Planta最新文献

{"title":"Complete assembly of Onobrychis viciifolia mitochondrial genome reveals evolutionary dynamics.","authors":"Jianjiang Niu, Lemeng Liu, Chunyu Tian, Yanting Yang, Wenlong Gong, Yumei Feng, Zhiyong Li, Bater Hasi, Zinian Wu","doi":"10.1007/s00425-026-05186-6","DOIUrl":"10.1007/s00425-026-05186-6","url":null,"abstract":"<p><strong>Main conclusion: </strong>This study presents the mitogenome characteristics analysis of Onobrychis viciifolia, including anatomization of repeat sequences, RNA editing site prediction, substitution rate estimation, and phylogenetic and collinearity analyses. Onobrychis viciifolia is a perennial forage legume with high crude protein content. Although its chloroplast genome has been characterized, the mitochondrial genome (mitogenome) had not previously been annotated. In this study, we assembled the first complete mitogenome of O. viciifolia using a hybrid approach, integrating Illumina NovaSeq short-read and Nanopore PromethION long-read data. The single master circular mitogenome spans 351,303 bp (GC content: 45.17%) and encodes 31 protein-coding genes (PCGs), 20 transfer RNAs, and 4 ribosomal RNAs. Through structural analysis, we identified 76 simple sequence repeats, 144 dispersed repeats, and 6 tandem repeats. Codon usage analysis of 9533 codons revealed a pronounced bias for TTA-encoded leucine (relative synonymous codon usage = 1.53). The analysis of synonymous (Ks) and nonsynonymous (Ka) substitution rates (Ka/Ks) of 21 core genes from 20 legume species revealed that the majority of genes were subject to purifying selection, whereas potential positive selection signals were detected in the ccmB and nad9 genes. We predicted 459 RNA editing sites, with nad4 and ccmB exhibiting higher editing frequencies of 45 and 34 events, respectively. Comparative mitogenomic analysis detected 37 chloroplast-derived sequences (total length: 11,539 bp; 3.28% of the mitogenome), including four transfer RNA genes (trnD-GUC, trnH-GUG, trnM-CAU, and trnF-GAA). Phylogenetic analysis indicated that O. viciifolia and Astragalus complanatus are most closely related, with the node supported by a bootstrap value of 100%, which was corroborated by the phylogenetic tree constructed from 23 plant species. Collinearity analysis further revealed the highly rearranged nature of its mitochondrial genome structure. The assembled and annotated mitogenome provides a valuable resource for investigating cytoplasmic inheritance mechanisms.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"264 5","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hyperspectral imaging-based early stress and disease detection for sustainable crop management.","authors":"Aditya Sharma, Deepali Tiwari, Bhanu Pratap, Vijay Shankar Singh","doi":"10.1007/s00425-026-05182-w","DOIUrl":"10.1007/s00425-026-05182-w","url":null,"abstract":"<p><strong>Main conclusion: </strong>This review highlights how hyperspectral imaging, artificial intelligence, spectral analysis, and plant physiology enable early, accurate, non-destructive stress detection, advancing precision agriculture and sustainable food production. Early detection of plant diseases and stress is vital to sustaining crop productivity under increasingly climatic and environmental pressures. Hyperspectral imaging (HSI) enables the identification of physiological and biochemical changes in plants before visible symptoms emerge, supporting timely diagnosis and precision agriculture. This review examines the spectral mechanisms underlying plant responses to biotic and abiotic stresses across the visible, near-infrared, and shortwave infrared regions, focusing on how pigment composition, cellular structure, and water status affect spectral signatures. Here, we explain the  key aspects of hyperspectral data acquisition, calibration, and preprocessing, including radiometric correction, illumination normalization, spectral noise reduction, and dimensionality reduction, essential for analysing high-dimensional datasets. Furthermore, the integration of HSI data with machine learning and deep learning algorithms for disease classification, severity quantification, and early stress detection is also reviewed.  Therefore, this review summarizes  the potential of hyperspectral imaging and artificial intelligence for advancing precision crop monitoring and data-driven agricultural management.