Nature PlantsPub Date : 2025-03-14DOI: 10.1038/s41477-025-01967-1
Brian D. Gregory
{"title":"A NERDy effect on flowering","authors":"Brian D. Gregory","doi":"10.1038/s41477-025-01967-1","DOIUrl":"10.1038/s41477-025-01967-1","url":null,"abstract":"Identification of NERD-interacting proteins reveals a role for this protein in N6-methyladenosine deposition at the FLC locus to regulate flowering time.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 3","pages":"383-384"},"PeriodicalIF":15.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143618505","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":"Hordeum I genome unlocks adaptive evolution and genetic potential for crop improvement","authors":"Hao Feng, Qingwei Du, Ying Jiang, Yong Jia, Tianhua He, Yibin Wang, Brett Chapman, Jiaxin Yu, Haiwen Zhang, Mengxue Gu, Mengwei Jiang, Shanshan Gao, Xinjie Zhang, Yameng Song, Vanika Garg, Rajeev K. Varshney, Jianhua Wei, Chengdao Li, Xingtan Zhang, Ruifen Li","doi":"10.1038/s41477-025-01942-w","DOIUrl":"10.1038/s41477-025-01942-w","url":null,"abstract":"Crop wild relatives (CWRs) are invaluable for crop improvement. Among these, Hordeum I-genome species exhibit exceptional tolerance to alkali and salt stresses. Here we present a chromosome-scale genome assembly of Hordeum brevisubulatum (II, 2n = 2x =14) and genome resequencing of 38 diploid germplasms spanning 7 I-genome species. We reveal that the adaptive evolution of the H. brevisubulatum genome is shaped by structural variations, some of which may contribute to its adaptation to high alkali and salt environments. Evolutionary duplication of the stress sensor-responder module CaBP-NRT2 and the horizontally transferred fungal gene Fhb7 were identified as novel alkaline–saline tolerance mechanisms. We also demonstrate the potential of the Hordeum I genome in crop breeding through the newly synthesized hexaploid Tritordeum (AABBII) with enhanced alkaline–saline tolerance. Our study fills critical gaps in Hordeum genomics and CWR research, advancing introgression of CWR resources into current crops for sustainable agriculture. The authors present a reference genome for Hordeum I-genome species. This work unravels genomic features that drive adaptation to salt and alkali environments and could aid in improving crop resilience.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 3","pages":"438-452"},"PeriodicalIF":15.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-025-01942-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143618506","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":"NERD-dependent m6A modification of the nascent FLC transcript regulates flowering time in Arabidopsis","authors":"Yanlin Shao, Jinqi Ma, Songyao Zhang, Yifeng Xu, Hao Yu","doi":"10.1038/s41477-025-01945-7","DOIUrl":"10.1038/s41477-025-01945-7","url":null,"abstract":"N6-methyladenosine (m6A) is the most prevalent internal modification on messenger RNA. Although recent studies have shown m6A effects on determining the fate of mRNA through modulating various aspects of plant mRNA metabolism, whether and how m6A affects gene transcription in plants remains elusive. Here we show that NEEDED FOR RDR2-INDEPENDENT DNA METHYLATION (NERD), a plant-specific protein, is an essential component of the m6A methyltransferase complex required for regulating the transcription of a central floral repressor FLOWERING LOCUS C (FLC) in Arabidopsis. NERD interacts with and stabilizes the two core methyltransferases, mRNA adenosine methylases A and B, to promote m6A modification of nascent RNA, conferring an overall negative effect on gene transcription. At the FLC locus, NERD-mediated m6A modification on the nascent transcript negatively affects H3K36me3 deposition and FLC transcription through NERD interaction with the H3K36me3 methyltransferase SET DOMAIN GROUP 8. Collectively, our findings reveal that NERD mediates the crosstalk between epitranscriptomic and epigenetic regulation of FLC to modulate flowering in Arabidopsis. This study reveals NERD, a zinc finger protein, as an essential component of the plant m6A methyltransferase complex that mediates epitranscriptomic and epigenetic regulation of the floral repressor gene FLC to modulate flowering in Arabidopsis.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 3","pages":"468-482"},"PeriodicalIF":15.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143618714","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}
