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Growth-limiting drought increases sensitivity of Asian rice (Oryza sativa) leaves to heat shock through physiological and spatially distinct transcriptomic responses.

Growth-limiting droughts (GLD) impair tissue expansion and delay developmental transitions but are often not considered as stressors, as many physiological traits are only slightly altered relative to well-watered counterparts. Concurrently, cell size, biochemical makeup, and transcriptome profiles vary along the leaf blade in accordance with the partitioning of distinct functions to spatially defined regions of the leaf. This suggests that because different parts of the leaf have underlying differences in their transcriptome profiles, they might respond to GLD in distinctive ways. Moreover, how antagonistic stressors influence physiology and gene expression in different zones of leaves is an open question. In this study, we profiled growth, anatomy, and gas exchange in Asian rice (Oryza sativa) leaves developed in well-watered and GLD conditions, with or without a secondary heat shock. We dissected leaves into seven equal-length segments for transcriptome analysis in these conditions. We hypothesized that GLD would make the leaves more sensitive to heat shock and would disrupt the underlying heterogeneity of the leaf transcriptome. GLD plants were more strongly affected by heat shock with respect to gas exchange and the number and types of genes that were differentially expressed and that these differences varied along the leaf blade. We developed an eFP browser tool with these data to facilitate exploration and hypothesis testing. These findings show that even mild drought treatments are sufficient to impact responses to antagonistic stressors and that substantial within-organ variance exists with respect to stress responses.

Oryza

WRKY14-DPB Module Enhances Drought Tolerance by Activating the Expression of UGT84B1 Involved in Hydrolyzable Tannin Biosynthesis.

Drought stress severely limits the growth and development of trees. Tannins, which serve as vital secondary metabolites in plant roots, help mitigate drought stress. The Lauraceae family, which holds major economic and ecological value, faces substantial developmental challenges due to its sensitivity to drought conditions. Despite this, research on the regulatory mechanisms governing tannin-specific accumulation under drought stress remains limited. In this study, we aim to explore how WRKY14 interacts with DPB to regulate the metabolism of hydrolyzable tannin (HT) via the key enzyme UGT84B1, thereby enhancing drought tolerance in Litsea cubeba, a main species within the Lauraceae family. The WRKY-DPB-UGT84B1 module was specifically expressed in roots in response to drought stress. LcUGT84B1 was found to generate 1-O-Galloyl-β-d-glucose in vitro and in overexpressing L. cubeba. Moreover, molecular biology and transformation experiments demonstrated that LcWRKY14 and LcDPB formed a complex that directly bound to the LcUGT84B1 promoter, activating its expression and thereby facilitating HT synthesis. Co-overexpression of LcWRKY14 and LcDPB significantly enhanced drought tolerance by increasing HT accumulation. These findings provide new insights into the regulatory mechanisms of the WRKY-DPB-UGT84B1 module in promoting drought tolerance and offer a potential breeding strategy for developing drought-resistant varieties.

Drought Resistance

Genome-Wide Analysis of Triticum aestivum Root Meristem Growth Factor (RGF) Gene Family Highlights TaRGF5 as a Putative Component of Root-Associated Signaling.

