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Molecular Mechanisms of Plant Adaptation and Stress Tolerance Under Changing Environmental Conditions

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 31 August 2026 | Viewed by 3660

Special Issue Editor


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Guest Editor
1. Guangdong-Hong Kong Joint Laboratory for Carbon Neutrality, Jiangmen Laboratory of Carbon Science and Technology, Jiangmen 529199, China
2. College of Education Sciences (CES), The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511453, China
Interests: plant genetics and genomics; molecular plant physiology; plant breeding and genetics; synthetic biology; abiotic stress; secondary metabolism; plant growth and development
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Special Issue Information

Dear Colleagues,

Rapid environmental change is reshaping the way plants grow, develop, and survive. Extreme temperatures, prolonged droughts, salinity intrusion, flooding, nutrient imbalances, shifting photoperiods, and emerging pathogens now occur more frequently and often in combination. Elevated CO2 (eCO2) adds another layer: it can enhance photosynthesis and biomass, yet rewire carbon–nitrogen balance, stomatal behavior, secondary metabolism, and defense mechanisms. eCO2 rarely acts alone; its effects modulate and are modulated by water deficit, heat, ozone, and nutrient limitations, yielding outcomes that are genotype-, tissue-, and stage-specific. These stresses trigger complex and sometimes antagonistic molecular responses, challenging the resilience of even the most adaptable species.

Despite extensive progress in plant genomics, physiology, and breeding, we still lack an integrated understanding of how plants perceive, prioritize, and coordinate defense and adaptation across diverse and fluctuating environmental conditions. This Special Issue seeks contributions that move beyond single-factor analyses to unravel the molecular circuitry, signaling crosstalk, and physiological adjustments underpinning tolerance to combined and sequential stresses. By integrating molecular biology, systems-level omics, physiology, and predictive modeling studies, we aim to bridge the gap between controlled experiments and real-world agricultural and ecological contexts.

Topics of interest include, but are not limited to, the following:

  • Decoding integrators and crosstalk among hormone, redox, sugar, TOR/SnRK1, and calcium signaling under multi-stress conditions.
  • Understanding carbon–nitrogen reallocation and metabolic remodeling (primary, secondary, and structural) that govern tolerance vs. yield.
  • Disentangling root–soil–microbiome mechanisms, including rhizosphere signaling and nutrient acquisition under eCO2 and abiotic stress.
  • Mapping spatial and temporal heterogeneity via single-cell/spatial omics, real-time imaging, and high-throughput phenotyping.
  • Leveraging natural variation, pangenomes, epigenetic memory, and genome editing to identify deployable tolerance traits.
  • Mechanism-anchored engineering (CRISPR/prime editing, synthetic circuits) and predictive modeling/AI that generalize from growth chambers to fields.

Original research, short communications, methods/resources, data papers, and concise mechanistic reviews that integrate multi-omics, physiology, and modeling are encouraged. Studies on crops, trees, and model plants are all in scope, especially those validating targets across environments.

Dr. Naveed Ahmad
Guest Editor

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Keywords

  • elevated CO2
  • drought–heat–salinity
  • carbon–nitrogen balance
  • TOR/SnRK1
  • hormone crosstalk
  • redox signaling
  • microbiome
  • single-cell/spatial omics
  • phenomics
  • genome editing
  • predictive breeding

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Published Papers (5 papers)

