Plant Cell最新文献

{"title":"Inferring cell division from cell shape.","authors":"Zining Wang, Yujie Zhao, Hokuto Nakayama, Gorou Horiguchi, Yasuhiro Inoue, Atsushi Mochizuki, Hirokazu Tsukaya","doi":"10.1093/plcell/koag279","DOIUrl":"10.1093/plcell/koag279","url":null,"abstract":"<p><p>Cell division patterns shape developing organs, but their systematic analysis remains limited by the technical difficulty of existing detection methods. Here, we present a practical method for inferring recent daughter-cell pairs from static cell shapes. Although cell divisions have long been inferred by expert judgment, the accuracy of this approach has rarely been quantified. Using live imaging of Arabidopsis leaf primordia, we evaluated 49 features from 7,573 neighboring cell pairs, including 1,114 direct daughter pairs and 6,459 non-daughter pairs. A simple junction-angle criterion correctly inferred 1,030 daughter pairs with 94.1% precision and 92.5% recall, whereas symmetry-based indices performed poorly. Temporal analysis revealed that junction angles were initially high after division, decreased during growth, and were altered by subsequent divisions, thus separating daughter pairs from non-daughter pairs. This method also achieved 98.4% precision and 97.2% recall in an independent shoot apical meristem live-imaging dataset. Application to the pointed-tip Arabidopsis mutant rpl4d-3 and 2 nonmodel species further supported its potential applicability for analyzing division patterns in diverse leaf morphologies. For community use, we provide FIJI/ImageJ and Qt-based graphical user interface implementations. Overall, this study quantitatively validates empirical geometric cues and provides a practical framework for inferring daughter pairs from static tissue images.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":13.5,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Natural variant of microProtein SMART1 confers 3S plant architecture traits and high-density tolerance in maize.","authors":"Yun Meng, Jiashuai Wu, Xiaoxue Luan, Nuonuo Zhang, Jiapeng Zha, Atiq Ur Rahman, Nengquan Zhong, Xi Wang, Haiyang Jiang, Qingqing Wu","doi":"10.1093/plcell/koag277","DOIUrl":"10.1093/plcell/koag277","url":null,"abstract":"<p><p>High-density planting is a critical strategy for maximizing maize (Zea mays L.) yield. The ideotype for maize dense planting requires shade-tolerant traits characterized by semi-dwarf, sturdy stems, and smart-canopy structure (termed 3S traits), which collectively enhance lodging resistance and light capture efficiency. However, the genetic basis of these 3S traits regulation in maize remains unclear. Here, we identify Shade-responsive MicroProtein Architecture Remodeling Target 1 (SMART1) as a pivotal regulator that enhances 3S traits, manifesting as semi-dwarf plant height, robust stems and upright upper leaves. Field trials demonstrate that SMART1 overexpression significantly improves density tolerance, photosynthetic capacity and grain yield. Association analysis revealed that natural variations in SMART1 influence its binding affinity to a phytochrome-interacting factor, ZmPIF5.2, thereby modulating its allosteric deactivation. These molecular interactions subsequently repress the expression of ZmMYBs, ZmCRRs, and ZmCYPs genes, contributing to phenotypic variation in shade-related traits across maize inbred lines and haplotype-specific overexpression lines. Evolutionary analysis further reveals that the shade-tolerant haplotype SMART1Hap2 underwent positive selection during maize domestication and modern breeding. Our findings identify SMART1 as a key regulator of 3S traits under normal and high-density conditions and provide a promising genetic target for breeding maize varieties with enhanced density tolerance.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":13.5,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148970187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A cellular view of seed development and germination.","authors":"Cunman He, Lucas Auroux, Mathew Lewsey, James Whelan","doi":"10.1093/plcell/koag286","DOIUrl":"10.1093/plcell/koag286","url":null,"abstract":"<p><p>Seeds are fundamental to global food security, yet their encapsulated structure, dense storage compounds, and spatial heterogeneity have created a \"hidden box\" problem, often restricting research to bulk and tissue approaches that mask cell type-specific regulatory programs. Advances in single-cell and spatial transcriptomics now enable systematic dissection of seed biology at cellular resolution. This review provides a cellular view spanning the developmental continuum from fertilization to seedling establishment by synthesizing single-cell and spatial transcriptomic studies in Arabidopsis thaliana and major crops (Oryza sativa-rice, Zea mays-maize, Hordeum vulgare-barley, Glycine max-soybean, Triticum aestivum-wheat). These technologies reveal previously undetected cellular