Wheat (Triticum aestivum), a key global crop, faces rising drought stress that limits root growth and water uptake. Root meristem growth factors (RGFs) are small peptides that regulate root stem cell maintenance, meristem activity, and lateral root formation in model plants, yet the RGF gene family remains unexplored in wheat. Here, we performed a comprehensive genome-wide analysis of the TaRGF gene family, identifying 15 genes distributed across the A, B, and D subgenomes and classified into five homeologous groups (TaRGF1-TaRGF5), predominantly located on chromosomes 2 and 6. All TaRGFs contained a characteristic RGF motif, with dibasic cleavage sites and Asp-Tyr motifs indicating conserved maturation mechanisms. Based on the phylogenetic analysis, the TaRGF5 homeologs showed the highest similarity to Arabidopsis thaliana RGF5. Tested RNA-seq data revealed predominantly root-enriched expression for all TaRGF genes, with TaRGF5 exhibiting the most root-preferential and downregulation under drought stress. Quantitative real-time PCR (qRT-PCR) confirmed that drought stress suppressed the expression of TaRGF5A, TaRGF5B, and TaRGF5D in roots of wheat cultivar Sids-13 across all time points, unlike the higher accumulation seen in controls. Promoter analysis predicted a unique BES1 transcription factor binding site exclusively in TaRGF5B, linking brassinosteroid signaling to peptide-mediated root regulation. Structural modeling and molecular docking predicted an interaction between wheat TaRGF5 homeologs and root growth factor-insensitive receptor kinase (TaRGI3), characterized by conserved sulfotyrosine-mediated binding and favorable interaction energetics. Based on this characterization of the wheat RGF gene family, particularly the potential role of TaRGF5 in root development and drought-adaptation signaling, we propose targeting this gene for functional analysis to improve wheat resilience under water-limited conditions.

Triticum

Genome-wide analysis of the plant-specific PLATZ gene family in Taraxacum kok-saghyz and its roles in response to drought and salt tolerance.

Abiotic stress severely limits plant growth and productivity. Taraxacum kok-saghyz Rodin (TKS), known for its environmental resilience, represents a valuable resource for identifying stress-tolerant genes to improve stress-adaptive crops. Plant AT-rich protein and zinc-binding protein (PLATZ) transcription factors serve as core regulators of plant growth, developmental processes, and adaptive responses to various stress conditions; however, they remain uncharacterized in TKS. Here, we identified 10 TksPLATZ genes through a whole-genome analysis. Phylogenetically, these genes were grouped into five distinct evolutionary branches. Promoter sequence analysis revealed multiple types of cis-acting regulatory elements that are connected with hormonal signal responses and environmental stress adaptation. Integrated analysis of transcriptome datasets and RT-qPCR validation demonstrated that TksPLATZ genes display tissue-specific expression profiles and show distinct responsive patterns to drought and salt stress treatments. Among them, TksPLATZ1, TksPLATZ2 and TksPLATZ7 were markedly induced under both stressors and were selected for further functional study. We demonstrated that TksPLATZ1, TksPLATZ2 and TksPLATZ7 localize to the cell nucleus and act as transcriptional activators and repressors, respectively. Phenotypic data from overexpression experiments in plants confirm that heterologous expression of TksPLATZ1, TksPLATZ2, and TksPLATZ7 enhances the tolerance of Arabidopsis to salt and osmotic stress. These findings provide valuable genetic resources for improving plant tolerance to environmental stresses.

Salt Tolerance

Functional characterization of the MdFLZ2 gene in drought and salt stress tolerance in apple.

Drought and salt stress are significant environmental limitations that severely constrain plant growth and productivity, therefore, enhancing stress tolerance is a key goal in crop improvement. The plant-specific FCS-like zinc finger (FLZ) proteins have been identified as important regulators of stress adaptation. In this study, we conducted a genome-wide characterization of the FLZ gene family in apple and functionally characterized MdFLZ2. qRT-PCR analysis revealed that MdFLZ2 was differentially expressed across various tissues and transcriptionally induced by both drought and salt stress. Subcellular localization assays demonstrated that the MdFLZ2 protein is localized to both the nucleus and the cytoplasm. The overexpression of MdFLZ2 in apple calli, Arabidopsis and tomato conferred increased resistance to drought and salt stress. In addition, yeast two-hybrid (Y2H) assays confirmed that MdFLZ2 interacted with MdSnRK1.1, and similar interactions were also detected between other MdFLZ family members and MdSnRK1.1. Collectively, our findings suggest MdFLZ2 as a positive regulator of drought and salt tolerance and highlight its potential to serve as a genetic resource for abiotic stress improvement.

Malus

Overexpression of the tomato SlLEA_2-26 gene enhances the tolerance to drought and salt stresses in Arabidopsis thaliana.

