The Plant Cell最新文献

{"title":"The miR167- ARF8 Module Integrates HSFA1-HSFA2 and RVE4/8-ERF53/54 Transcriptional Cascades to Enhance Plant Thermotolerance","authors":"Jie Li, Yixin Li, Chen Chen, Chenghao Ma, Guiliang Tang, Zhong Zhao, Jun Yan","doi":"10.1093/plcell/koag300","DOIUrl":"https://doi.org/10.1093/plcell/koag300","url":null,"abstract":"Heat stress (HS) is a major environmental factor limiting plant survival and crop productivity, prompting the evolution of adaptive responses driven by transcriptional reprogramming coordinated by Class A1 HS TRANSCRIPTION FACTORS (HSFA1s). Here, we demonstrate that the miR167–AUXIN RESPONSE FACTOR 8 (ARF8) module functions as a central regulatory hub, enhancing thermotolerance by integrating both HSFA1-dependent and HSFA1-independent signaling cascades. Under HS, the expression of ARF6 and ARF8 is repressed, while miR167 is induced. Disruption of ARF6/ARF8 or overexpression of miR167 significantly improves heat tolerance, whereas ARF8 overexpression increases HS sensitivity. ARF8 directly binds to the promoters of HSFA1 genes and heat shock protein (HSP) genes, repressing their transcription and thereby impairing the heat-responsive gene network. In addition, ARF8 physically interacts with HSFA1 proteins, further inhibiting their transactivation activity post-translationally. Notably, ARF8 also regulates HSFA2, a major amplifier of the HS response, through both HSFA1-dependent and HSFA1-independent mechanisms. Genetic evidence supports a model in which the HSFA1–HSFA2 axis functions downstream of the miR167–ARF8 module, but contributes only partially to the overall thermotolerance phenotype. Beyond the HSFA1–HSFA2 pathway, ARF8 also suppresses the RVE4/8–ERF53/54 transcriptional cascade, a circadian-regulated, HSFA1-independent module that promotes thermotolerance. This dual regulation allows ARF8 to fine-tune HS adaptation through integration of both canonical and noncanonical signaling routes. Together, these findings establish the miR167–ARF8 module as a central integrator of HS response pathways. This work not only reveals new mechanistic complexity in plant heat response networks but also identifies a conserved regulatory node with promising potential for genetic improvement of heat-resilient crops.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149048873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell epigenomics in plants","authors":"Cheng Tong, Chaofan Liu, Zhe Liang, Xiaofeng Gu","doi":"10.1093/plcell/koag298","DOIUrl":"https://doi.org/10.1093/plcell/koag298","url":null,"abstract":"Single-cell technologies enable epigenomics characterization at single-cell resolution, offering novel insights into gene expression regulation and a wide range of biological processes, including cell fate determination, developmental differentiation, and environmental adaptation. In recent years, plant single-cell epigenomics has witnessed rapid progress, empowering the construction of cell type–specific chromatin accessibility atlases, the identification of candidate cis-regulatory elements (CREs), the inference of gene regulatory networks, and the elucidation of regulatory mechanisms underlying plant development, stress responses, species evolution, and complex agronomic traits. Nevertheless, single-cell methodologies for profiling histone modifications, DNA methylation, three-dimensional genome organization, and spatial epigenomic states in plants are still in their infancy. In this review, we systematically elaborate the technological framework, bioinformatic workflows, key research advances, and existing challenges in the field of plant single-cell epigenomics, and highlight future perspectives for its in-depth development.