Rice frequently encounters diverse abiotic stresses under changing climatic conditions, including high temperature, osmotic stress, and nutrient deficiencies, which severely limit productivity. Nagina 22 (N22), an aus rice cultivar, is widely recognized as an important donor for drought and heat tolerance traits. However, its sensitivity to phosphorus deficiency poses a significant limitation, particularly under drought and high-temperature conditions, which further reduce the availability of inorganic phosphate (Pi). We hypothesized that mutagenesis of N22 would yield superior variants with enhanced agronomic performance and conserved stress-response mechanisms. One of the Ethyl methanesulfonate (EMS) mutants, NH733, outperformed N22 by maintaining higher photosynthetic efficiency, biomass, reproductive fertility, and grain yield, supported by a more efficient antioxidant machinery under high temperature and low-soil-phosphorus (P) conditions. RNA sequencing under diverse (osmotic stress, high temperature, and low-P) stresses revealed the potential roles of HSFA2D, PCF3, and GHD7 in broad-spectrum stress adaptation of NH733, thereby establishing this mutant line as a valuable genetic resource for breeding climate-resilient rice varieties. Functional validation of the genes and regulators identified in this study will further facilitate their exploitation in genome editing or genomic assisted breeding–driven crop improvement programs.
Salinized soil is a potential resource for agricultural development, and cotton can improve and rehabilitate saline-alkali soil. Therefore, identifying, analyzing, and validating salt tolerance genes in cotton are of great significance for remediating saline-alkali land. Flavonol synthase (FLS) plays a key role in flavonol biosynthesis in plant, and it is also important in plant growth, development, and abiotic stress tolerance. However, the function of the FLS gene in cotton under salt stress remains unclear. In this study, the function of GhFLS1 under salt stress was analyzed through combined transcriptomic and metabolomic, exogenous quercetin, 3-3’diaminobenzadine (DAB) and 2-aminoethyl diphyenylborate (DPBA) staining in cotton, and the generation and characterization of GhFLS1-overexpressing lines in Arabidopsis and cotton. Differentially expressed genes and differentially accumulated metabolites were significantly enriched in the flavonoid metabolic pathway. DAB and DPBA staining revealed significant reactive oxygen species (ROS) and flavonol accumulation in cotton leaves under salt stress. Exogenous quercetin application enhanced the salt stress tolerance of cotton. GhFLS1 expression was significantly upregulated in response to salt stress. GhFLS1-overexpressing Arabidopsis exhibited enhanced salt stress tolerance, and ROS accumulation was significantly reduced in GhFLS1-overexpressing cotton under salt stress. This study presents the first functional characterization of a cotton FLS gene in response to salt stress by overexpression in Arabidopsis and cotton. We integrated transcriptomic and metabolomic, identifying quercetin as the key downstream metabolite, and validated its protective role through exogenous application. These results establish a functional link from GhFLS to quercetin-mediated ROS homeostasis, providing a candidate gene and a metabolic marker for breeding salt-tolerant cotton.
Sugarcane bagasse (SCB) curing supports a diverse bacterial community with potential biocontrol activity against soil-borne phytopathogens. In this study, twenty bacterial isolates obtained during SCB curing were screened for antagonistic activity against Fusarium oxysporum f. sp. lycopersici (Fol) FOLViF, the causal agent of tomato Fusarium wilt. All isolates inhibited Fol FOLViF mycelial growth in dual culture assays, with inhibition ranging from 32.08% to 52.08%. The isolate KRBA1 exhibited the strongest antifungal activity and was identified as Burkholderia dolosa based on 16S rRNA gene sequencing (GenBank accession no. PX590031). Metabolite profiling of the Fol FOLViF & B. dolosa KRBA1 interaction zone revealed a distinct set of bioactive compounds not detected in either organism grown alone. Transcriptome analysis of Fol FOLViF exposed to B. dolosa KRBA1 led to the detection of 189 differentially expressed genes, indicating extensive transcriptional reprogramming. Genes involved in translation, membrane transport, and DNA replication were downregulated, whereas genes associated with oxidative stress response and secondary metabolism were upregulated. KEGG pathway analysis revealed the disruption of metabolic pathways, oxidative phosphorylation, endocytosis, and protein turnover in Fol. Molecular docking demonstrated strong binding affinities of the B. dolosa KRBA1 derived metabolite procyclidine toward multiple essential Fol proteins, exceeding those of the commercial fungicide carbendazim. Glasshouse evaluation using tomato cv. Kalyan confirmed that B. dolosa KRBA1 significantly reduced Fusarium wilt severity and enhanced plant growth compared to pathogen-inoculated controls. These results showed that B. dolosa KRBA1 inhibits Fol by combining transcriptional interference with metabolite-mediated inhibition, emphasizing its potential as a strong biological control agent against Fusarium wilt.