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"264 5","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Calcium-ROS-NO signalling integration in plant immunity: mechanistic interactions and feedback regulation.","authors":"Deepak Siruka, Sneha Jha, Alka Shankar","doi":"10.1007/s00425-026-05180-y","DOIUrl":"10.1007/s00425-026-05180-y","url":null,"abstract":"<p><strong>Main conclusion: </strong>This review establishes Ca²⁺, ROS and NO signalling as an integrated feedback network that links pathogen perception, calcium decoding, local and systemic defence, and maintenance of immune homeostasis across tissues. Calcium (Ca²⁺) signalling is a central component of plant immune responses and provides a mechanistic link between pathogen perception and downstream defence activation. Immune stimuli generate distinct spatial and temporal Ca²⁺ signatures that are decoded by calcium sensor proteins, including calcium-dependent protein kinases, calcineurin B-like protein-interacting protein kinases, calmodulins and calmodulin-like proteins. These sensors regulate defence gene expression, hormone signalling, reactive oxygen species (ROS) production and programmed cell death. Recent structural and functional studies have further demonstrated that nucleotide-binding leucine-rich repeat (NLR) resistosomes can function as Ca²⁺-permeable channels, providing a direct connection between effector recognition and Ca²⁺ influx during effector-triggered immunity. Increasing evidence also shows extensive bidirectional communication amongst Ca²⁺, ROS and nitric oxide (NO). Ca²⁺-dependent activation of NADPH oxidases promotes ROS production, whereas ROS and NO can modulate Ca²⁺ fluxes and signalling components through redox-dependent mechanisms. These reciprocal interactions generate feedback circuits that regulate the intensity, duration and spatial propagation of immune responses. This review summarizes current knowledge of Ca²⁺ channels and sensor proteins involved in plant immunity and integrates recent findings on Ca²⁺-ROS-NO crosstalk. Particular emphasis is placed on feedback regulation and unresolved mechanisms governing the spatio-temporal coordination of these signals. Understanding this integrated signalling network will advance mechanistic approaches for improving crop disease resistance whilst limiting detrimental effects of excessive immune activation.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"264 5","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tree grafting: an introspection with reference to breeding, production and productivity in Hevea brasiliensis.","authors":"Rekha Karumamkandathil, Kumari Jayasree, Supriya Radhakrishnan, Athira Pandara Valappil, Raheena Kallarakuzhi Thajudeen, Thomas Kadampanattu Uthup","doi":"10.1007/s00425-026-05172-y","DOIUrl":"10.1007/s00425-026-05172-y","url":null,"abstract":"<p><strong>Main conclusion: </strong>Grafting has transformed the propagation and productivity of perennial tree crops, but genetically variable rootstocks and functional stock-scion interactions can limit the uniform expression of elite scion potential. Evidence from Hevea brasiliensis highlights the need for compatible and uniform rootstocks, self-rooted planting material, and emerging graft assisted biotechnological approaches to improve plantation uniformity and productivity. Due to high heterozygosity and difficulty in fixing desirable traits, grafting has long been the preferred method of propagation in many perennial crops. Hevea brasiliensis, a perennial tree and the primary source of natural rubber (NR), is widely propagated through grafting. As an outbreeding, highly heterozygous species, grafting preserves traits of hybrids developed through prolonged selection. Combined with genetic improvement, grafting has substantially increased rubber productivity worldwide, from ~300 kg ha^-1 to ~3000 kg ha^-1. However, actual plantation yields remain below potential due to significant tree-to-tree variation in latex production, even among genetically uniform clones. In addition to environmental factors, stock-scion interactions are recognized as important determinants of intra-clonal variation, although their underlying molecular mechanisms remain poorly understood. Research integrating anatomical, physiological, and genetic approaches generating genome, metabolome, and proteome data has identified several key contributors to this phenomenon. This review discusses the current knowledge on factors influencing stock-scion interactions in rubber and provides a general framework to address hetero-grafting related variability issues in perennial crops propagated by grafting. The issues discussed are of use to breeders and geneticists to optimize growth and yield in such crops via more precise and sustainable exploitation of their elite genotypes.