Nature PlantsPub Date : 2025-03-14DOI: 10.1038/s41477-025-01920-2
Amber N. Hafeez, Laetitia Chartrain, Cong Feng , Florence Cambon, Martha Clarke, Simon Griffiths, Sadiye Hayta, Mei Jiang , Beat Keller, Rachel Kirby, Markus C. Kolodziej, Oliver R. Powell, Mark A. Smedley, Burkhard Steuernagel, Wenfei Xian , Luzie U. Wingen, Shifeng Cheng , Cyrille Saintenac, Brande B. H. Wulff, James K. M. Brown
{"title":"Septoria tritici blotch resistance gene Stb15 encodes a lectin receptor-like kinase","authors":"Amber N. Hafeez, Laetitia Chartrain, Cong Feng \u0000 , Florence Cambon, Martha Clarke, Simon Griffiths, Sadiye Hayta, Mei Jiang \u0000 , Beat Keller, Rachel Kirby, Markus C. Kolodziej, Oliver R. Powell, Mark A. Smedley, Burkhard Steuernagel, Wenfei Xian \u0000 , Luzie U. Wingen, Shifeng Cheng \u0000 , Cyrille Saintenac, Brande B. H. Wulff, James K. M. Brown","doi":"10.1038/s41477-025-01920-2","DOIUrl":"10.1038/s41477-025-01920-2","url":null,"abstract":"Septoria tritici blotch (STB), caused by the Dothideomycete fungus Zymoseptoria tritici, is one of the most damaging diseases of bread wheat (Triticum aestivum)1 and the target of costly fungicide applications2. In line with the fungus’s apoplastic lifestyle, STB resistance genes isolated to date encode receptor-like kinases (RLKs) including a wall-associated kinase (Stb6) and a cysteine-rich kinase (Stb16q)3,4. Here we used genome-wide association studies on a diverse panel of 300 whole-genome shotgun-sequenced wheat landraces (WatSeq consortium5) to identify a 99-kb region containing six candidates for the Stb15 resistance gene. Mutagenesis and transgenesis confirmed a gene encoding an intronless G-type lectin RLK as Stb15. The characterization of Stb15 exemplifies the unexpected diversity of RLKs conferring Z. tritici resistance in wheat. Stb15 provides resistance to Septoria tritici blotch in wheat and encodes a G-type lectin receptor-like kinase. The three cloned Stb genes, which are effective against different pathogen isolates, encode diverse receptor-like kinases with extracellular domains potentially involved in sugar binding.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 3","pages":"410-420"},"PeriodicalIF":15.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-025-01920-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143618503","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":"Sporophyte-directed gametogenesis in Arabidopsis","authors":"Prakash Sivakumar, Saurabh Pandey, A. Ramesha, Jayeshkumar Narsibhai Davda, Aparna Singh, Chandan Kumar, Hardik Gala, Veeraputhiran Subbiah, Harikrishna Adicherla, Jyotsna Dhawan, L. Aravind, Imran Siddiqi","doi":"10.1038/s41477-025-01932-y","DOIUrl":"10.1038/s41477-025-01932-y","url":null,"abstract":"Plants alternate between diploid sporophyte and haploid gametophyte generations1. In mosses, which retain features of ancestral land plants, the gametophyte is dominant and has an independent existence. However, in flowering plants the gametophyte has undergone evolutionary reduction to just a few cells enclosed within the sporophyte. The gametophyte is thought to retain genetic control of its development even after reduction2. Here we show that male gametophyte development in Arabidopsis, long considered to be autonomous, is also under genetic control of the sporophyte via a repressive mechanism that includes large-scale regulation of protein turnover. We identify an Arabidopsis gene SHUKR as an inhibitor of male gametic gene expression. SHUKR is unrelated to proteins of known function and acts sporophytically in meiosis to control gametophyte development by negatively regulating expression of a large set of genes specific to postmeiotic gametogenesis. This control emerged late in evolution as SHUKR homologues are found only in eudicots. We show that SHUKR is rapidly evolving under positive selection, suggesting that variation in control of protein turnover during male gametogenesis has played an important role in evolution within eudicots. Ancestral land plants had a free-living gametophyte, but in flowering plants the gametophyte develops within the sporophyte. This study shows that male gametophyte development in Arabidopsis is directed by the sporophyte through repression of gametogenesis genes.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 3","pages":"398-409"},"PeriodicalIF":15.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143618504","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}