Cadmium (Cd) contamination in farmland soils severely threatens wheat productivity and human health via food chain transmission. Although ATP-binding cassette (ABC) transporters are known to participate in heavy metal uptake and detoxification in plants, the genetic mechanisms coordinating Cd uptake, root retention and long-distance translocation in wheat remain poorly understood. In this study, we identified the wheat ABC transporter ABCG42 as a key regulator of Cd bioaccumulation and partitioning by regulating cell wall sequestration and interacting with ABA-, stress- and ripening-induced protein 1 (ASR1). Knockout of ABCG42 reduced Cd retention in root cell walls, thereby decreasing root Cd uptake and root-to-shoot translocation. Conversely, ABCG42 overexpression enhanced Cd sequestration in root cell walls and reduced Cd translocation to shoots, revealing a dual role of ABCG42 in promoting root Cd uptake and limiting long-distance Cd transport. Unlike previously reported plasma‑membrane‑localized ABCG homologs that extrude Cd out of plant cells, this ER‑resident transporter facilitates root cell‑wall Cd sequestration. ABCG42 physically interacted with ASR1, and both proteins were co-localized to the endoplasmic reticulum (ER). ABCG42 overexpression upregulated ASR1 expression and increased abscisic acid (ABA), salicylic acid (SA), and gibberellic acid (GA) levels under Cd stress. Transcriptomic and proteomic analyses revealed that the ABCG42-ASR1 module modulates Cd tolerance by regulating hormone signaling, mitogen-activated protein kinase (MAPK) cascades, and antioxidant enzyme activity. Our findings elucidate a novel molecular module that integrates Cd transport and ABA signaling to coordinate wheat Cd tolerance and accumulation. Collectively, these findings establish ABCG42 as a key genetic determinant of wheat Cd uptake and partitioning, providing a mechanistic basis for developing genetic strategies to mitigate Cd accumulation and reduce Cd entry into the food chain.
The upper leaves of flue-cured tobacco exhibit distinct developmental and metabolic gradients; however, the regulatory mechanisms underlying spatial metabolic reprogramming remain largely unclear. In this study, transcriptomic, metabolomic, phytohormone profiling, and physiological analyses were integrated to characterize molecular and metabolic changes across five consecutive upper leaf positions. Transcriptomic analysis revealed progressively increased transcriptional divergence with increasing leaf position, with 2,493 differentially expressed genes (DEGs) identified in the L15_vs_L11 comparison and 1,309 position-specific DEGs detected in L15, indicating enhanced transcriptional specialization in the uppermost leaves. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed a gradual transition from primary metabolic processes toward secondary metabolism, carbon assimilation, hormone signaling, and stress-related pathways along the leaf-position gradient. Metabolomic profiling identified alkaloids and terpenoids as major differentially accumulated metabolite classes, with the highest number of DAMs observed in the L13_vs_L11 comparison, suggesting that L13 represents a potential metabolic transition-associated position rather than a universal developmental switch. Nicotine accumulation peaked at L13, whereas total nitrogen content, chlorophyll content, net photosynthetic rate (Pn), and transpiration rate (Tr) progressively increased toward L15, indicating enhanced photosynthetic activity and altered carbon–nitrogen allocation in upper leaves. Phytohormone profiling revealed three major distribution patterns: position-dependent accumulation represented by 1-aminocyclopropane-1-carboxylic acid (ACC), jasmonic acid (JA), and cis-zeatin riboside (cZR); relatively stable fluctuation of indole-3-acetic acid (IAA); and developmental stage-associated variations in abscisic acid (ABA), gibberellic acid 3 (GA₃), brassinolide (BL), and salicylic acid (SA). Weighted gene co-expression network analysis (WGCNA) identified gene modules associated with nitrogen, sugar, and