complexity and heterogeneity: distinct transcriptional subpopulations within morphologically uniform tissues, specialized endosperm microdomains mediating nutrient transfer and metabolic polarity, cell type-specific genomic imprinting patterns, and spatially segregated hormone signaling hubs controlling dormancy and germination. Integration of transcriptional profiling with chromatin accessibility and transcription factor binding data has enabled construction of cell type-specific gene regulatory networks for seeds, advancing from correlation to causal inference and identifying master regulators of developmental transitions. These approaches illuminate how early embryonic patterning establishes transcriptional identities, how metabolic zonation coordinates storage compound accumulation and mobilization, how chromatin states maintain dormancy and license germination competence, and how spatiotemporal coordination integrates hormone signaling with energy metabolism across tissues. Single-cell and spatial approaches are establishing seeds not as opaque structures but as assemblies of coordinated cellular programs amenable to systematic analysis and targeted manipulation for crop improvement.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":"38 10","pages":""},"PeriodicalIF":13.5,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13673986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: The spliceosome's secret life: PRP8 silences transposons through 3D chromatin organization.","authors":"","doi":"10.1093/plcell/koag311","DOIUrl":"10.1093/plcell/koag311","url":null,"abstract":"","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":"38 10","pages":""},"PeriodicalIF":13.5,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13673983/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BR-ENHANCED EXPRESSION 1/2/3 fine-tune plant photomorphogenesis by regulating the phyA/B-SPA1 cascade.","authors":"Jiale Yuan, Jing Cao, Qizhang Wang, Qian Xu, Yuxia Liang, Ruiyun Wang, Can Huang, Hua Zhou, Dongqing Xu, Fang Lin","doi":"10.1093/plcell/koag284","DOIUrl":"10.1093/plcell/koag284","url":null,"abstract":"<p><p>BR-ENHANCED EXPRESSION1 (BEE1), BEE2, and BEE3, key transcriptional components of brassinosteroid signaling, have been shown to play critical roles in regulating light signaling. However, the precise molecular mechanism by which BEE1/2/3 repress photomorphogenesis remains elusive. In this study, we found that light triggers the degradation of BEE1/2/3 proteins through the 26S proteasome system. BEE1/2/3 interact with PHYTOCHROME A (phyA) and phyB, and this interaction promotes the degradation of BEE3. Mutations in BEE1/2/3 exhibit short hypocotyls and partially suppress the long hypocotyl phenotype of the phyA phyB double mutant. BEE1/2/3 attenuate the interaction between phyB and PHYTOCHROME-INTERACTING FACTOR 3 (PIF3), leading to PIF3 stabilization and subsequent repression of photomorphogenesis. In addition, BEE1/2/3 interact with SUPPRESSORs OF PHYTOCHROME A (SPAs) to disrupt the phyA/B-SPA1 association, thereby further attenuating the exaggerated light signaling. The COP1-SPAs complexes stabilize BEE1/3 under both dark and light conditions. Mutations in BEE1/2/3 enhance the constitutively photomorphogenic phenotype of spa1/2/4, whereas overexpression of BEE1/3 partially rescue the short hypocotyls of cop1 and spa1/2/4. Collectively, these findings demonstrate that BEE1/2/3 fine-tune the phyA/B-COP1/SPA1 signaling hub to negatively regulate photomorphogenesis in response to excessive light signaling. Our study provides insights into the pivotal roles of BEE1/2/3 as photomorphogenic repressors, facilitating adaptation to complex light conditions.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":13.5,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149012691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulatory network unveils the molecular architecture governing seed vigor in watermelon (Citrullus lanatus).","authors":"Xinyi Wu, Mengxue Cheng, Xuyang Li, Chunyu Zhang, Yingying Zhou, Bing Bai","doi":"10.1093/plcell/koag263","DOIUrl":"10.1093/plcell/koag263","url":null,"abstract":"<p><p>Seed vigor, a determinant of agricultural productivity, diminishes during aging but can be restored through priming. We integrated multi-omics approaches to dissect molecular mechanisms governing watermelon seed vigor under controlled deterioration and priming. Controlled deterioration progressively impaired germination speed (t50) and uniformity (AUC) before reducing maximum germination (Gmax), whereas priming reversed these effects even under aging conditions. Transcriptome analyses revealed that aging upregulated oxidative-stress genes (e.g., cytochrome c oxidase) and suppressed translation machinery. Priming activated stress-response pathways and ribosomal proteins through DOF/ERF-mediated transcriptional reprogramming via cis-element recognition, and molecular docking