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149027562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Branching out or bearing fruit: how MADS-box transcription factors orchestrate maize ovule development","authors":"Ved Prakash","doi":"10.1093/plcell/koag296","DOIUrl":"https://doi.org/10.1093/plcell/koag296","url":null,"abstract":"","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149021252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"When Fungi Knock, Nitrilases Unlock the Auxin Arsenal","authors":"Jiajun Wang,Yueyao Wang","doi":"10.1093/plcell/koag295","DOIUrl":"https://doi.org/10.1093/plcell/koag295","url":null,"abstract":"","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149021251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The circadian clock protein CmLHY integrates strigolactone signaling to regulate short-day-induced flowering in chrysanthemum","authors":"Yi Zhang, Yingying Xing, Xinhui Wang, Fei Li, Guosheng Xiong, Tao Huang, Yonggang Liu, Lisheng Zhai, Ting Zhang, Jiafu Jiang, Likai Wang, Fadi Chen, Sumei Chen","doi":"10.1093/plcell/koag291","DOIUrl":"https://doi.org/10.1093/plcell/koag291","url":null,"abstract":"Flowering is a key ornamental trait in chrysanthemum and a major agronomic trait affecting rice yield. Strigolactones (SLs) are a class of phytohormones that regulate diverse aspects of plant growth and development, including flowering time. However, the molecular mechanisms underlying SL-mediated regulation of flowering remain poorly understood. Here, we show that SL promotes flowering in chrysanthemum under inductive short-day conditions. The SL-specific signaling complex CmMAX2–CmD14.1–CmD53 was first identified in chrysanthemum. Silencing CmD14.1 or CmMAX2 causes late-flowering and SL insensitivity, while their overexpression accelerates flowering upon SL treatment. In contrast, overexpression of CmD53 or the degradation-resistant variant CmD53m delayed flowering. SL-induced CmD53 degradation depends on both CmD14.1 and CmMAX2. RNA-seq analysis reveals that overexpression of CmD53 or CmD53m significantly downregulates the florigen gene CmFTL3. We confirmed that CmD53 directly binds to the CmFTL3 promoter to repress its transcription, thereby delaying flowering. Moreover, the central circadian clock protein CmLHY represses CmMAX2 and CmD14.1 transcription and subsequently modulates SL-mediated CmD53 degradation. This regulatory cascade fine-tunes CmFTL3 expression and controls flowering in chrysanthemum under inductive SD conditions. Similarly, in rice, OsD3 (a MAX2 homolog) and OsD14 act downstream of OsCCA1 (an LHY/CCA1 homolog) to regulate flowering. Our findings demonstrate that LHY/CCA1-mediated integration of SL signaling in the flowering regulatory pathway is conserved between chrysanthemum and rice, providing new insights into the novel crosstalk between the circadian clock and SL signaling in flowering-time control.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149021261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tangential single-cell spatial transcriptomics resolves early ray lineage trajectory in poplar","authors":"Cheng Qi, Rui Ding, Ruoya Zhao, Sarmad Khalid, Shiyi Yang, Zhiyang Pei, Chengcheng Li, Longwei Mei, Jing Zhang, Long Dang, Jinfang Luo, Jinlong Wang, Chunmei Shi, Yongjian Wang, Manzhu Bao, Quanzi Li, Bo Zheng, Xueping Shi","doi":"10.1093/plcell/koag275","DOIUrl":"https://doi.org/10.1093/plcell/koag275","url":null,"abstract":"Vascular cambium drives secondary growth in woody plants, yet its closely related stem-cell populations—fusiform and ray initials—are difficult to distinguish, limiting resolution of early ray fate specification. In Populus tremula × P. alba clone 717, we integrated a two-year biweekly field survey of xylem ray anatomy with time-series stem transcriptomes and single-cell-resolution tangential spatial transcriptomics to resolve early ray-lineage states in situ. Across two growing seasons, ray cell number and size/area traits showed reproducible dynamics and were most strongly associated with daylength, radiation and temperature averaged over the preceding 1-4 weeks. Co-expression analysis identified gene modules that covary with ray traits and these environmental indices. By enhancing recovery of ray cambial cells through tangential sectioning, we generated a single-cell-resolution spatial transcriptomic atlas that distinguishes fusiform initial cells (FICs) and ray initial cells (RIC_1/2), and reconstructs a continuous early ray trajectory from FICs to RICs and xylem ray precursor cells (XRP_1-3), supported by RNA in situ hybridization. Integrating field-linked candidates, public scRNA-seq resources, and spatial markers, we identified 227 ray-lineage candidates, enriched for chromatin/nuclear functions and ribosome biogenesis, with relatively few transcription factors. These results provide stage-resolved markers and candidates for dissecting ray development and its seasonal environmental covariation.