nicotine-related traits, containing candidate transcription factors from the WRKY, TIFY, GRAS, and NAC families. Integrated transcriptomic and metabolomic analyses further revealed coordinated remodeling of starch and sucrose metabolism, phenylpropanoid metabolism, flavonoid metabolism, and glutathione metabolism, reflecting a redistribution of metabolic flux toward specialized metabolism and antioxidant-related processes in mature upper leaves. Collectively, this study provides a multi-omics framework for understanding leaf-position-dependent metabolic reprogramming and highlights the coordinated roles of hormonal dynamics, carbon–nitrogen allocation, and secondary metabolism during upper-leaf development in flue-cured tobacco.
Microplastics (MPs) are widespread pollutants, raising increasing environmental concerns. Nowadays, bio-based and biodegradable plastics are commonly used as alternatives to conventional plastics. Yet, their ecological impacts and potential interactive effects with other global change factors, such as drought, on organisms are largely unknown. We investigated interactive effects of soil amendment with different MP glitter types [conventional polyethylene terephthalate (PET), bio-based polylactic acid (PLA), and biodegradable modified regenerated cellulose (RC)] and drought on the common crop savoy cabbage (Brassica oleracea var. sabauda) in a full-factorial design. We measured photosynthetic parameters, transpiration, shoot and root biomass, and leaf amino acid profiles. MP had no impact on photosynthetic parameters, but influenced shoot and root biomass as well as their ratio, also in interaction with drought. Especially RC glitter led to a pronounced reduction of shoot and root biomass. MP had no effects on total amino acid concentrations, but glitter amendment impacted the concentrations of four amino acids which may indicate stress responses. Drought led to enhanced total amino acid and especially proline concentrations, with interactive effects on six amino acids. We assume that the negative effects of MP amendment on biomass may be due to reduced water and nutrient uptake or to additives leaching from MPs; slower degradation of MPs under drought may lessen the acute toxicity of the additives. The pronounced growth retardation under RC glitter amendment highlights the potential ecological risk of biodegradable plastic. Toxicity may decrease over time, but the long-term impacts and degradation dynamics of MPs warrant further investigation.
Soil salinization and alkalinity are major threats to maize production worldwide. To dissect the dynamic molecular responses and co-expression network underlying salt-alkali tolerance, we conducted a time-series multi-omics study using two maize inbred lines contrasting in salt tolerance: HCL195 (tolerant) and HCL660 (sensitive). Root samples were collected at 0, 12, 24, 48, and 72 h after treatment with 100 mmol/L saline-alkali solution for RNA sequencing, and at 0, 24, and 72 h for protein quantification. HCL195 showed superior growth and a markedly stronger and sustained transcriptional response, with 2,492 genes differentially expressed at all stress time points, compared to 700 in HCL660. KEGG enrichment analysis revealed that phenylpropanoid and diterpenoid biosynthesis pathways were significantly enriched in both lines across all time points. Most genes in these pathways exhibited overall upregulation with temporal dynamics in response to salt-alkali stress. Proteomic profiles corroborated the transcriptomic result that HCL195 maintained a higher proportion of up-regulated proteins. Joint transcriptome-proteome analysis identified 36 up- and 142 down-regulated concordant genes at 72 h in HCL195. Through construction of a transcription factor (TF)–target gene co-expression network, we identified seven hub TFs that collectively regulate 271 genes, three of which are known to be related to salt tolerance. These results highlight that sustained activation of key secondary metabolic pathways and antioxidant modules, driven by a core set of TFs, underpins maize salt tolerance.