and yeast one-hybrid assays confirmed this interaction. Two biomarkers, Cla97C04G070560 (cytochrome c oxidase) and Cla97C03G062270 (ribosomal protein), were identified as quantitative predictors of germination decline. Machine-learning-based proteomic models and a regulatory network, SeedWatermelonNet, were constructed. These analyses uncovered hub genes (e.g., OHCU-decarbox, HSPs, LIM, NADPH-dependent aldehyde reductase 1, RPL32) coordinating uric acid metabolism, stress responses, energy metabolism, and translation. Experimental validation confirmed the regulatory roles of these candidates, including physical interactions mediating seed-vigor transduction cascades and their predicted function as direct regulators of seed vigor via SeedWatermelonNet. Maternal alleles dominated transcriptional regulation of stored mRNAs, with aging reducing maternal-specific gene expression. Promoter SNPs in these genes implicated BPC and DOF transcription factors in maternal bias. These findings establish molecular thresholds for vigor loss, validate priming as a resilience strategy, and provide biomarkers for seed quality assessment. Integrating transcriptomic, proteomic, and allele-specific insights advances precision breeding and storage practices, offering targets to enhance seed resilience against climate-driven challenges in agricultural.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":13.5,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148913166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single cell transcriptome reveals the molecular pathways of MADS-box genes in maize ovule development.","authors":"Yunfu Li, Jimin Zhan, Binfei Tang, Guangliang Lin, Zhen Li, Yanwen Wang, Qin Sun, Juan Huang, Yanfang Du, Haijun Liu, Ning Yang, Mingqiu Dai, Zuxin Zhang, Lei Liu","doi":"10.1093/plcell/koag280","DOIUrl":"10.1093/plcell/koag280","url":null,"abstract":"<p><p>Flowers are the reproductive structures of flowering plants, involved in seed production. A mature flower has 4 whorls of specialized organs that differentiate from heterogeneous cell clusters in the floral meristem. However, the mechanisms controlling the specialization of floral meristem cells remain elusive. Our early research identified a double mutant of 2 MADS-box genes (mads8;14) that lacks floral organs and repeatedly produces branch-like structures in the female inflorescence of maize (Zea mays L.). Here, single-cell transcriptomic analysis revealed that ZmMADS8/14 regulate ovule cell specialization and that branch-like structures are associated with defective floral meristem termination and enhanced proliferation of ovule epidermal cells in the mads8;14 mutant. ZmMADS8/14 restrict ZMM3 expression to the nucellus, whereas their loss results in ectopic ZMM3 expression co-localizing with KNOTTED1. ZMM3 suppresses the expression of floral organ identity genes, such as B-class gene Zmm16/sterile tassel silky ear1, C-class gene Zea AGAMOUS1, E-class gene Bearded-ear1, and Drooping leaf1/Indeterminate floral apex1, while activating key factors involved in meristem maintenance. This indicates that ZmMADS8/14 suppress meristematic activity but promote floral organ development by precisely regulating the level and domain of ZMM3 expression, leading to the formation of fertile florets and ovules. Additionally, knocking out ZMM3 partially rescues the defective phenotypes of the double mutant mads8;14, as well as increases the kernel number in the zmm3 mutant. These findings provide a new perspective for in-depth analysis of heterogeneous cell clusters, functions, and regulatory pathways in female floral organs, as well as potential targets for improving maize ear traits.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":13.5,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148970122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Direct coupling of PSK peptide signaling to ROS generation by PSKR1-RBOHB safeguards pollen thermotolerance in tomato.","authors":"Xiao Liang, Fangfang Li, Lu Han, Ping Wang, Qifei Gao, Anran Wang, Xiaotian Liu, Jiren Huang, Fei Li, Huan Liu, Jingquan Yu, Christine H Foyer, Kai Shi","doi":"10.1093/plcell/koag266","DOIUrl":"10.1093/plcell/koag266","url":null,"abstract":"<p><p>Heat stress poses a major threat to global crop productivity, with the male gametophyte being the most thermosensitive stage. While peptide hormones are known orchestrators of plant vegetative adaptation, their roles in reproductive thermotolerance remain largely undefined. Here, we show that phytosulfokine (PSK) signaling determines tomato pollen thermotolerance, as heat-induced anther PSK precursor expression correlates with pollen germination, and exogenous PSK application mitigates heat-induced pollen abortion. Loss of the PSK receptor (PSKR) PSKR1 or the NADPH oxidase Respiratory burst oxidase homolog B (RBOHB) compromises reactive oxygen species (ROS) homeostasis and pollen thermotolerance, causing severe