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"264 5","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149081753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TML functions in Arabidopsis pollen tube penetration into the stigma and style.","authors":"Xiao Han, Meng-Xing Cao, Zi-Ming Wang, Xin-Qi Gao","doi":"10.1007/s00425-026-05171-z","DOIUrl":"10.1007/s00425-026-05171-z","url":null,"abstract":"<p><strong>Main conclusion: </strong>Decreased TML expression compromises pollen tube growth in the stigma and style, indicating that TML is critical for the penetration of pollen tubes into the stigma and style during pollination. In flowering plants, the penetration of the pollen tube into the maternal stigma tissue is a crucial step for successful pollination. Endocytosis is a vital process for pollen tube growth in vitro and in vivo. TML is one subunit of the TPLATE/TSET complex, the core complex for clathrin-dependent endocytosis. TML is localized in the lateral region of growing pollen tubes, but its function is unknown in pollen tube. In this study, we found that decreased TML expression compromises pollen tube growth in the stigma and style, despite comparable growth in vitro to the wild type. Our results indicate that TML plays a role in the penetration of pollen tubes into the stigma and style during pollination.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"264 5","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149075676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cross talk between plant photoreceptor signaling and chloroplast signaling: implications for physiological regulation.","authors":"Huiting Yang, Tianen Zhang, Yang Liu, Yao Shan, Li Yang, Yuanyuan Liu, Zhaoen Yang, Fuguang Li, Jun Peng, Zhi Wang","doi":"10.1007/s00425-026-05179-5","DOIUrl":"10.1007/s00425-026-05179-5","url":null,"abstract":"<p><strong>Main conclusion: </strong>This review focuses on the bidirectional integrated network formed by light signaling and photosynthesis, providing insights for research aimed at optimizing plant energy balance, resource allocation, and stress resilience to facilitate crop improvement. Photoreceptor-mediated light signaling constitutes the core pathway through which plants perceive light quality, intensity, and duration to precisely modulate growth and development. Crucially, this signaling network extensively interacts with and engages in cross talk with the photosynthetic system, forming a sophisticated regulatory circuit. This integration allows plants to balance energy harvest (photosynthesis) with energy consumption (growth and development), thereby optimizing resource allocation and stress resilience under fluctuating environmental conditions. This review systematically examines the key components and molecular mechanisms that define photoreceptor signaling over the past two decades, including phytochromes, cryptochromes, and downstream factors such as COP1, PIFs, and HY5. A central focus of this review is the bidirectional interaction mechanism between photoreceptor signaling and chloroplast function. In this context, bidirectional regulation refers to two interconnected processes: (i) anterograde control, in which nuclear photoreceptor signaling regulates chloroplast biogenesis, photosynthetic gene expression, and chloroplast positioning; (ii) retrograde signaling, whereby chloroplast functional status generates metabolic and redox-derived signals that feed back to the nucleus to reshape light signaling outputs. Importantly, emerging evidence suggests that these pathways do not operate independently but instead converge at shared transcriptional and signaling nodes, forming an integrated regulatory network that coordinates energy capture with growth and stress responses. Finally, the review summarizes major advances and open questions in light signaling theory, discusses innovative applications in intelligent, spectral-tunable lighting systems for controlled-environment agriculture, and offers future perspectives on applying light resource research to sustainable crop improvement.