High light stress is common during plant production. However, we still lack of powerful tools to deal with high light stress. In this study, poly(acrylic acid) coated Mn3O4 nanoparticles (PMO) were used to increase high light tolerance of cotton. Our results showed that the fluorescence intensity of hydrogen peroxide (H2O2), hydroxyl radical, and superoxide anion (O2•-) was significantly lower in PMO treated cotton plants than control plants under high light, accompanied with increased activities of peroxidase and catalase in PMO treated cotton plants. Further, under high-light stress, PMO treatment significantly downregulated actin depolymerization factor GhADF7 expression by 64.0% (first true leaf) and 41.0% (second true leaf) compared with the control, accompanied by a marked increase in actin filament (AF) fluorescence intensity and integrated density. Under normal growth conditions, foliar application of actin polymerization inhibitor and excessive H2O2 demonstrated that AF depolymerization led to increased ROS accumulation, whereas PMO effectively alleviated high-light-induced ROS accumulation. This result indicated that the ROS content and the stability of AF skeleton were mutually affected. Moreover, cotton plants with silencing of GhADF7 showed increased actin filament fluorescence intensity and integrated density while reducing H2O2 and O2•- levels in seedlings under high-light stress. Collectively, these results demonstrate that PMO enhances high-light tolerance in cotton by suppressing AF depolymerization through downregulation of GhADF7 expression and modulation of ROS homeostasis, thereby maintaining cytoskeletal stability. It highlights the potential of nanotechnology approach as a powerful tool to resist plant high light stress.
The root iron plaque is a film of iron-manganese oxide coatings formed on the surface of submerged plant roots. It results from root radial oxygen loss, which oxidizes Fe(II) to Fe(III) and combines with elements such as manganese, ultimately covering the root tips and root hair surfaces. Owing to its large specific surface area and abundant functional groups, the iron plaque can regulate the migration and accumulation of heavy metals through adsorption, co-precipitation, and other mechanisms, serving as a natural barrier against heavy metal pollution. This article systematically reviews the barrier mechanisms at the root surface and the internal adaptation mechanisms of the iron plaque in regulating the transport and accumulation of heavy metals in the plant-soil system. It also analyzes the influence of agronomic measures (such as water management and fertilization methods), the rhizosphere microenvironment (including root exudates and microbial communities), and root-related genes (such as Radial oxygen loss (ROL) related genes and iron-regulated transporters) on the formation of the iron plaque and its effects on heavy metal migration and accumulation. Furthermore, potential risks associated with the iron plaque in the plant-soil system are discussed, and future research directions are proposed.
Silver-based materials are widely used in medical, industrial, and consumer applications, increasing the likelihood of environmental release of both nanoparticulate and ionic forms of silver. Despite growing concern over plant exposure, the molecular mechanisms of how different silver forms affect membrane transport and stress-response pathways remain poorly understood. Here, we investigated how nanoparticulate silver (AgNPs) versus ionic silver (AgNO₃) differentially modulates transcriptional and post-transcriptional responses in tomato using wild-type and aquaporin-deficient genotypes. Plants were exposed for 30 days to 30 mg L⁻¹ AgNPs (2 nm) or AgNO₃, followed by integrated analyses of membrane transport, metal homeostasis, and oxidative stress responses using RT-qPCR, western blotting, and confocal immunofluorescence imaging. Ionic silver elicited stronger transcriptional activation of transport and stress-related genes, including H⁺-ATPase (2.16–4.32-fold), CAT2 (3.97–4.06-fold), and MET2 (up to 6.28-fold), while suppressing aquaporin transcripts (PIP2;1 reduced to 0.76–0.79-fold at Day 30). Under AgNP exposure, CAT2 increased to 3.87-fold in the aquaporin-deficient genotype, and MET2 increased to 6.28-fold at Day 30, indicating a stronger stress-response activation in this line. At the protein level, AgNO₃ caused pronounced loss of PIP2:1 abundance (∼3.5-fold lower in aquaporin-deficient plants), whereas AgNPs preserved higher aquaporin levels. Immunofluorescence analyses further showed retention of membrane-associated aquaporin signal under AgNPs exposure and enhanced vacuolar proton pump activity under AgNO₃. Collectively, these findings demonstrate that silver form influences plant response more strongly, rather than nanoparticle presence alone or aquaporin disruption per se, highlighting membrane transport networks and post-transcriptional regulation as potential determinants of resilience to silver exposure.
