viewed by 1189

Abstract

Previous studies have demonstrated that γ-Aminobutyric acid (GABA) effectively alleviates heavy metal stresses by maintaining the redox balance and reducing the accumulation of reactive oxygen species (ROS). However, little is known about the role of GABA on programmed cell death (PCD) under Cd treatments in plants. The present study investigated the effects of GABA on Cd-induced PCD in two Brassica species, oilseed rape (Brassica napus, Bn), and black mustard (Brassica juncea, Bj). We observed that GABA significantly alleviated Cd-induced PCD by enhancing antioxidant systems, inhibiting chromatin condensation in the nucleus, and reducing DNA fragmentation under Cd stress. Moreover, GABA may not only reduce caspase-3-like activity by repressing gene expression, but also regulate transcription of PCD-related genes. Bn showed lower Cd accumulation and lower tolerance, with more pronounced PCD, compared with Bj. Our results provide new insights into the mechanism that GABA enhances Cd tolerance in plants. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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20 pages, 2466 KiB

Open AccessArticle

Silicon-Mitigated Effect on Zinc-Induced Stress Conditions: Epigenetic, Morphological, and Physiological Screening of Barley Plants

by Marzena Mazurek, Renata Tobiasz-Salach, Barbara Stadnik and Dagmara Migut

Int. J. Mol. Sci. 2025, 26(1), 104; https://doi.org/10.3390/ijms26010104 - 26 Dec 2024

Viewed by 576

Abstract

Plants are increasingly exposed to stress-induced factors, including heavy metals. Zinc, although it is a microelement, at high concentrations can be phytotoxic to plants by limiting their growth and development. The presented research confirmed the inhibition effect of Zn on morphological and physiological parameters in barley plants. However, the effect was Zn dose dependent (50 µM, 100 µM, and 200 µM), as well as part of the plants (above ground or roots). To mitigate the negative effects of Zn, plants were sprayed with 0.1% silicon. Silicon was proven to have a positive effect on mitigating the inhibitory effects of Zn-induced stress. In most cases, an increase in both morphological (length, elongation, fresh and dry weights, and weather content) and physiological (relative chlorophyll content and fluorescence) parameters was observed. This occurrence was dependent on the Zn dose. Epigenetic analyses confirmed differences in the DNA methylation level, both between plants subjected to stress at different strengths (50 µM, 100 µM, and 200 µM Zn) and between plants sprayed with Si or not. The differences indicate that silicon affects the epigenome of barley plants, thereby modifying the response of plants to stress factors. This modification may be the basis for plants to acquire resistance as “epigenetic memory”. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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16 pages, 41800 KiB

Open AccessArticle

Genome-Wide Characterization and Analysis of the bHLH Gene Family in Perilla frutescens

by Jiankang Chen, Jiayi Xu, Ping Wang, Yihan Wang, Yumeng Wang, Junmei Lian, Yan Yan, Lin Cheng, Yingping Wang and Peng Di

Int. J. Mol. Sci. 2024, 25(24), 13717; https://doi.org/10.3390/ijms252413717 - 22 Dec 2024

Viewed by 1123

Abstract

Perilla frutescens (L.) Britt. is a traditional medicinal and culinary plant with a long history of cultivation and significant potential for broader utilization. The basic helix-loop-helix (bHLH) gene family is essential for regulating plant growth, development, stress responses, and secondary metabolism. However, the bHLH gene family in P. frutescens has not yet been characterized. In this study, a total of 205 bHLH genes were identified in P. frutescens through genome mining and analysis. Phylogenetic analysis classified these PfbHLH genes into 23 distinct subfamilies. Promoter analysis revealed an enrichment of cis-acting elements linked to plant hormone signaling and stress responses, suggesting their potential regulatory roles in development, growth, and stress adaptation. Expression profiling based on publicly available RNA-seq data demonstrated tissue-specific expression patterns of PfbHLH genes in roots, stems, and leaves. Four PfbHLH genes (PfbHLH66, PfbHLH45, PfbHLH13, and PfbHLH5) showed significant responses to methyl jasmonate (MeJA) induction. Yeast one-hybrid assays confirmed that these PfbHLH proteins could bind to the cis-acting G-box (CACGTG) element. This study offers new perspectives on the evolution, regulatory mechanisms, and functional roles of the bHLH gene family in P. frutescens. The findings deepen our understanding of the functional diversity within this gene family and establish a foundation for genetic enhancement and the biosynthesis of medicinal compounds in the species. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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17 pages, 8848 KiB