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"264 5","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149075747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Medicinal-plant immunity and specialized metabolism in plant-pathogen interactions: mechanisms and applications.","authors":"Atif Ali Khan Khalil, Hanhong Bae","doi":"10.1007/s00425-026-05176-8","DOIUrl":"10.1007/s00425-026-05176-8","url":null,"abstract":"<p><strong>Main conclusion: </strong>Medicinal-plant immunity and specialized metabolism are mechanistically linked, but rigorous receptor validation, causal multi-omics, and field trials are needed for reliable translational applications. Medicinal plants combine classical immune signaling with lineage-specific specialized metabolism. This review focuses on the immune systems of medicinal plants and on how pathogen perception reshapes the biosynthesis of pharmacologically valuable secondary metabolites. We synthesize evidence for pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), emphasizing pattern-recognition receptors (PRRs), nucleotide-binding leucine-rich repeat (NLR) proteins, MAP kinase (MAPK) signaling, calcium influx, reactive oxygen species (ROS), salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) crosstalk. Examples from Atractylodes macrocephala, Panax ginseng, Cannabis sativa, Catharanthus roseus, Artemisia annua, Hypericum perforatum, Salvia miltiorrhiza, and Withania somnifera illustrate both progress and major knowledge gaps. We distinguish well-validated medicinal-plant mechanisms from inferences based on Arabidopsis, rice, tomato, and Nicotiana reference systems. The review further evaluates elicitor treatments, microbial inoculants, genetic engineering, genome editing, integrated pest management (IPM), multi-omics, and microbiome engineering as strategies to improve both disease resistance and metabolite quality. We propose that future studies should test mechanistic links between receptor activation, transcription-factor networks, metabolite flux, and field-level medicinal quality through paired transcriptomics, proteomics, metabolomics, microbiome profiling, and targeted perturbation experiments. This synthesis provides a focused framework for translating plant-pathogen biology into resilient and chemically consistent medicinal-plant production.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"264 5","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149070015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Involvement of cytokinin response factor 6 in the integration of abiotic stress responses with metabolism and growth in Arabidopsis thaliana.","authors":"Ivan Couée","doi":"10.1007/s00425-026-05181-x","DOIUrl":"10.1007/s00425-026-05181-x","url":null,"abstract":"<p><strong>Main conclusion: </strong>This review highlights the importance of the CYTOKININ RESPONSE FACTOR 6 transcription factor as a plant regulatory nexus integrating responses to multiple abiotic stresses with metabolism, growth and development. Cytokinin Response Factors constitute a subfamily of plant transcription factors that have been identified as cytokinin-responsive APETALA2/ethylene-responsive element binding proteins and further characterised as components of cytokinin signalling. Besides being involved in the canonical cytokinin signalling pathway, they are part of complex networks of interactive regulation. Their mode of action, their interactions and their functions however remain to be fully understood. Among cytokinin response factors that are currently identified and characterised in Arabidopsis thaliana, CYTOKININ RESPONSE FACTOR 6 has been extensively studied as it is related to numerous developmental, nutritional, hormonal, abiotic stress and biotic stress processes. CYTOKININ RESPONSE FACTOR 6 was thus recently shown to be part of a SNF1-related kinase1/Jumonji C domain-containing JMJ15 regulatory axis involved in energy, oxidative stress and growth co-regulation. This review focusses on involvement of CYTOKININ RESPONSE FACTOR 6 in the integration of abiotic stress responses with metabolism, growth and development, and on the underlying mechanisms of this integration. The characterisation of CYTOKININ RESPONSE FACTOR 6 as a stress-growth nexus will be highlighted in terms of regulatory processes and mechanisms. The essential roles of this stress-growth nexus will be discussed in the context of multiple stresses and global changes with potential implications for plant biodiversity dynamics and agricultural sustainability.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"264 5","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MicroRNA172 regulates growth under low nitrogen conditions in Arabidopsis thaliana.","authors":"Nidhi Gandhi, Kratika Singh, Ananda Kumar Sarkar, Amar Pal Singh","doi":"10.1007/s00425-026-05175-9","DOIUrl":"10.1007/s00425-026-05175-9","url":null,"abstract":"<p><strong>Main conclusion: </strong>miR172 and its target genes TOE1 and TOE2 regulate low nitrogen (LN) dependent root elongation growth in Arabidopsis thaliana. Overexpression of miR172 suppresses LN mediated PR elongation. Reduced responses of miR172 overexpression lines and toe1-2;toe2-1 mutants to LN are associated with impaired nitrate