Wheat serves as a fundamental pillar of global food security, functioning as a primary source of dietary energy and protein for a substantial proportion of the world’s population. Recent progress in wheat science has driven notable gains in productivity, largely attributable to advances in breeding technologies, genomics and molecular biology. In this review, we synthesize key developments in wheat research, with particular emphasis on the convergence of modern biotechnological tools and an increasingly refined understanding of wheat genetic architecture and physiology. We highlight the transition from conventional multi-omics frameworks, which typically analyze individual datasets in isolation to integrative pan-omics paradigms that unify diverse omics layers across pangenomic scales to shift from simple data integration to context-driven causal inference. This shift has markedly improved the resolution at which genome organization, allelic variation, and complex regulatory networks are characterized, thereby facilitating the dissection of multifactorial agronomic traits. By incorporating genomics, transcriptomics, proteomics, metabolomics, phenomics, and epigenomics into unified analytical platforms, pan-omics enables a systems-level interpretation of genotype–phenotype relationships, particularly under complex and combined abiotic stress environments. Furthermore, the integration of pan-omics with advanced methodologies including genome editing, high-throughput phenotyping, and artificial intelligence provides a robust foundation for predictive breeding and precision crop design. We also highlight critical knowledge gaps, emerging research priorities, and strategic technological interventions required to accelerate wheat improvement over the coming decade. Given projections that global wheat demand will rise by approximately 60% by 2050, sustained innovation, interdisciplinary collaboration, and the deployment of integrative pan-omics-driven approaches will be indispensable. Such efforts are essential to enhance yield potential, nutritional quality, and resilience to climate variability, thereby ensuring sustainable wheat production systems for future generations.
Ethyl methanesulfonate (EMS) mutagenesis is a common technique for developing genetic diversity in microorganisms. The present study investigates the genetic and biological effects of EMS mutagenesis in Fusarium proliferatum (F. proliferatum), the causative agent of Pokkah Boeng Disease (PBD) of sugarcane in China. F. proliferatum wild-type strain (PB6–3) was treated with different EMS concentrations of 0.0%, 1.0%, 2.5%, 5.0%, and 7.5%, and exposure times were kept at 30, 60, 90, and 120 min (mins) for the development of EMS mutagenesis. The EMS-mutagenized strains were screened for changes in virulence using detached sugarcane leaf assays. The strain with the most notable mutations relative to PB6–3, denoted MPB6–3, showed reduced virulence, an altered phenotype, and reduced growth and sporulation. Molecular markers were used to validate the successful induction of EMS mutagenesis in MPB6–3, and subsequent research showed that varying nitrogen (N) sources affected growth and sporulation rate, as well as the synthesis rate of secondary metabolites (SMs), e.g., phytohormones and mycotoxins. The study showed that N sources significantly affected metabolic rates in both PB6–3 and MPB6–3. Notably, the MPB6–3 showed varied rates of N assimilation. The results highlighted the applicability of EMS mutagenesis for developing biological mutants with altered virulence and metabolite profiles, and also provided valuable insights into F. proliferatum, enabling the development of a novel disease control strategy for sugarcane.