Open AccessArticle

A CsWRKY48 Gene from Tea Plants Intercropped with Chinese Chestnut Plays an Important Role in Resistance to Biotic and Abiotic Stresses

by Jianzhao Wang, Yikai Gong, Meng Li, Yan Bai and Tian Wu

Int. J. Mol. Sci. 2024, 25(24), 13526; https://doi.org/10.3390/ijms252413526 - 17 Dec 2024

Viewed by 765

Abstract

Tea plant (Camellia sinensis) is an important horticultural crop. The quality and productivity of tea plants is always threatened by various adverse environmental factors. Numerous studies have shown that intercropping tea plants with other plants can greatly improve the quality of their products. The intercropping system of Chinese chestnut (Castanea mollissima) and tea plants is an agricultural planting model in which the two species are grown on the same piece of land following a specific spacing and cultivation method. Based on a comparative transcriptome analysis between Chinese chestnut tea intercropped plantations and a pure tea plantation, it was found that the expression levels of the WRKY genes were significantly upregulated under the intercropping pattern. In this study, we cloned a candidate gene, CsWRKY48, and verified its functions in tobacco (Nicotiana tabacum) via heterologous transformation. The contents of protective enzyme activities and osmoregulatory substances were significantly increased, and the trichomes length and density were improved in the transgenic tobacco lines. This phenotype offered an enhanced resistance to both low temperatures and aphids for transgenic lines overexpressing CsWRKY48. Further analysis indicated that the CsWRKY48 transcription factor might interact with other regulators, such as CBF, ERF, MYC, and MYB, to enhance the resistance of tea plants to biotic and abiotic stresses. These findings not only confirm the elevated resistance of tea plants under intercropping, but also indicate a potential regulatory network mediated by the WRKY transcription factor. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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16 pages, 2381 KiB

Open AccessArticle

Genome-Wide Association Study and Marker Development for Fusarium Oxysporum Root Rot Resistance in Soybean

by Yuhe Wang, Jinfeng Han, Xiangkun Meng, Maolin Sun, Shuo Qu, Yuanyuan Liu, Yongguang Li, Yuhang Zhan, Weili Teng, Haiyan Li, Xue Zhao and Yingpeng Han

Int. J. Mol. Sci. 2024, 25(23), 12573; https://doi.org/10.3390/ijms252312573 - 22 Nov 2024

Viewed by 983

Abstract

Fusarium oxysporum root rot (FORR) is an important disease threatening soybean production. The development of marker-assisted selection (MAS) molecular markers will help accelerate the disease resistance breeding process and achieve the breeding goal of improving soybean disease resistance. This study evaluated the FORR disease resistance of 356 soybean germplasm accessions (SGAs) and screened resistance-related loci using genome-wide association analysis (GWAS) to develop molecular markers for MAS. A total of 1,355,930 high-quality SNPs were analyzed, 150 SNP sites significantly associated with FORR resistance were identified, and these sites were distributed within 41 QTLs. Additionally, 240 candidate genes were screened near these QTL regions, involving multiple functions such as hormone metabolism, signal transduction, stress defense, and growth regulation. Cleaved amplified polymorphic sequence (CAPS) and Kompetitive Allele-Specific PCR (KASP) molecular markers were developed based on candidate genes with significant SNP loci and beneficial haplotypes. The CAPS markers, S15_50486939-CAPS1 and S15_50452626-CAPS2, can effectively distinguish resistant and sensitive genotypes through enzyme digestion. The KASP marker is based on S07_19078765-G/T and exhibits a genotype clustering pattern consistent with disease resistance, demonstrating its application value in breeding. The CAPS and KASP markers developed in this study can provide reliable tools for MAS in FORR disease-resistant varieties. The research results will help reveal the genetic structure of FORR disease resistance and provide support for efficient breeding. Full article

(This article belongs to the Special Issue Plant Responses to Biotic and Abiotic Stresses)

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