assimilation, suggesting a role of the miR172-TOE1/TOE2 module in regulating plant growth under LN conditions. MicroRNAs (miRNAs), a class of small non-coding regulatory RNAs, play important roles in various aspects of plant growth and stress responses, including nutrient deficiency. The availability of nitrogen (N), an essential mineral for plant growth, affects the expression of several miRNAs. However, the function of miRNAs in modulating root responses under low nitrogen (LN) condition remains elusive. Here we report that LN differentially regulates miR172 expression levels, which modulate plant response. Overexpression of miR172 (miR172OE) reduced the plant response to LN-mediated PR elongation, whereas miR172-target mimic (MIM172) lines exhibited enhanced LN-dependent PR elongation in Arabidopsis thaliana (Arabidopsis). Cellular analysis at the root tip revealed that miR172OE plants exhibited a reduced response to LN-mediated root cell elongation and meristem zone (MZ) inhibition, whereas MIM172 plants maintained LN-responsive regulation of these cellular parameters comparable to wild-type. Consistent with these findings, LN-mediated suppression of chlorophyll levels was compromised in miR172OE plants. Analysis of miR172 target genes suggests that among the known targets [SCHLAFMUTZE (SMZ), SCHNARCHZAPFEN (SNZ), APETALA2 (AP2), TARGET OF EAT1 (TOE1), TOE2, and TOE3], TOE1 and TOE2 are involved in LN-dependent elongation of PR through modulation of cellular activities at the root tip. The toe1-2;toe2-1 double mutants showed reduced response to PR elongation and compromised cell elongation under LN condition. Further, chlorate sensitivity assay data suggest that reduced response of miR172OE lines and toe1-2;toe2-1 double mutants under LN condition is associated with a reduced nitrate assimilation pathway. Together, our findings suggest the role of miR172 and its targets TOE1 and TOE2 in regulating nitrogen-responsive growth and the nitrate assimilation pathway.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"264 5","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exogenous regulators that alleviate waterlogging stress in plants: mechanisms, integration, and translational strategies.","authors":"Shanshan Sha, Chengcheng Zeng, Xuyi Shang, Bingchen Zou, Yuju Yang","doi":"10.1007/s00425-026-05178-6","DOIUrl":"10.1007/s00425-026-05178-6","url":null,"abstract":"<p><strong>Main conclusion: </strong>Exogenous regulators mitigate waterlogging stress via a three-tier framework; integrated strategies boost field waterlogging resilience effectively. Waterlogging, an increasingly critical constraint on crop productivity with climate change amplifying extreme precipitation, limits rhizospheric O₂ diffusion to induce hypoxia. This rapidly impairs mitochondrial respiration, forces a shift to low-efficiency glycolysis and fermentation, and accumulates potentially toxic by-products. Upon postanoxic stress, plants face an oxidative burst that compromises membrane integrity, suppresses photosynthesis, and destabilizes yield. Despite inherent adaptive programs (e.g., aerenchyma formation, adventitious rooting), most crops remain vulnerable to prolonged/recurrent waterlogging, necessitating practical interventions complementing genetic improvement. Here, we synthesize evidence that exogenous inputs-including phytohormones, osmoprotectants, antioxidants, gaseous signaling molecules, mineral nutrients, and beneficial microorganisms-mitigate injury by coordinating early signaling, metabolic maintenance, and rhizosphere stabilization. We integrate these effects into a three-tier framework: (i) resetting hypoxia perception/response thresholds, (ii) sustaining energy/redox homeostasis via balanced mitochondrial function and fermentation, and (iii) converting short-term tolerance to sustained recovery through morphological remodeling and rhizosphere improvement. Finally, we outline a translational strategy coupling exogenous regulation with functional microbiomes, targeted genetic improvement, and agronomic management to enhance field robustness and reduce environment-driven \"effect drift\". Highlights Exogenous regulators improve plant-waterlogging tolerance via a three-layer regulatory framework. A combined application of exogenous substances, microbiome, genetics, and agronomy enhances field waterlogging resistance. Hypoxia response, energy metabolism, and ROS homeostasis are core regulatory targets for stress alleviation.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"264 5","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149063866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}