The Plant Cell最新文献

Rational design of induced regeneration via somatic embryogenesis in the absence of exogenous phytohormones 无外源植物激素诱导体细胞胚胎再生的合理设计

The Plant Cell Pub Date : 2025-10-19 DOI: 10.1093/plcell/koaf252

Jana Wittmer, Menno Pijnenburg, Tristan Wijsman, Sieme Pelzer, Kelvin Adema, Merijn Kerstens, An-Nikol Kutevska, Joke Fierens, Hugo Hofhuis, Robert Sevenier, Bjorn Kloosterman, Michiel de Both, Wouter Kohlen, Harm Nijveen, Ben Scheres, Renze Heidstra

{"title":"Rational design of induced regeneration via somatic embryogenesis in the absence of exogenous phytohormones","authors":"Jana Wittmer, Menno Pijnenburg, Tristan Wijsman, Sieme Pelzer, Kelvin Adema, Merijn Kerstens, An-Nikol Kutevska, Joke Fierens, Hugo Hofhuis, Robert Sevenier, Bjorn Kloosterman, Michiel de Both, Wouter Kohlen, Harm Nijveen, Ben Scheres, Renze Heidstra","doi":"10.1093/plcell/koaf252","DOIUrl":"https://doi.org/10.1093/plcell/koaf252","url":null,"abstract":"Plants have a remarkable regenerative capacity, but this varies widely among species and tissue types. Important crop cultivars show regenerative recalcitrance, which is a major obstacle for the application of modern plant propagation and breeding techniques. Regeneration generally involves empirically determined tissue culture methods that are based on the principle of inducing totipotency. Cells are first persuaded to change fate towards root stem cell-like identity and then are reprogrammed to acquire shoot fate. Alternatively, pluri- or totipotent cells can lead to the formation of a complete plantlet through somatic embryogenesis. We applied our knowledge of root stem cell niche biology to directly use the implicated stem cell factors, including RETINOBLASTOMA (RBR), SCARECROW (SCR), SHORT ROOT (SHR) and members of the AINTEGUMENTA-LIKE/PLETHORA (AIL/PLT) and WUSCHEL-related homeobox (WOX) gene families, as a tool to induce regeneration in a way similar to the principle of induced pluripotent stem cells in the animal field. We show that stem cell factors synergistically induce regeneration involving the somatic embryogenesis pathway and can break recalcitrance in Arabidopsis (Arabidopsis thaliana) and pepper (Capsicum annuum).","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145314588","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}

引用次数: 0

Single-cell and spatial omics reveal progressive loss of xylem developmental complexity across seed plants 单细胞组学和空间组学揭示了种子植物木质部发育复杂性的逐渐丧失

The Plant Cell Pub Date : 2025-10-19 DOI: 10.1093/plcell/koaf253

Peng Shuai, Jo-Wei Allison Hsieh, Chung-Ting Kao, Chen-Wei Hu, Ray Wang, Shang-Che Kuo, Ming-Ren Yen, Pin-Chien Liou, Yi-Chi Ho, Chia-Chen Chu, Shuotian Huang, Jiao Liu, Lixia Zhang, Chia-Chen Wu, Yi-Jyun Luo, Quanzi Li, Chuan-Chih Hsu, Chao-Li Huang, Jung-Chen Su, Mei-Chun Tseng, Ying-Lan Chen, Te-Lun Mai, Ying-Chung Jimmy Lin

{"title":"Single-cell and spatial omics reveal progressive loss of xylem developmental complexity across seed plants","authors":"Peng Shuai, Jo-Wei Allison Hsieh, Chung-Ting Kao, Chen-Wei Hu, Ray Wang, Shang-Che Kuo, Ming-Ren Yen, Pin-Chien Liou, Yi-Chi Ho, Chia-Chen Chu, Shuotian Huang, Jiao Liu, Lixia Zhang, Chia-Chen Wu, Yi-Jyun Luo, Quanzi Li, Chuan-Chih Hsu, Chao-Li Huang, Jung-Chen Su, Mei-Chun Tseng, Ying-Lan Chen, Te-Lun Mai, Ying-Chung Jimmy Lin","doi":"10.1093/plcell/koaf253","DOIUrl":"https://doi.org/10.1093/plcell/koaf253","url":null,"abstract":"Secondary growth is a key characteristic evolved from seed plants and generates secondary xylem—the most abundant tissue on Earth. Recent studies have uncovered xylem developmental lineages in eudicots and magnoliids of angiosperms. However, xylem development in gymnosperms, the other representative clade of seed plants, remained elusive. We performed single-cell transcriptomics for xylem cells of conifers (Cunninghamia lanceolata), the major clade in gymnosperms. Using Seurat and scVI-based cross-species integration, we reconstructed the xylem differentiation trajectories and revealed that the radial system is conserved across seed plants, while the axial system in C. lanceolata exhibits a composite lineage architecture resembling both eudicots and magnoliids. To validate these trajectories, we established a multi-modal spatial framework incorporating spatial transcriptomics, spatial proteomics, and spatial metabolomics. These three spatial layers provided orthogonal evidence confirming cell-type identities and trajectory inference. Additionally, we identified a xylem cell population unique to gymnosperms, suggesting a lineage-specific specialization. Together, our findings uncover a more complex ancestral xylem architecture in gymnosperms and propose a progressive simplification of axial developmental programs from gymnosperms to angiosperms, highlighting a trajectory of reductive evolution in seed plant vascular development.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"45 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145314589","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}