Aeroterrestrial algae often encounter a semi-hydrated state between full hydration and dehydration, in which the cytoplasm has fluidity but metabolism is impaired, potentially inducing stress. We hypothesised that not all desiccation tolerant (DT) algae tolerate semi-hydration equally, but that longevity in a semi-hydrated state aligns with species habitat. To test this, we monitored photochemical activity between 75-99% relative humidity (RH), as well as resistance to being held at ∼90% RH, 20°C, under a diurnal light cycle, in six DT algae from a range of habitats. Compositions of photosynthetic pigments, tocopherols (lipid antioxidant) and lipid peroxidation-derived reactive carbonyl species were assessed as stress markers after 0 and 3 weeks of semi-hydration. Initial dehydration activated the photoprotective xanthophyll cycle in all species and on average elevated carbonyls 14-fold more in species less tolerant of semi-hydration, while tocopherols accumulated ∼4-fold in more tolerant species. The least DT species, Zygnema circumcarinatum, with primarily an aquatic habit, had barely detectable photochemistry at 95% RH and pigments broke down during desiccation. In contrast, Asterochloris glomerata (aeroterrestrial lichen photobiont) was photochemically active at 87.5% RH and least stressed by semi-hydration. However, even in aeroterrestrial species, cells aged at ∼90% RH, showing that cellular repair was impaired in a semi-hydrated state. Overall, semi-hydration is a vulnerable state, whereby certain algal species have adapted to tolerate it more than others.
Typha angustifolia is a wetland macrophyte used in aquatic phytoremediation, yet the short-term physiological and molecular mechanisms underlying its responses to different heavy metals, and the potential modulatory role of carbon dots (CDs), remain insufficiently understood. In this study, we evaluated metal accumulation, biomass response, oxidative stress, and antioxidant defense after 48 h of exposure to Pb, Cd, Zn, Cr, Ni, and Cu, with or without CDs. Additionally, the early molecular response was assessed by quantifying the expression of two detoxification-related genes (PCS1 and HMA3) after 8 h of treatment. Metal accumulation occurred predominantly in roots, with Pb showing the highest root retention and Cr the lowest accumulation. High root bioconcentration factors and very low transfer factors, particularly for Pb and Cd (TF < 0.15), are consistent with a short-term phytostabilization-like response in T. angustifolia under acute exposure conditions. Metal exposure significantly reduced plant biomass, with Zn and Cu causing the strongest growth inhibition, whereas Pb and Cd had comparatively weaker effects under the tested conditions. Oxidative stress was evident from elevated malondialdehyde (MDA) levels and increased antioxidant enzyme activities, with Cd producing the strongest induction of CAT and POD, and Pb eliciting the highest SOD activity. RT-qPCR analysis further showed that metal stress significantly upregulated PCS1 and HMA3, especially in roots, where PCS1 reached a 6-fold increase and HMA3 a 4.5-fold increase relative to the control. Co-application of CDs attenuated these responses, reducing PCS1 expression from 6-fold to approximately 4-fold and HMA3 from 4.5-fold to 3.3-fold under high metal stress, consistent with a possible reduction in apparent detoxification demand under these conditions. In shoots, PCS1 and HMA3 were likewise reduced by CDs from nearly 6-fold to 4.4-fold and from 4.6-fold to 3.5-fold, respectively. These findings provide integrated short-term physiological and molecular evidence that T. angustifolia responds to heavy metal exposure through root-based retention, antioxidant activation, and detoxification-related pathways, while CDs attenuate stress-related molecular responses, particularly the induction of PCS1 and HMA3, under acute exposure conditions.