Late embryogenesis abundant (LEA) proteins are pivotal in conferring cellular tolerance to abiotic stresses and sustaining plant growth and development. However, systematic functional characterization of the tomato SlLEA_2 gene family remains limited. To elucidate the role of tomato SlLEA_2-26 in abiotic stress responses, this study cloned its full-length cDNA. Quantitative real-time PCR (qRT-PCR) analysis revealed that SlLEA_2-26 exhibits predominant expression in flowers and fruits, and is strongly induced by drought, salt, Cu2+, and Pb2+ stresses. Three homozygous Arabidopsis thaliana T3 SlLEA_2-26-overexpression lines were generated and confirmed via genomic PCR. Under drought and salt stress, T3 A. thaliana lines overexpressing SlLEA_2-26 exhibited significantly enhanced seed germination rates, root elongation, and fresh weights compared to wild type (WT) plants, indicating improved stress tolerance during early seedling development. Furthermore, transgenic plants accumulated higher levels of soluble sugar and proline, and displayed elevated antioxidant enzyme activity compared to the WT, whereas contents of malondialdehyde (MDA) and reactive oxygen species (ROS) were markedly reduced relative to WT. qRT-PCR analysis confirmed the significant upregulation of SlLEA_2-26 in transgenic lines under drought and salt stress conditions, accompanied by elevated expression of AtP5CS1, AtCSD1, AtRD29A, AtRD26, and AtNCED3. Collectively, these results demonstrate that SlLEA_2-26 overexpression enhances drought and salt stress tolerance in A. thaliana by promoting the accumulation of osmoregulatory substances, augmenting antioxidant defense capacity, and activating stress-responsive gene expression. This study provides a theoretical foundation and valuable genetic resources for breeding stress-tolerant tomatoes and other crops.

SlLEA_2–26

Temporal proteomic analysis reveals a three-phase adaptation strategy in Phytophthora cinnamomi during salinity stress.

Phytophthora cinnamomi, a highly invasive hemibiotrophic oomycete, threatens global agriculture, forestry, and native ecosystems. Although drought and temperature effects on P. cinnamomi-host interactions are well studied, current knowledge of abiotic stress responses in P. cinnamomi remains largely centered on infection and phytopathology, with limited molecular insight into the pathogen's direct response to salinity independent of its host. To address this gap, we combined growth assays, time-resolved proteomics, and network analysis to define how P. cinnamomi responds and adapts to salinity exposure. Growth assays showed that NaCl-modified agar enhanced mycelial expansion in a concentration-dependent manner, with 100 mM NaCl significantly increasing growth at 48, 72, and 96 h compared with controls, while 50 mM NaCl remained comparable to control conditions. Temporal proteomic analysis of 100 mM NaCl treatment at 0, 1, 6, 12, and 24 h post treatment revealed dynamic shifts in protein abundance. Early induction of ROS (Reactive Oxygen Species)-detoxifying enzymes, including glutathione S-transferases and peroxidases, was consistent with ROS-specific staining assays. Network analysis identified modules enriched for redox regulation, ATP generation, ion transport, and translational control, highlighting multi-layered adaptation to elevated NaCl levels. Notably, clusters of conserved hypothetical proteins were strongly upregulated, indicating unexplored stress tolerance components in Phytophthora species. Here, we propose that P. cinnamomi rapidly activates a three-phase strategy involving metabolism readjustments, redox defenses, and cellular structure alterations under salinity conditions. With increasing soil salinization due to climate change, our study provides first mechanistic insights into P. cinnamomi's adaptive plasticity and ecological resilience to abiotic stress. SIGNIFICANCE: This study represents the first temporal proteomic analysis of salinity stress adaptation in Phytophthora cinnamomi, revealing a sophisticated three-phase adaptation strategy. This research fundamentally advances our understanding of how this globally destructive plant pathogen, P. cinnamomi, maintains environmental resilience. Our findings reveal proteome remodelling as a mechanistic framework for understanding stress tolerance in oomycetes, a group of microorganisms responsible for some of the world's most destructive agricultural and forest diseases. Our results show proteins involved in emergency damage control through metabolic recalibration to sustained adaptation. These findings have relevance for predicting pathogen behavior under climate change scenarios, where increasing soil salinity threatens agricultural productivity while simultaneously enhancing pathogen survival and virulence. Understanding how P. cinnamomi responds to prolonged salinity exposure may inform targeted biocontrol strategies and improve predictive models of disease pressure in salt-affected agricultural regions. The temporal analysis framework we present offers a broadly applicable approach for understanding microbial stress adaptation, with implications extending beyond plant pathology to environmental microbiology and biotechnology applications where stress tolerance is paramount.