引用次数: 0

Multi-omics identifies key genetic and metabolic networks regulating spike organ development in wheat 多组学鉴定小麦穗器官发育的关键遗传和代谢网络

The Plant Cell Pub Date : 2025-10-18 DOI: 10.1093/plcell/koaf250

Yangyang Liu, Lili Zhang, Anting Zhu, Liping Shen, Jiaqi Zhang, Jun Chen, Guowei Chang, Changbin Yin, Ziying Wang, Zhiwen Sun, Kuocheng Shen, Xiaowan Xu, Mengjing Sun, Mingming Xin, Jianhui Wu, Zefu Lu, Yiping Tong, Zhonghu He, Fei Lu, Yuanfeng Hao, Wei Chen, Zifeng Guo

{"title":"Multi-omics identifies key genetic and metabolic networks regulating spike organ development in wheat","authors":"Yangyang Liu, Lili Zhang, Anting Zhu, Liping Shen, Jiaqi Zhang, Jun Chen, Guowei Chang, Changbin Yin, Ziying Wang, Zhiwen Sun, Kuocheng Shen, Xiaowan Xu, Mengjing Sun, Mingming Xin, Jianhui Wu, Zefu Lu, Yiping Tong, Zhonghu He, Fei Lu, Yuanfeng Hao, Wei Chen, Zifeng Guo","doi":"10.1093/plcell/koaf250","DOIUrl":"https://doi.org/10.1093/plcell/koaf250","url":null,"abstract":"Wheat (Triticum aestivum L.) spike development is tightly regulated by genetic and metabolic programs that drive organ growth and morphological changes. However, the dynamic interplay between metabolic shifts, gene expression patterns, and their regulatory roles during spike development, remains poorly characterized. To address this knowledge gap, we performed integrated metabolomic and transcriptomic profiling across 12 stages of wheat spike organ development. Our analysis detected 1,105 metabolites in 233 spike, spikelet, and floret samples, uncovering an uneven distribution of phytohormone-related metabolites. The exogenous phytohormone treatments validated the regulatory roles of phytohormones in spike morphogenesis. High-resolution spatiotemporal data from carpel organs enabled the reconstruction of a regulatory network, identifying key genes (including 12-oxo-phytodienoic acid reductase3 (TaOPR3), Grain Length1 (GL1), and Grain Length2 (GL2)) as critical determinants of grain size. Genomic analyses revealed geographical differentiation in gene haplotypes and their selective retention during breeding, with superior alleles associated with increased grain size. This comprehensive dataset provides a valuable resource for understanding the molecular basis of wheat grain yield and offers potential targets for crop improvement.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"102 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145314590","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}

引用次数: 0

Two to tango: DTT1 regulates barley tapetum transition as part of a paired key. 二对探戈：DTT1调节大麦绒毡层过渡作为配对键的一部分。

The Plant Cell Pub Date : 2025-10-16 DOI: 10.1093/plcell/koaf249

Julie Robinson

引用次数: 0

The H3R2me2a demethylase JMJ10 regulates tomato fruit size through its interaction with the transcription factor BZR1.3. H3R2me2a去甲基化酶JMJ10通过与转录因子BZR1.3相互作用调控番茄果实大小。

The Plant Cell Pub Date : 2025-10-16 DOI: 10.1093/plcell/koaf251

Jing Zeng,Zhiwei Li,Xiaochun Ding,Hanzhi Liang,Keqiang Wu,Yueming Jiang,Xuewu Duan,Guoxiang Jiang