The current changes in climatic conditions including frequent droughts, become a huge threat to the sustainability of grape production particularly in water-limited regions, including Cyprus. Intercropping has gained increasing interest as a promising strategy for improving soil health and providing agroecosystem services. However, it remains unclear whether intercropping could contribute to grapevine resilience, and how plant species interact under drought stress conditions. This study therefore investigates the effects of intercropping with oregano (Origanum dubium-OD) on drought stress responses of three grapevine cultivars (Syrah; Xynisteri and Giannoudi) focusing on their secondary metabolites, oxidative stress markers, mineral profiles, defense-related genes and the structure of their rhizosphere microbial communities. Soil analysis revealed significant differences in soil pH and electrical conductivity in drought-stressed grapevine monocultures and those intercropped with OD. The physiological response to intercropping under drought stress was highly cultivar-dependent. While intercropping did not significantly alter the chlorophyll levels or overall physiological state of Xynisteri, it induced a significant increase in chlorophyll content in Syrah and a significant decrease in Giannoudi. Furthermore, intercropping significantly promoted the accumulation of phenolics, flavonoids, and antioxidant markers across all cultivars. In monocultured vines, drought induced distinct mineral profiles depending on cultivars. Both drought and intercropping induced differential expression of genes related to defense, photosynthesis, and oxidative stress mitigation. Intercropping also reshaped bacterial diversity, enriching beneficial genera under drought stress. Functional predictions indicated that intercropping increased beneficial bacteria prevalence and supported improved acclimatation process to drought stress. These findings provide novel mechanistic insights into how aromatic intercropping enhances vine drought tolerance, improves soil health, and shapes grapevine-microbe-soil dynamics under water deficit. This model could serve as an innovative ecological tool to enhance climate resilience in dryland viticulture, without compromising vine physiological health.
Heavy metal (HM) contamination poses severe threats to agricultural productivity and ecosystem health, necessitating innovative phytoremediation strategies. Phytoremediation remains a dynamic and expanding research domain, and an updated overview of recent advances, particularly those linking hormonal regulation with transport physiology and multi-omics reprogramming, is urgently needed. The central aim of this review is therefore to delineate how phytohormone networks orchestrate plant responses to HM stress and translate those responses into improved phytoremediation outcomes. Specifically, we examine how major phytohormones, auxin, cytokinin, ethylene, abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), brassinosteroids, and gibberellins, modulate metal uptake, translocation, sequestration, and tolerance. Multi-omics approaches have revealed that these hormones regulate metal transporter expression (NRAMP, HMA, ZIP, ABC families), coordinate antioxidant defense, and reprogram primary and specialized metabolism. Transcriptomic analyses identify hormone-responsive transcription factors (ERFs, WRKYs, MYBs) as master controllers of metal-stress gene networks, while metabolomic profiling highlights phytohormone-driven changes in phenylpropanoid biosynthesis, amino acid metabolism, and organic acid production. Systems-biology integration of these datasets uncovers extensive hormone-crosstalk networks that fine-tune metal accumulation patterns and underpin rational phytoremediation design through genetic engineering, exogenous hormone application, and targeted breeding. Critical knowledge gaps, including tissue-specific hormone dynamics, long-distance signalling mechanisms, and the translation of laboratory findings to field-scale remediation, are identified, providing a roadmap for developing climate-resilient, metal-tolerant crops and optimising phytoremediation technologies.
Drought stress during the grain-filling stage severely limits sunflower (Helianthus annuus L.) productivity. Here, physiological, transcriptomic, and widely targeted metabolomic analyses were conducted in the drought-tolerant inbred line TDR1 and the drought-sensitive line ZDA279. TDR1 exhibited stronger osmotic adjustment and antioxidant responses under drought stress. Integrated multi-omics analysis revealed genotype-dependent changes in sucrose metabolism, amino acid metabolism, and phenylpropanoid biosynthesis. Ha4CL2, a gene associated with phenylpropanoid metabolism, was strongly induced by drought in TDR1. Silencing Ha4CL2 reduced lignin accumulation, impaired antioxidant-related responses, and increased drought sensitivity in TDR1. Yeast one-hybrid assays showed that HaMYB62 binds to the Ha4CL2 promoter, while transient dual-luciferase assays demonstrated that HaMYB62 represses Ha4CL2 promoter activity in plant cells. Moreover, HaMYB62 silencing compromised drought tolerance and altered antioxidant- and lignin-related traits. These findings identify Ha4CL2 as a contributor to drought adaptation and suggest that HaMYB62 and Ha4CL2 function within a broader regulatory network associated with phenylpropanoid-mediated drought responses in sunflower.