Phytophthora

Plant-derived and microbial biostimulants in sustainable agriculture: mechanisms, applications, and challenges.

Plant biostimulants have emerged as transformative and sustainable tools for improving crop productivity, resource-use efficiency, and resilience under rapidly intensifying environmental stresses. Unlike conventional agrochemicals, biostimulants function by activating physiological, biochemical, and molecular processes that optimize plant performance without directly supplying nutrients or exerting pesticidal effects. This review comprehensively examines the integrated roles of plant-derived and microbial biostimulants in sustainable agriculture, with particular emphasis on microbial-mediated mechanisms underlying plant stress adaptation and rhizosphere functioning. Plant-derived biostimulants, including seaweed extracts, humic substances, protein hydrolysates, amino acids, and chitosan, enhance nutrient acquisition, root architecture, hormonal regulation, and antioxidant defense systems. More importantly, microbial biostimulants, such as plant growth-promoting rhizobacteria (PGPR), endophytic microorganisms, mycorrhizal fungi, actinomycetes, yeasts, and cyanobacteria, exert multifunctional effects through biological nitrogen fixation, mineral solubilization, phytohormone biosynthesis, volatile signaling, osmolyte accumulation, pathogen suppression, and modulation of stress-responsive genes. These beneficial microorganisms reshape rhizosphere microbial communities, improve nutrient cycling, and enhance plant tolerance to drought, salinity, heat, and heavy metal toxicity. Emerging evidence from genomics, transcriptomics, metabolomics, and microbiome-based investigations has further revealed the molecular networks and signaling pathways governing biostimulant-induced resilience and plant-microbe interactions. Despite their substantial promise, inconsistent field performance, formulation instability, regulatory limitations, and inadequate mechanistic understanding continue to restrict their large-scale adoption. This review highlights recent advances in microbial and plant-derived biostimulants while identifying critical knowledge gaps and future opportunities for precision biostimulant engineering, microbiome manipulation, and climate-resilient crop management. The integration of next generation biostimulant technologies into sustainable agricultural systems may significantly reduce dependence on agrochemicals while improving crop productivity, environmental sustainability, and global food security.

Agriculture

Morphological, Physiological and Transcriptomic Changes in Response to Water Deficit Stress in Brassica napus L.

Yield losses due to water-deficit (WD) conditions, especially during the reproductive stages of plant development, pose a significant threat to global canola (Brassica napus L.) production. Therefore, it is critical to investigate traits contributing to improved productivity under increased WD conditions. Here we present phenotypic, physiological and transcriptomic changes in response to WD across contrasting canola accessions exhibiting variation in drought resistance-related traits. WD significantly reduced shoot biomass, plant height, harvest index, leaf water content, photosynthetic CO2 assimilation rate, intrinsic water-use efficiency and carbon isotope discrimination. WD caused 49 to 100% of the seed yield reduction: the minimum seed yield reduction (49.66%) was observed in a doubled-haploid (DH) line, 06-5101.137, while the maximum yield reduction (94.1 to 100%) occurred in the late-flowering DH lines (06.5101.088 and 06-5101.306). Seed yield showed a positive correlation (r = 0.29 to 0.95) with shoot biomass and harvest index, leaf water content, photosynthetic CO2 assimilation rate, intrinsic water use efficiency and carbon isotope discrimination. However, it showed negative correlations with days to flower, leaf specific weight, root length, root biomass (r = -0.04 to -0.79) across water treatments. The specific leaf transcriptome analysis of the two parental lines of DH population that exhibit variation for effective water use under well-watered and water-deficient conditions revealed different categories of differentially expressed genes (DEGs): WD-responsive DEGs in BC1329 parental line (1116) and BC9102 (1205) with 754 and 853 DEGs unique to BC1329 and BC9102, respectively, WD-responsive DEGs (906), genotype-dependent DEGs (8465) and genotype × treatment interaction DEGs (353). DEG annotations revealed that the WD-treatment-affected genes were involved in stress responses and growth and development. We further located 235 DEGs within the QTL regions underlying agronomic and physiological performance. Our study provides a conceptual framework for the morphological, physiological and molecular determinants involved in water-use efficiency. Seedlings' traits with high heritability values, such as shoot biomass, leaf weight, leaf water content and Δ13C, serve as proxies for trait-based selection for improved seed yield under both water-limited and non-water-limited conditions.