yield losses under both controlled and natural field heat-stress conditions. Mechanistically, genetic rescue experiments establish that RBOHB-dependent ROS signaling functions downstream of PSK perception driven by PSKR1-mediated phosphorylation of RBOHB at threonine-266 and serine-340 in pollen grains, which triggers protective ROS bursts to activate the downstream heat shock transcription factor/heat shock protein pathway. Genetic complementation with phospho-mimic variants confirms that phosphorylation at these residues is sufficient to enhance pollen thermotolerance. Our findings define a PSK peptide-ROS signaling axis that safeguards male thermotolerance, providing both genetic targets and peptide-based strategies for sustaining crop yields in a warming climate.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":13.5,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148906992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA m6A methylation fine-tunes the jasmonic acid biosynthesis pathway to modulate plant aging.","authors":"Yu Zhang, Ping Li, Changmei Hua, Jinqi Ma, Kuan Nam Kong, Songyao Zhang, Xiaowei Wu, Jean Loi, Ian Kin Yuen Choi, Chongsheng He, In-Cheol Jang, Lisha Shen","doi":"10.1093/plcell/koag287","DOIUrl":"10.1093/plcell/koag287","url":null,"abstract":"<p><p>N 6-Methyladenosine (m6A) is a context-dependent mRNA modification, yet how its dynamics integrate with endogenous signaling to shape plant development remains unclear. Here, we provide further evidence for HIZ2 as an essential component of the m6A writer complex in Arabidopsis, which methylates and destabilizes mRNAs decoding multiple enzymes acting in sequential steps of jasmonic acid biosynthesis, thereby ensuring jasmonic acid homeostasis required for timely leaf senescence. HIZ2 interacts with and is indispensable for maintaining the abundance of key m6A writer complex components, including MTA. HIZ2 is required for transcriptome-wide m6A deposition, notably on transcripts of multiple jasmonic acid biosynthesis genes, which are subsequently recognized and destabilized by the m6A readers ECT2/3/4. During aging, reduced m6A deposition on these transcripts permits their accumulation, thus elevating jasmonic acid levels that drive the progression of leaf senescence. Our findings indicate that coordinated m6A-dependent regulation of multiple jasmonic acid biosynthesis transcripts fine-tunes jasmonic acid homeostasis and contributes to the timely progression of leaf senescence.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":13.5,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647280/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149002096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.","authors":"Min-Yao Jhu, Max Minne, Ziliang Luo, Hannah Dörpholz, Jie Yao, M Shahid Mukhtar, Fern Mathieu, Marta Peirats-Llobet, Travis Lee, Pau Formosa-Jordan, Siyu Song, Marc Libault, Che-Wei Hsu, Trevor M Nolan, Tatsuya Nobori, Christopher R Anderton, Robert J Schmitz, David Jackson, Miguel Moreno-Risueno, Hilde Nelissen, Rüdiger Simon, Rosangela Sozzani, Keiko Sugimoto","doi":"10.1093/plcell/koag282","DOIUrl":"10.1093/plcell/koag282","url":null,"abstract":"<p><p>Spatial omics technologies provide new opportunities for plant biology by enabling molecular profiling within structurally intact tissues, revealing spatially organized cell states, developmental gradients, and regulatory interactions. While spatial transcriptomics has driven early advances, the field is rapidly expanding toward integrated spatial multi-omics by combining single-cell and spatial transcriptomic, epigenomic, proteomic, and metabolomic data. These approaches offer new opportunities to study development, physiology, and plant biotic and abiotic interactions in spatially preserved cellular contexts. However, despite rapid adoption, the field remains constrained by plant-specific challenges when applying technologies largely developed for animal systems. Compared with animal systems, plant tissues pose additional challenges due to rigid cell walls and diverse chemistries, complicating sample preparation, cell and subcellular segmentation, signal detection, and data integration. As a result, many studies rely on bespoke protocols and analysis pipelines that are often difficult to reproduce or generalize. Here, we provide a practical, solution-oriented synthesis of current bottlenecks across experimental and computational pipelines, highlight emerging strategies to overcome these limitations, and propose a roadmap for community-driven protocol sharing, benchmarking, and integration across spatial and multi-omics modalities. Addressing these challenges will be essential to establish spatial omics as a routine and scalable tool for plant biology.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":13.5,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148970117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}