{"title":"The H3R2me2a demethylase JMJ10 regulates tomato fruit size through its interaction with the transcription factor BZR1.3.","authors":"Jing Zeng,Zhiwei Li,Xiaochun Ding,Hanzhi Liang,Keqiang Wu,Yueming Jiang,Xuewu Duan,Guoxiang Jiang","doi":"10.1093/plcell/koaf251","DOIUrl":"https://doi.org/10.1093/plcell/koaf251","url":null,"abstract":"Fruit weight and size are fundamental traits in tomato breeding and critical determinants of yield. Although several histone-modifying enzymes have been implicated in tomato fruit ripening, the role of histone arginine methylation in fruit development remains unknown. Here, we identify the histone H3R2me2a demethylase Jumonji C-domain-containing proteins 10 (JMJ10) as a key regulator of fruit size in tomato (Solanum lycopersicum). Loss of JMJ10 function reduces fruit size, whereas JMJ10 overexpression enhances fruit growth, primarily by promoting pericarp cell expansion. JMJ10 specifically demethylates H3R2me2a at key fruit size-associated genes, including FW11.3, CDF4, EXP2, EXP5, XTH8, and PRE2, thereby promoting their transcription. Furthermore, we show that JMJ10 physically interacts with the transcription factor Brassinazole-Resistant 1.3 (BZR1.3), which recruits JMJ10 to its target genes. The jmj10 bzr1.3 double mutants exhibit a more severe reduction in fruit size compared to either single mutant, confirming a synergistic interaction between JMJ10 and BZR1.3. ChIP-qPCR analysis showed that JMJ10 occupancy at its target loci is significantly reduced in the bzr1.3 mutant, suggesting that JMJ10 binding is BZR1.3-dependent. Additionally, BZR1.3 recruits JMJ10 to enhance the expression of these genes by facilitating H3R2me2a removal. Collectively, our findings reveal a mechanism by which BZR1.3 recruits JMJ10, a H3R2me2a demethylase, to coordinate the epigenetic regulation of fruit size in tomato.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145305583","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}

引用次数: 0

The CYP71A, NIT, AMI, and IAMH gene families are dispensable for indole-3-acetaldoxime-mediated auxin biosynthesis in Arabidopsis CYP71A、NIT、AMI和IAMH基因家族对于拟南芥中吲哚-3-乙酰氧肟介导的生长素生物合成是必不可少的

The Plant Cell Pub Date : 2025-10-15 DOI: 10.1093/plcell/koaf242

M Fenech, J Brumos, A Pěnčík, B Edwards, S Belcapo, J DeLacey, A Patel, M M Kater, X Li, K Ljung, O Novak, J M Alonso, A N Stepanova

{"title":"The CYP71A, NIT, AMI, and IAMH gene families are dispensable for indole-3-acetaldoxime-mediated auxin biosynthesis in Arabidopsis","authors":"M Fenech, J Brumos, A Pěnčík, B Edwards, S Belcapo, J DeLacey, A Patel, M M Kater, X Li, K Ljung, O Novak, J M Alonso, A N Stepanova","doi":"10.1093/plcell/koaf242","DOIUrl":"https://doi.org/10.1093/plcell/koaf242","url":null,"abstract":"The auxin indole-3-acetic acid (IAA) governs plant development and environmental responses. Although the indole-3-pyruvic acid (IPyA) pathway is the predominant route for IAA biosynthesis, other pathways have been proposed, such as the indole-3-acetaldoxime (IAOx) pathway. The IAOx pathway has garnered attention due to its supposed activation in auxin-overproducing mutants (e.g., sur1, sur2, ugt74b1) and the auxin-like responses triggered by exogenous application of its proposed intermediates IAOx, indole-3-acetonitrile (IAN), and indole-3-acetamide (IAM). However, despite the supporting evidence for individual steps of the IAOx pathway, its overall physiological relevance remains inconclusive. Here, using a comprehensive genetic approach combined with metabolic and phenotypic profiling, we demonstrate that mutating gene families proposed to function in the IAOx pathway in Arabidopsis (Arabidopsis thaliana) does not result in prominent auxin-deficient phenotypes, nor are these genes required for the high auxin production in the sur2 mutant. Our findings also challenge the previously postulated linear IAOx pathway. Exogenously provided IAOx, IAN, and IAM can be converted to IAA in vivo, but they do not act as precursors for each other. Finally, our findings question the physiological relevance of IAM and IAN as IAA precursors in plants and suggest the existence of a yet-uncharacterized route for IAA production in the sur2 mutant, likely involving IAOx as an intermediate. The identification of the metabolic steps and the corresponding genes in this pathway may uncover another IAA biosynthesis route in plants.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145295587","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}

引用次数: 0

Beyond the PEL surveyance: Genome editing of the OsPEL family enhances photosynthesis efficiency in Rice. 超越PEL调查：OsPEL家族的基因组编辑提高了水稻的光合效率。