Brassica napus

Genomics control of biostimulant-induced stress tolerance and crop yield enhancement.

Biostimulants are changing modern agriculture, as they have the potential to secure healthy and sustainable food production while preserving the environment. They have two main biological effects: growth promotion and stress protection. Both effects can lead to enhancement of the yield and improvement of the marketable grade of the produce in crops, without compromising crop quality. Their use increased exponentially in the past decade, as they are highly efficient, ecologically friendly (non-toxic, biodegradable), and applicable to all major crops. While exponential data on the physiological mechanisms of stress protection is accumulating in recent years, the information as to how biostimulants act at the molecular level is still rather limited. Here we review the growing evidence of the biostimulants role in stress protection and yield enhancement of crops, as well as the recent transcriptomic and metabolomic data, which indicate biostimulants' molecular mode of action. In particular, we outline the role of genes encoding signaling components, plant hormones (abscisic acid, brassinosteroids, and ethylene), genes encoding transcription factors from ERF, WRKY, NAC, and MYB families, and genes related to growth, photosynthesis, and stress response. Finally, we describe strategies to study the genetic and genomics control of biostimulants mode of action, with foci on stress tolerance and yield enhancement. In Arabidopsis, established systems for biostimulants-induced protection against drought and oxidative stress will allow both forward and reverse genetics approaches to identify key genes from the biostimulants network. Mutations in such genes compromise the stress-protective effect of biostimulants. In major crops such as pepper and tomato, large Genome Wide Association Studies (GWAS) panels can be utilized to study crops responses to biostimulants in terms of drought tolerance, fruit qualities, and yield in order to pinpoint genes controlling biostimulants-induced stress protection and yield enhancement. The combination of these approaches allows identification and verification of important genes involved in the pathways of biostimulant-induced stress protection and yield enhancement, as well as deciphering parts of the intricate biostimulant-signaling network.

Crops, Agricultural

Genome-Wide Analysis of the AT-Hook Gene Family in Malus sieversii and Functional Characterization of MsAHL13.

AT-hook motif nuclear-localized (AHL) proteins are pivotal in plant growth, development, and stress responses. Nevertheless, there is limited research on AHL proteins in Malus sieversii. Our study identified 25 AHL genes from the M. sieversii genome, named MsAHL1-MsAHL25. The encoded protein sequences had lengths ranging from 195 to 554 amino acids, molecular weights from 19.17 to 58.53 kDa, and isoelectric points from 4.67 to 10.09. Chromosomal mapping revealed that these 25 genes were unevenly distributed across 10 chromosomes. Collinearity analysis of AHL genes in M. sieversii implied that gene loss might have occurred during its evolution. The phylogenetic tree classified the AHL proteins of M. sieversii into two subfamilies, showing a close relationship with multiple proteins of M. domestica. Promoter analysis indicated that the AHL genes in M. sieversii harbored numerous stress- and hormone-responsive elements, suggesting their potential role in various stress responses. qRT-PCR analysis of six representative MsAHLs under biotic and abiotic stresses demonstrated that the expression of MsAHL13, MsAHL15, and MsAHL17 was significantly upregulated under salt, drought, and cold stresses, while MsAHL01 expression was inhibited under low-temperature stress. All six MsAHLs were induced by the pathogen Valsa mali. Subcellular localization analysis of the specifically expressed protein MsAHL13 showed its nuclear location. Furthermore, luciferase and yeast two-hybrid assays confirmed the in vitro physical interaction between the MsAHL13 and MsMYB1 proteins. This research offers an important theoretical basis for further exploration of the functional mechanisms of this gene family in responding to environmental stresses.