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Research

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17 pages, 2757 KB  
Article
Time-Series-Based Co-Expression Network Analysis Reveals Key Regulatory Modules and Hub Genes in Salt-Tolerant Wheat Under Salt Stress
by Guiqiang Fan, Jianan Huang, Hong-Jin Wang, Yuxiang Huo, Peiyu Liu, Uzair Ullah, Guohang Hu, Munib Ahmad, Abdullah Shalmani, Hui Fang and Tianrong Huang
Curr. Issues Mol. Biol. 2026, 48(3), 317; https://doi.org/10.3390/cimb48030317 - 16 Mar 2026
Viewed by 482
Abstract
Salt stress severely constrains wheat growth and yield by inducing osmotic imbalance, ion toxicity, and excessive accumulation of reactive oxygen species (ROS). Although salt-tolerant cultivars can adapt through rapid signaling transduction and maintenance of cellular homeostasis, the underlying dynamic regulatory networks remain insufficiently [...] Read more.
Salt stress severely constrains wheat growth and yield by inducing osmotic imbalance, ion toxicity, and excessive accumulation of reactive oxygen species (ROS). Although salt-tolerant cultivars can adapt through rapid signaling transduction and maintenance of cellular homeostasis, the underlying dynamic regulatory networks remain insufficiently characterized. In this study, we reanalyzed publicly available time-series RNA-seq data (0, 1, 3, 6, 12, and 24 h) from the salt-tolerant wheat cultivar Xiaoyan22 under salt stress and constructed a time-series-based co-expression network using weighted gene co-expression network analysis (WGCNA). Multiple gene modules were identified, among which the black module showed significant positive correlations with both salt treatment (treatment_bin) and stress duration (time_h). This module displayed a progressively increasing eigengene expression pattern throughout the stress period. Gene significance (GS) was positively correlated with module membership (MM), facilitating the identification of highly connected hub genes within this module. Functional enrichment analysis indicated that genes in the black module were primarily associated with DNA replication and genome stability maintenance, RNA metabolic regulation, phenylpropanoid metabolism, and cuticle/suberin/wax biosynthesis. Physiological analysis further revealed enhanced activities of superoxide (SOD), peroxide (POD), and catalase (CAT), enhanced accumulation of proline and soluble sugars, and a time-dependent increase in MDA under salt stress. qRT-PCR confirmed significant induction of candidate genes, including a ZAR1-like receptor kinase, Remorin, and NETWORKED 1D. Collectively, these findings integrate co-expression network inference with physiological and molecular validation, providing candidate regulators and pathways for understanding salt tolerance and supporting future molecular breeding efforts. Full article
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21 pages, 7702 KB  
Article
Genome-Wide Identification and Characterization of C3H-ZFP Genes and Their Expression Under Salt and Cadmium Stress Conditions in Soybean
by Intikhab Alam, Khadija Batool, Hui-Cong Wang and Fang Qiao
Curr. Issues Mol. Biol. 2026, 48(3), 287; https://doi.org/10.3390/cimb48030287 - 8 Mar 2026
Viewed by 495
Abstract
Zinc finger proteins (ZFPs) are a diverse group of plant transcription factors essential for regulating development, signaling, and stress responses. In this study, we performed a genome-wide identification and integrative analysis of 140 C3H-type zinc finger transcription factor genes in the soybean genome, [...] Read more.
Zinc finger proteins (ZFPs) are a diverse group of plant transcription factors essential for regulating development, signaling, and stress responses. In this study, we performed a genome-wide identification and integrative analysis of 140 C3H-type zinc finger transcription factor genes in the soybean genome, exhibiting an uneven distribution across all 20 chromosomes. These C3H-ZFPs contained one (37), two (58), three (19), four (7), five (17), or six (2) C3H domains and were classified into 14 subsets based on their domain architecture. All C3H genes encoding proteins harbored the conserved C3H-ZFP domain and displayed various physicochemical characteristics. Phylogenetic analysis grouped them into 10 clades, closely related to other species like Arabidopsis, rice and alfalfa. Promoter analysis revealed cis-elements associated with stress response (~39.1%), light response (~37.3%), phytohormones (~18.5%), and development (~4.97%). Duplication analysis revealed 78 pairs of segmental and eight tandem duplication events, with purifying selection indicated by Ka/Ks (nonsynonymous/synonymous) ratios, indicating that these C3H-ZFP duplicates were largely maintained under purifying selection. A total of 388 miRNAs from 196 gene families were predicted to target 140 C3H-ZFP genes, with most enriched miRNAs targeting C3H-ZFP genes, including the miR156, miR395, and miR396 families. Transcription factor binding sites for MYB, AP2, MIKC_MADS, BBR-BPC, ERF, C2H2, and Dof were found upstream of most C3H-ZFP genes. RNA-Seq and qRT-PCR analyses showed tissue-specific expression and stress-responsive expression patterns, with several C3H-ZFP genes, especially GmC3H1, GmC3H63, GmC3H124, and GmC3H127, being significantly upregulated under abiotic stress conditions. Together, these results provide a comprehensive overview of soybean C3H-ZFP genes and identify promising candidates for future functional studies on development and abiotic stress adaptation. Full article