The Plant Cell Pub Date : 2025-10-15 DOI: 10.1093/plcell/koaf247

Christian Damian Lorenzo

引用次数: 0

Whispers in the Genome: The Hidden Grammar of Tomato Fruit Development. 基因组中的低语：番茄果实发育的隐藏语法。

The Plant Cell Pub Date : 2025-10-15 DOI: 10.1093/plcell/koaf248

Andrea Gómez-Felipe

引用次数: 0

Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes 空间分解植物转录组中基因和基因组复制后的基因表达差异

The Plant Cell Pub Date : 2025-10-15 DOI: 10.1093/plcell/koaf243

Fabricio Almeida-Silva, Yves Van de Peer

{"title":"Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes","authors":"Fabricio Almeida-Silva, Yves Van de Peer","doi":"10.1093/plcell/koaf243","DOIUrl":"https://doi.org/10.1093/plcell/koaf243","url":null,"abstract":"Gene and genome duplications expand genetic repertoires and facilitate functional innovation. Segmental or whole-genome duplications generate duplicates with similar and somewhat redundant expression profiles across multiple tissues, while other modes of duplication create genes that show increased divergence, leading to functional innovations. How duplicates diverge in expression across cell types in a single tissue remains elusive. Here, we used high-resolution spatial transcriptomic data from Arabidopsis thaliana, Glycine max, Phalaenopsis aphrodite, Zea mays, and Hordeum vulgare to investigate the evolution of gene expression following gene duplication. We found that genes originating from segmental or whole-genome duplications display increased expression levels, expression breadths, spatial variability, and number of coexpression partners. Duplication mechanisms that preserve cis-regulatory landscapes typically generate paralogs with more preserved expression profiles, but such differences generated by mode of duplication fade or disappear over time. Paralogs originating from large-scale (including whole-genome) duplications display redundant or overlapping expression profiles, indicating functional redundancy or subfunctionalization, while most small-scale duplicates diverge asymmetrically, consistent with neofunctionalization. Expression divergence also depends on gene functions, with dosage-sensitive genes displaying highly preserved expression profiles, and genes involved in more specialized processes diverging more rapidly. Our findings offer a spatially resolved view of expression divergence following duplication, elucidating the tempo and mode of gene expression evolution, and helping understand how gene and genome duplications shape cell identities.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145295586","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}

引用次数: 0

A triose phosphate/phosphate translocator triggers antimicrobial immunity by exporting glyceraldehyde 3-phosphate from chloroplasts. 磷酸三糖/磷酸转运体通过从叶绿体输出3-磷酸甘油醛触发抗微生物免疫。

The Plant Cell Pub Date : 2025-10-14 DOI: 10.1093/plcell/koaf245

Deng-Pan Zuo,Bin Wang,Yu-Zi Liu,Zheng-Song Chen,Ru-Jian Hu,Meng-Jun He,Zong-Ying Zhang,Ying Wang,Cheng-Gui Han

{"title":"A triose phosphate/phosphate translocator triggers antimicrobial immunity by exporting glyceraldehyde 3-phosphate from chloroplasts.","authors":"Deng-Pan Zuo,Bin Wang,Yu-Zi Liu,Zheng-Song Chen,Ru-Jian Hu,Meng-Jun He,Zong-Ying Zhang,Ying Wang,Cheng-Gui Han","doi":"10.1093/plcell/koaf245","DOIUrl":"https://doi.org/10.1093/plcell/koaf245","url":null,"abstract":"Chloroplasts play a crucial role in plant immunity against invading microbes. However, whether photosynthetic metabolites from chloroplasts participate directly in host defenses remains poorly understood. Here, we uncovered that an Arabidopsis thaliana triose phosphate/phosphate translocator (TPT) in the inner membrane of the chloroplast envelope suppresses viral infection and evokes defense responses. AtTPT overexpression impairs virus accumulation in plants, and loss-of-function tpt-3 mutants exhibit an increased viral load. The antiviral activity of AtTPT requires its metabolite transport capacity, implying that it indeed functions through its metabolite(s). To this end, we found that glyceraldehyde 3-phosphate (GAP), one the metabolites translocated by AtTPT, drastically enhances the expression of defense-related genes and induces defense signaling pathways. Moreover, AtTPT or GAP robustly impairs the proliferation of diverse phytopathogens. Therefore, we propose that AtTPT exports GAP to mediate broad-spectrum pathogen resistance, which provides insights into the mechanisms underlying chloroplast-mediated immunity induced by a photosynthetic metabolite.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145296051","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}

引用次数: 0