Nature PlantsPub Date : 2025-03-11DOI: 10.1038/s41477-025-01937-7
Dan Zhang, Sanyuan Tang, Junyu Chen, Fangyuan Liu, Kangxu Zhao, Lu Kang, Chao Li, Ran Xia, Fang Yang, Feifei Yu, Cheng-Guo Duan, Peng Xie, Qi Xie
{"title":"Chromosomal inversion at the DG1 promoter drives double-grain spikelets and enhances grain yield in sorghum","authors":"Dan Zhang, Sanyuan Tang, Junyu Chen, Fangyuan Liu, Kangxu Zhao, Lu Kang, Chao Li, Ran Xia, Fang Yang, Feifei Yu, Cheng-Guo Duan, Peng Xie, Qi Xie","doi":"10.1038/s41477-025-01937-7","DOIUrl":"10.1038/s41477-025-01937-7","url":null,"abstract":"The phenomenon of multiple-grain spikelets is frequently observed in gramineous crops. In the case of dual-floret spikelets, the upper fertile floret develops normally to form a single grain, while the lower sterile floret undergoes abortion. Here we elucidate the role of Double-Grain 1 (DG1), a gene encoding a homeobox-domain-containing protein, in regulating the lower floret meristem activity and double-grain spikelet trait in sorghum. A 35.7-kb paracentric inversion in the DG1 promoter region leads to increased DG1 expression, probably by reducing repressive histone modifications. This increase in DG1 expression transforms the degenerated lower floret into a fertile one. The use of the superior DG1 allele results in an increase of approximately 40.7% to 46.1% in grain number per panicle and a 10.1% to 14.3% increase in overall grain yield. Our findings shed light on the sorghum double-grain spikelet characteristic, offering valuable insights for high-yield breeding designs in cereals. A 35.7-kb inversion in the DG1 promoter increased DG1 expression in sorghum, inducing double-grain spikelets by restoring fertility to the lower floret. The superior DG1 allele boosted grain number and yield, providing insights for high-yield breeding.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 3","pages":"453-467"},"PeriodicalIF":15.8,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143589837","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":"Regulation of alternative splicing by CBF-mediated protein condensation in plant response to cold stress","authors":"Diyi Fu, Yue Song, Shifeng Wu, Yue Peng, Yuhang Ming, Zhuoyang Li, Xiaoyan Zhang, Wen Song, Zhen Su, Zhizhong Gong, Shuhua Yang, Yiting Shi","doi":"10.1038/s41477-025-01933-x","DOIUrl":"10.1038/s41477-025-01933-x","url":null,"abstract":"Cold acclimation is critical for the survival of plants in temperate regions under low temperatures, and C-REPEAT BINDING FACTORs (CBFs) are well established as key transcriptional factors that regulate this adaptive process by controlling the expression of cold-responsive genes. Here we demonstrate that CBFs are involved in modulating alternative splicing during cold acclimation through their interaction with subunits of the spliceosome complex. Under cold stress, CBF proteins accumulate and directly interact with SKI-INTERACTING PROTEIN (SKIP), a key component of the spliceosome, which positively regulates acquired freezing tolerance. This interaction facilitates the formation of SKIP nuclear condensates, which enhances the association between SKIP and specific cold-responsive transcripts, thereby increasing their splicing efficiency. Our findings uncover a regulatory role of CBFs in alternative splicing and highlight their pivotal involvement in the full development of cold acclimation, bridging transcriptional and post-transcriptional regulatory mechanisms. CBF transcription factors facilitate the formation of SKIP nuclear condensates to increase the splicing efficiency of cold-responsive transcripts, bridging transcriptional and post-transcriptional regulation during cold acclimation.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 3","pages":"505-517"},"PeriodicalIF":15.8,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546239","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}
Nature PlantsPub Date : 2025-03-05DOI: 10.1038/s41477-025-01940-y
Jia Li, Lei Cao, Yaqian Zhao, Jinghan Shen, Lei Wang, Mingfeng Feng, Min Zhu, Yonghao Ye, Richard Kormelink, Xiaorong Tao, Xiangxi Wang