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22 pages, 4179 KB  
Article
C2H2 Zinc-Finger Transcription Factors Coordinate Hormone–Stress Crosstalk to Shape Expression Bias of the Flavonoid Pathway in Safflower (Carthamus tinctorius L.)
by Yue Chang, Abdul Wakeel Umar, Minghui Ma, Yuru Zhang, Naveed Ahmad and Xiuming Liu
Curr. Issues Mol. Biol. 2025, 47(12), 1023; https://doi.org/10.3390/cimb47121023 - 8 Dec 2025
Cited by 1 | Viewed by 675
Abstract
C2H2-type zinc-finger transcription factors (ZFPs) play essential roles in plant stress signaling and development; however, their putative functions in safflower have not been systematically characterized. Leveraging the reference genome of the safflower cultivar ‘Jihong-1’ (Carthamus tinctorius L.), we investigated the C2H2 family [...] Read more.
C2H2-type zinc-finger transcription factors (ZFPs) play essential roles in plant stress signaling and development; however, their putative functions in safflower have not been systematically characterized. Leveraging the reference genome of the safflower cultivar ‘Jihong-1’ (Carthamus tinctorius L.), we investigated the C2H2 family and identified 62 CtC2H2 genes. Comparative phylogeny with Arabidopsis revealed six subfamilies characterized by shared features such as exon–intron organization and conserved QALGGH motif. Promoter analysis identified multiple light- and hormone-responsive cis-elements (e.g., G-box, Box 4, GT1-motif, ABRE, CGTCA/TGACG), suggesting potential multi-layered regulation. RNA-seq and qRT-PCR analysis identified tissue-specific candidate genes, with CtC2H2-22 emerging as the most petal-specific (6-fold upregulation), alongside CtC2H2-02, CtC2H2-23, and CtC2H2-24 in seeds (~3-fold), and CtC2H2-21 in roots (3-fold). Under abiotic stresses, CtC2H2 genes also demonstrated rapid and dynamic responses. Under cold stress, CtC2H2 genes showed a rapid temporal pattern of expression, with early increase for genes like CtC2H2-45 (>4-fold at 3–6 h) and a delayed increase for CtC2H2-23 at 9 h. A majority of CtC2H2 genes (8/12) were upregulated by ABA treatment, with CtC2H2-47 suggesting 3.5-fold induction. ABA treatment also led to a significant increase (2.5-fold) in total leaf flavonoid content at 24h, which is associated with the significant upregulation of flavonoid pathway genes CtANS (5-fold) and CtCHS (3.3-fold). Simultaneously, UV-B radiation induced two distinct expression patterns: a significant suppression of four genes (CtC2H2-23 decreased to 30% of control) and a complex fluctuating pattern, with CtC2H2-02 upregulated at 48 h (2.8-fold). MeJA elicitation revealed four complex expression profiles, from transient induction (CtC2H2-02, 2.5-fold at 3 h) to multi-phasic oscillations, demonstrating the functional diversity of CtC2H2-ZFPs in jasmonate signaling. Together, these results suggest stress and hormone-responsive expression modules of C2H2 ZFPs for future functional studies aimed at improving stress adaptation and modulating specialized metabolism in safflower. Full article
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13 pages, 979 KB  
Article
Key Genes Involved in the Saline–Water Stress Tolerance of Aloe vera
by María Mota-Ituarte, Jesús Josafath Quezada-Rivera, Aurelio Pedroza-Sandoval, Jorge Sáenz-Mata and Rafael Minjares-Fuentes
Curr. Issues Mol. Biol. 2025, 47(12), 1000; https://doi.org/10.3390/cimb47121000 - 28 Nov 2025
Viewed by 700
Abstract
Aloe vera is well known for its high tolerance to adverse environmental conditions. However, the molecular pathways governing its adaptive response mechanisms to abiotic stress remain unclear. Thus, the expression of AOG, ABA2, and GMMT genes in Aloe vera plants subjected [...] Read more.
Aloe vera is well known for its high tolerance to adverse environmental conditions. However, the molecular pathways governing its adaptive response mechanisms to abiotic stress remain unclear. Thus, the expression of AOG, ABA2, and GMMT genes in Aloe vera plants subjected to saline–water stress was evaluated, with the expression of key genes significantly influenced by stress response. AOG and GMMT expression levels were higher under field capacity (FC) than under water deficit (PWP), with AOG reaching ~4.3% under 40 mM salinity at FC. In contrast, ABA2 was strongly upregulated under PWP, particularly at 40 mM salinity, with expression increasing up to fivefold compared to the control. However, salinity above 40 mM led to reduced ABA2 expression. GMMT was overexpressed (~6%) under severe stress, while mannose content increased significantly with salinity but remained unaffected by soil moisture. These findings highlight gene-specific responses to combined stress. Full article
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Review