Malus sieversii

β-carotene enhances drought tolerance in fenugreek by modulating antioxidant defense and redox homeostasis.

Drought stress is one of the main abiotic factors that modulates the morphology and physiology of crops. This study investigated the effect of foliar application of β-carotene on the growth, physiological, and biochemical responses of fenugreek (Trigonella foenum-graecum L.) under drought stress conditions. A pot experiment was conducted using two varieties, Kasuri and Local, under two drought stress levels (control and 50% field capacity), and three β-carotene concentrations (0, 100, and 200 ppm) were applied. Drought stress significantly declined shoot fresh weight up to 35.02% and 58.04%, and shoot length to 17.12% and 17.14%, while increasing the root fresh weight by 133% and 26.2% and the root length to 109.1% and 13.4%, respectively, in the Kasuri methi and Local. Drought stress decreases the total Chl. by 55.4% and 59.3% and carotenoids 42.1% and 59.3% and increased the MDA by 6.35% and 24.2%, respectively, and the content of hydrogen peroxides increased by 12.05% and 44.2% in Kasuri and Local as compared to control. By the application of 200  ppm β-carotene, the shoot fresh weight increased by 95.06% and 66.7%, the shoot length increased by 49.6% and 44.5%, and the total Chl. increased by 194.3% and 144.3%, and carotenoids 71.6% and 63%, and MDA decreased by 14.7% and 15.8%, hydrogen peroxides 26.6% and 27.8%, in Kasuri methi and Local under drought stress conditions. Additionally, with the application of β-carotene, antioxidant enzyme activities (SOD, POD, and CAT) and osmoprotectants (total soluble proteins and sugars) improved significantly, indicating enhanced oxidative defense. Overall, foliar β-carotene application, especially at 200 ppm, proved highly effective in improving fenugreek's drought tolerance by enhancing antioxidant capacity, maintaining pigment stability, and supporting metabolic homeostasis, thereby highlighting its potential role in sustainable crop management under water-limited conditions.

beta Carotene

Research progress on the regulatory mechanisms of the PSY promoter.

Carotenoids are essential pigments in the plant photosynthetic apparatus, functioning in light harvesting, photoprotection, and signal transduction, and serving as precursors of vital nutrients such as vitamin A. Phytoene synthase (PSY) is the first rate-limiting enzyme in the plant carotenoid biosynthetic pathway, and its transcriptional regulation primarily depends on cis-acting promoter elements, associated transcription factors, and epigenetic status. The PSY promoter region contains core cis-elements as well as multiple light-, hormone-, and stress-responsive elements, which collectively function as key regulatory sites governing spatiotemporal expression. This review systematically summarizes recent advances in PSY promoter regulation by plant hormones (e.g., abscisic acid, ethylene, jasmonic acid), environmental factors (light signaling, temperature, salinity, and drought), and epigenetic mechanisms (DNA methylation, histone modifications, and chromatin remodeling). In addition, the application of transgenic and biotechnological approaches to PSY promoter regulation is further summarized. Including promoter sequence engineering with precise editing of cis-elements and promoter-targeted CRISPR activation/interference (CRISPRa/i) for tunable transcriptional control. Emphasis is placed on how these signals are integrated at the promoter level. Deeper insights into these mechanisms will provide both theoretical foundations and practical strategies for enhancing carotenoid accumulation and stress tolerance in crops through molecular design.

Promoter Regions, Genetic