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148922781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A SNP in the 4-Coumarate CoA ligase 1-likeα promoter induces juice sac granulation by promoting BR-mediated lignin synthesis in citrus","authors":"Lele Chu, Hang Zhang, Shaoqiang Hu, Wenqiang Hu, Ligang He, Haowei Chen, Qiyu Chen, Jihua Ding, Liming Wu, Ji-Hong Liu","doi":"10.1093/plcell/koag276","DOIUrl":"https://doi.org/10.1093/plcell/koag276","url":null,"abstract":"Juice sac granulation (also known as ‘Kushui’), characterized by hardening and dehydration, is a widespread physiological disorder that severely compromises fruit quality. However, the molecular mechanism and signaling pathways underlying this disorder remain largely unexplored. In this study, we identified a unique hybrid from a cross between Kiyomi (Citrus unshiu Marc × C. sinensis Osbeck) and Egan No. 1 tangerine (C. reticulata Blanc.) that exhibits the juice sac granulation from the onset of fruit development. Compared to normal fruits, ‘Kushui’ fruit (KS) exhibited significantly elevated levels of lignin and brassinolide (BR). Through resequencing and transcriptome analyses, we identified 4-Coumarate CoA ligase 1-likeα (Ci4CL1-likeα) as a key gene involved in lignin biosynthesis. Notably, a single nucleotide polymorphism (SNP, A/T) in the promoter region of Ci4CL1-likeα between KS (carrying T) and normal (carrying A) allowed the former to be successfully targeted and positively regulated by CiMYB306. In addition, both CiMYB306 and Ci4CL1-likeα were positively regulated by CiNAC9 through interacting with the NARC motifs in a BR-inducible way. Genetic evidences confirmed that CiMYB306 and CiNAC9 regulated lignin biosynthesis in a Ci4CL1-likeα-dependent manner. Taken together, our findings reveal that the mutation of A into T in the promoter of Ci4CL1-likeα creates a binding site recognized and positively activated by CiMYB306, which acts in synergy with CiNAC9 in a BR-responsive way, leading to enhanced lignin synthesis and fruit granulation. These findings gain valuable insight into the BR-mediated transcriptional regulatory module involved in fruit granulation and unravel potential targets for mitigating this disorder.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148946745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A brassinosteroid signaling protein acts as an integrative regulator of K+ and Na+ transport in rice response to salt stress","authors":"Di Chen, Quanxiang Tian, Qi Wu, Hongwei Cao, Kai Ding, Wen Jing, Chenxue Jing, Xiaoxia Tang, Wenjing Zhang, Jingya Yuan, Qun Zhang, Wenhua Zhang, Like Shen","doi":"10.1093/plcell/koag274","DOIUrl":"https://doi.org/10.1093/plcell/koag274","url":null,"abstract":"Maintaining the cytosolic K+/Na+ homeostasis is crucial for plants’ salt tolerance. Therefore, elucidating the regulatory mechanism governing K+/Na+ transport is pivotal to engineering salt-tolerant crops. Although many regulators have been shown specifically to modulate either Na+ or K+ transporters, little is known about integrative regulators that orchestrate the transport of both cations. In this study, we reveal that a rice basic helix-loop-helix (bHLH) transcription factor, BES1-INTERACTING MYC-LIKE1 (OsBIM1), negatively regulates K+/Na+ homeostasis under salt stress. Loss of OsBIM1 function conferred salt tolerance and K+/Na+ homeostasis in rice, whereas its overexpression produced the opposite effect. The K+ transporter OsHAK5 and transcription factor OsWRKY53 were identified as the targets of OsBIM1. By binding to E-box elements in their promoter regions, OsBIM1 not only repressed OsHAK5 expression and the root K+ uptake, but also trans-activated OsWRKY53 to suppress transcription of the Na+ transporter gene OsHKT1;5 and the Na+ unloading from xylem. OsBIM1 expression was attenuated by salt stress, and the loss of OsBIM1 function leads to synergistic upregulation of OsHAK5 and OsHKT1;5, thereby enhancing salt tolerance. As a positive regulator of Brassinosteroid (BR) signaling, OsBIM1 was also found to be indispensable for BR-induced attenuation of salt tolerance and involved in BR-mediated regulation of OsHAK5 and OsWRKY53 expression. This study reveals an integrative regulator of K+/Na+ transport and a negative regulatory mechanism by which BR affects salt tolerance, providing a promising strategy for breeding salt-tolerant rice.