{"title":"Structural basis for the activation of plant bunyavirus replication machinery and its dual-targeted inhibition by ribavirin","authors":"Jia Li, Lei Cao, Yaqian Zhao, Jinghan Shen, Lei Wang, Mingfeng Feng, Min Zhu, Yonghao Ye, Richard Kormelink, Xiaorong Tao, Xiangxi Wang","doi":"10.1038/s41477-025-01940-y","DOIUrl":"10.1038/s41477-025-01940-y","url":null,"abstract":"Despite the discovery of plant viruses as a new class of pathogens over a century ago, the structure of plant virus replication machinery and antiviral pesticide remains lacking. Here we report five cryogenic electron microscopy structures of a ~330-kDa RNA-dependent RNA polymerase (RdRp) from a devastating plant bunyavirus, tomato spotted wilt orthotospovirus (TSWV), including the apo, viral-RNA-bound, base analogue ribavirin-bound and ribavirin-triphosphate-bound states. They reveal that a flexible loop of RdRp’s motif F functions as ‘sensor’ to perceive viral RNA and further acts as an ‘adaptor’ to promote the formation of a complete catalytic centre. A ten-base RNA ‘hook’ structure is sufficient to trigger major conformational changes and activate RdRp. Chemical screening showed that ribavirin is effective against TSWV, and structural data revealed that ribavirin disrupts both hook-binding and catalytic core formation, locking polymerase in its inactive state. This work provides structural insights into the mechanisms of plant bunyavirus RdRp activation and its dual-targeted site inhibition, facilitating the development of pesticides against plant viruses. There are more than 2,100 known plant virus species. This work presents full-length three-dimensional structures of a plant virus’s replication machinery, providing insights into its activation and inhibition.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 3","pages":"518-530"},"PeriodicalIF":15.8,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-025-01940-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546240","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}
Nature PlantsPub Date : 2025-03-05DOI: 10.1038/s41477-025-01934-w
Guannan Jia, Guojingwei Chen, Zhaoheng Zhang, Chenghua Tian, Yaping Wang, Jie Luo, Kaina Zhang, Xiaoyun Zhao, Xiaoming Zhao, Zhen Li, Linfeng Sun, Wenqiang Yang, Yan Guo, Jiří Friml, Zhizhong Gong, Jing Zhang
{"title":"Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize","authors":"Guannan Jia, Guojingwei Chen, Zhaoheng Zhang, Chenghua Tian, Yaping Wang, Jie Luo, Kaina Zhang, Xiaoyun Zhao, Xiaoming Zhao, Zhen Li, Linfeng Sun, Wenqiang Yang, Yan Guo, Jiří Friml, Zhizhong Gong, Jing Zhang","doi":"10.1038/s41477-025-01934-w","DOIUrl":"10.1038/s41477-025-01934-w","url":null,"abstract":"Nitrogen (N) is an essential macronutrient for plant development and, ultimately, yield. Identifying the genetic components and mechanisms underlying N use efficiency in maize (Zea mays L.) is thus of great importance. Nitrate (NO3−) is the preferred inorganic N source in maize. Here we performed a genome-wide association study of shoot NO3− accumulation in maize seedlings grown under low-NO3− conditions, identifying the ferredoxin family gene ZmFd4 as a major contributor to this trait. ZmFd4 interacts and co-localizes with nitrite reductases (ZmNiRs) in chloroplasts to promote their enzymatic activity. Furthermore, ZmFd4 forms a high-affinity heterodimer with its closest paralogue, ZmFd9, in a NO3−-sensitive manner. Although ZmFd4 exerts similar biochemical functions as ZmFd9, ZmFd4 and ZmFd9 interaction limits their ability to associate with ZmNiRs and stimulate their activity. Knockout lines for ZmFd4 with decreased NO3− contents exhibit more efficient NO3− assimilation, and field experiments show consistently improved N utilization and grain yield under N-deficient conditions. Our work thus provides molecular and mechanistic insights into the natural variation in N utilization, instrumental for genetic improvement of yield in maize and, potentially, in other crops. Jia et al. uncover a molecular mechanism based on the balance of nitrate-sensitive protein–protein interaction between ferredoxins ZmFd4 and ZmFd9, together antagonistically targeting ZmNiR enzymes, thus regulating NO3– assimilation in maize.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 3","pages":"643-659"},"PeriodicalIF":15.8,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546238","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}