G-quadruplexes (GQSes) are highly stable DNA secondary structures, which exist as knots in the genome during different cellular processes like replication, transcription and translation. Although several studies have shown the role of Pif1-helicases regulating several cellular processes in yeast and human, the involvement of these helicases in GQS-mediated gene regulation remains largely unexplored in plants. In this study, we identified GQS-enriched regions by DNA affinity purification followed by sequencing from Arabidopsis Pif1-like helicase 1 (Atplh1) mutant. Differentially enriched peaks (DEPs) in the mutant showed preferential distribution in the exonic and promoter regions. The genes involved in various processes like transcriptional regulation, UDP-glycosylation, response to abiotic stress, ethylene biosynthesis and response to carbohydrate stimulus, were found to be differentially expressed (DEGs) between control and mutant plants. These DEGs showed enrichment of binding sites of ERF, WRKY, BBM and BIM transcription factors. Further, the DEGs harboring DEPs were found associated with response to wounding and salt stress, response to unfolded protein, heat stress response and UDP-glycosyl transferase activity. In addition, the mutants exhibited lesser growth inhibition under cold stress. Overall, our study identified genome-wide GQSes in Arabidopsis and altered gene expression regulated by AtPLH1.
Global climate change intensifies heat stress, severely threatening cotton production by impairing growth, reproduction, and fiber quality. Recent advances highlight that dynamic epigenetic mechanisms—including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs (ncRNAs)—orchestrate stress-responsive gene networks and establish heat stress memory in cotton. These reversible modifications provide a crucial regulatory layer for sensing, responding to, and potentially recalling thermal stress. Multi-omics integration has been pivotal in linking these epigenetic changes to physiological and agronomic outcomes. Translational tools such as epigenome editing and marker-assisted selection demonstrate the potential of harnessing epialleles (allelic variants defined by epigenetic modifications rather than DNA sequence changes) for breeding resilient varieties. However, challenges persist, including understanding epigenetic crosstalk and tissue-specificity. This review synthesizes current knowledge on epigenetic regulation in heat-stressed cotton, explores integrative omics approaches, and discusses their application in crop improvement. We conclude by outlining key research priorities to accelerate the development of epigenetics-informed breeding strategies for climate-resilient cotton.
Stress-associated proteins (SAPs) are a class of plant zinc-finger proteins that are primarily characterized by the canonical A20-AN1 domain architecture. In contrast, proteins containing only AN1 domains, repeated AN1 domains, or additional expanded domains are more appropriately classified as SAP-like variants. Across land plants, SAP-related genes have undergone lineage-specific expansion, whereas the canonical A20-AN1 configuration remains the predominant structural form.Available functional evidence indicates that perturbation of specific SAPs under drought and osmotic stress, salinity, temperature stress, oxidative stress, and heavy-metal stress is repeatedly associated with three major biological output layers: ubiquitin-proteasome-related proteostasis, hormone-associated signaling pathways, particularly abscisic acid (ABA)-related responses, and redox/ion homeostasis. These recurring outputs should not be interpreted as evidence for a single conserved mechanistic model across the entire SAP family. Current evidence instead supports a context-dependent framework in which SAP function is shaped by paralog identity, tissue context, developmental stage, interaction partners, and stress type. SAPs may function as either positive or negative regulators, making broad family-level generalizations unreliable.Direct biochemical evidence is currently available for only a limited subset of SAP members. For most SAP proteins, native substrates, in planta interaction networks, and stress-dependent post-translational regulatory mechanisms remain unresolved. In this review, we synthesize SAP biology within an evidence-weighted framework that integrates structural classification, evolutionary diversification, phenotype-level function, and mechanistic links to proteostasis, hormone signaling, and redox/ion homeostasis. We further propose that systematic substrate identification, post-translational modification (PTM)-resolved proteomics, proximity-labeling-based interactomics, and causal genetic analyses under multi-environment stress conditions will be essential for the development of paralog- and context-resolved SAP models. Such advances are expected to provide a stronger basis for identifying SAP targets with translational potential in breeding and genome-editing strategies aimed at improving climate resilience.