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148922784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cryptic Fate Priming and Lineage Stabilization during\u0000 Arabidopsis\u0000 Anther Development","authors":"Jianzheng Wang,Xueyi Zhou,Wenhui Sun,Yeqiao Liu,Shiting Zhang,Hanji Li,Yuhan Zhao,Xinyi Xie,Zhenze Lei,Hong Ma,Fang Chang","doi":"10.1093/plcell/koag262","DOIUrl":"https://doi.org/10.1093/plcell/koag262","url":null,"abstract":"Abstract Plant germ cells are specified de novo from somatic tissues, yet how early anther progenitors initiate divergent germline and somatic fates remains unclear. Here, we generated a high-resolution single-cell transcriptomic atlas of Arabidopsis anther development, profiling 66,864 cells from early lineage specification through pollen maturation. We resolved major anther cell types and identified an early L2-derived intermediate population, termed the archesporial-derived state (Ar-d), marked by REM22, ER/ERL1/2, SPL/NZZ, and BAM1. Although classical anatomical studies define archesporial cells, primary sporogenous cells, primary parietal cells, and secondary parietal derivatives based on developmental position and inferred lineage relationships, our analysis showed that these early L2-derived intermediates remain globally similar, forming a shared progenitor-like transcriptional state before lineage stabilization. Trajectory reconstruction, RNA velocity, and module analyses revealed that germline and somatic trajectories first emerge through restricted branch-biased transcriptional programs, which are later amplified into robust lineage-specific identities. Mutant single-cell analyses defined two regulatory steps: SPL/NZZ establishes early branch-associated transcriptional programs within the Ar-d state, whereas EMS1 stabilizes the somatic/tapetal trajectory and restricts inappropriate enrichment of germline-associated states. Lineage-resolved analyses further defined maturation programs in germline, tapetum, middle layer, and endothecium cells, and identified LBD transcription factors required for normal pollen development. Together, our study reveals a cryptic mode of anther fate priming in which shared early L2-derived intermediates progressively transform limited branch-biased transcriptional programs into distinct reproductive and somatic cell identities through SPL-dependent priming and EMS1-dependent somatic/tapetal stabilization.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148894510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diverse haplotypes at a complex\u0000 Solanum americanum\u0000 locus confer resistance to\u0000 Phytophthora infestans\u0000 and\u0000 P. capsici","authors":"Robert Heal,Andrea Carolina Olave-Achury,Maria Sindalovskaya,Ruth Norkor Annang,Shuting Sun,He Zhao,Qing Liu,Li Long,Hari Sharan Karki,Jodie Taylor,Aleksandra Wawryk-Khamdavong,Kinga Bachowska,Matthew Smoker,Maheen Alam,Sarah Pottinger,Vatsal Arora,Kee Hoon Sohn,Kamil Witek,Xiao Lin,Jonathan D G Jones","doi":"10.1093/plcell/koag264","DOIUrl":"https://doi.org/10.1093/plcell/koag264","url":null,"abstract":"Abstract Plants encounter diverse pathogens and have evolved a two-layered innate immune system to detect pathogen molecules and activate defense mechanisms that restrict infection. Most cloned plant Resistance (R) genes encode NLR immune receptors. NLR genes are often found in clusters of paralogs with sequence and copy number variation; whether these NLR clusters evolve in response to single or multiple pathogens has been unclear. We report here the isolation of a Phytophthora capsici resistance gene, Rpc2, along with a novel P. infestans resistance gene, Rpi-amr5, from two Solanum americanum accessions. These orthologous genes reside in the Rpi-amr1 cluster, which has previously been associated with resistance to P. infestans. By screening RXLR effector libraries of P. infestans and P. capsici, we identified multiple effectors recognised by both NLRs. Our findings highlight the complexity of NLR clusters and evolution driven by interactions with multiple pathogens. This work will underpin efforts to elevate resistance against Phytophthora pathogens and enhances our understanding of NLR evolution.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"82 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148894509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}