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21 pages, 13524 KB  
Review
From “Omics” to Field: Deciphering the Stress Adaptation Networks and Breeding Potential of Medicago ruthenica L.
by Chen Zhang, Yingfang Shen, Leping Qi and Xinxin Sun
Curr. Issues Mol. Biol. 2026, 48(4), 365; https://doi.org/10.3390/cimb48040365 - 1 Apr 2026
Viewed by 316
Abstract
Medicago ruthenica L., a superior forage crop within the genus Medicago (Fabaceae), is endowed with remarkable stress tolerance and an abundance of bioactive compounds, conferring significant ecological and forage value. Existing reviews primarily focus on a single research direction, and the most recent [...] Read more.
Medicago ruthenica L., a superior forage crop within the genus Medicago (Fabaceae), is endowed with remarkable stress tolerance and an abundance of bioactive compounds, conferring significant ecological and forage value. Existing reviews primarily focus on a single research direction, and the most recent findings are dated, failing to cover breakthroughs at the molecular level. This paper systematically synthesizes the latest research progress in five key areas: genetic diversity and genomic studies, biotic stress responses, abiotic stress tolerance mechanisms (drought, salinity, and low temperature, etc.), utilization (including genetic breeding, ecological restoration, and forage development), and future research prospects. This review addresses critical gaps in existing literature, particularly regarding advances in genomic sequencing, biotic stresses, and research on stress-associated microorganisms. Research indicates that M. ruthenica exhibits extensive genetic diversity, and its genome contains numerous positive selection signals associated with stress resistance. It can tolerate multiple abiotic and biotic stresses through morphoplasticity, physiological metabolic regulation, and transcriptional regulation. Furthermore, its symbiosis with microorganisms such as rhizobia significantly enhances its stress tolerance. M. ruthenica demonstrates outstanding application potential in degraded grassland restoration and high-quality forage production. Future research should focus on mining stress-resistant genes, optimizing molecular breeding techniques, and integrating artificial intelligence into breeding practices. That will facilitate its transformation from a regional endemic resource to a commercially viable functional species, thereby providing robust support for ecological security and the sustainable development of grassland-based livestock husbandry in cold and arid regions. Full article
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