Molecular Plant最新文献

{"title":"A highly efficient and environmentally friendly strategy to obtain transgene-free genome-edited progeny in flowering plants.","authors":"Tianhe Cheng, Meng-Xiang Sun","doi":"10.1016/j.molp.2025.03.014","DOIUrl":"10.1016/j.molp.2025.03.014","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"911-914"},"PeriodicalIF":17.1,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710011","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":"Seed dormancy and germination in rice: Molecular regulatory mechanisms and breeding.","authors":"Fan Xu, Hideki Yoshida, Chengcai Chu, Makoto Matsuoka, Jian Sun","doi":"10.1016/j.molp.2025.05.010","DOIUrl":"10.1016/j.molp.2025.05.010","url":null,"abstract":"<p><p>The transition from dormancy to germination marks the initial stage of the plant life cycle, with its intensity, synchronicity, and timing being critical for crop growth, development, and adaptation to complex climate conditions. This review synthesizes recent advances with classic molecular mechanisms of dormancy and germination, including environmental responses and signaling cascades. We integrate these independent studies to provide a comprehensive perspective on the complex regulatory networks and discuss novel insights into how rice seeds perceive and respond to environmental cues during this transition, particularly focusing on stress tolerance to temperature and flooding. We aim to bridge the understanding of the molecular mechanisms of dormancy and germination with their breeding applications. Specifically, we discuss gene targets and feasible strategies for the genetic improvement of pre-harvest sprouting and direct-seeded rice, two key traits essential for climate resilience, both of which involve dormancy and germination. Finally, we propose the concept of engineering germination-smart varieties endowed with intelligent environmental adaptation.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"960-977"},"PeriodicalIF":17.1,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151348","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":"The long noncoding RNA VIVIpary promotes seed dormancy release and pre-harvest sprouting through chromatin remodeling in rice.","authors":"Lu Yang, Yu Cheng, Chao Yuan, Yan-Fei Zhou, Qiao-Juan Huang, Wen-Long Zhao, Rui-Rui He, Jie Jiang, Yi-Chao Qin, Zheng-Tong Chen, Yu-Chan Zhang, Meng-Qi Lei, Jian-Ping Lian, Yue-Qin Chen","doi":"10.1016/j.molp.2025.04.010","DOIUrl":"10.1016/j.molp.2025.04.010","url":null,"abstract":"<p><p>Seed dormancy enables seeds to remain dormant until the environmental conditions are ideal for germination. Understanding the molecular mechanisms that underlie seed dormancy is essential for improving grain quality and preventing pre-harvest sprouting (PHS), a major challenge in global agriculture. Here, we address how long noncoding RNAs (lncRNAs) contribute to the regulation of seed dormancy in rice (Oryza sativa). We identified an lncRNA, VIVIpary, that is specifically expressed in embryos and is associated with shortened seed dormancy. VIVIpary exhibits higher expression in a PHS-sensitive variety, and its overexpression induces PHS, whereas its knockdown delays germination. Mechanistically, VIVIpary promotes the release of seed dormancy by regulating abscisic acid (ABA) signaling. VIVIpary serves as a spatial organizer that shapes chromatin architecture by directly binding to the chromatin adaptor protein OsMSI1 and enhancing its interaction with the histone deacetylase OsHDAC1, thereby reducing chromatin accessibility and fine-tuning ABA signaling. VIVIpary is differentially expressed between wild and cultivated rice, with higher expression in japonica rice, suggesting that it was a target of selection during rice domestication. Together, our findings reveal a domestication-associated lncRNA that modulates ABA signaling and chromatin architecture to regulate seed dormancy and PHS in rice, providing a potential target for improvement of rice agronomic traits.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"978-994"},"PeriodicalIF":17.1,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143973053","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":"WD40 protein-mediated crosstalk among three epigenetic marks regulates chromatin states and yield in rice.","authors":"Liwen Yang, Dongwei Li, Weijun Guo, Juqi Song, Chaofan Liu, Hanlin Liu, Cong Li, Xiaofeng Gu","doi":"10.1016/j.molp.2025.05.016","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.016","url":null,"abstract":"<p><p>Although there is increasing understanding of regulatory impacts from particular epigenetic marks, much less is known about how crosstalk occurring among multiple marks affects genetic regulation. Here, we show that Dwarf-related WD40 protein 1 (DRW1) mediates DNA 6mA demethylation, H3K27 trimethylation, and RNA m⁵C methylation in rice, based on its respective recruitment of the DNA demethylase AlkB homolog 1 (OsALKBH1), the histone methyltransferase CURLY LEAF (OsCLF), and NOP2/Sun RNA methyltransferase family member 2 (OsNSUN2). DRW1 knockout significantly reduces the extent of chromatin occupancy by OsALKBH1, OsCLF, and OsNSUN2, augments chromatin accessibility, and promotes the expression of brassinosteroid biosynthesis and signaling biomolecules. Gene editing at a CAAT-box (ATTGG→ATTGA) and a GATA motif (GATAGGG→GAT) in the DRW1 promoter leads to increased DRW1 transcription and to enhancement of both grain yield and salt tolerance. In field trials, DRW1-overexpressing rice lines display yield increases of ∼30.2% (on both normal and saline soils), accompanied by decreases in DNA 6mA and increases of H3K27me3 and RNA m⁵C levels for target genes. Overall, our study uncovers crosstalk among DNA 6mA, H3K27me3, and RNA m⁵C mediated by DRW1, and shows how this crosstalk controls transcriptional and post-transcriptional regulation affecting yield and salt tolerance.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226034","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":"SeedLLM·Rice: A large language model integrated with rice biological knowledge graph.","authors":"Fan Yang, Huanjun Kong, Jie Ying, Zihong Chen, Tao Luo, Wanli Jiang, Zhonghang Yuan, Zhefan Wang, Zhaona Ma, Shikuan Wang, Wanfeng Ma, Xiaoyi Wang, Xiaoying Li, Zhengyin Hu, Xiaodong Ma, Minguo Liu, Xi-Qing Wang, Fan Chen, Nanqing Dong","doi":"10.1016/j.molp.2025.05.013","DOIUrl":"https://doi.org/10.1016/j.molp.2025.05.013","url":null,"abstract":"<p><p>Rice biology research involves complex decision-making, requiring researchers to navigate a vast and growing body of knowledge that includes extensive literature and multiomics data. The exponential increase in biological data and scientific publications has posed significant challenges in efficiently extracting meaningful insights. While large language models (LLMs) show promise for knowledge retrieval, their application to rice-specific research is hindered by the absence of specialized models and the challenge of synthesizing multimodal data integral to the field. Moreover, the lack of standardized evaluation frameworks for domain-specific tasks impedes the assessment of model performance in this area. To address these challenges, we introduce SeedLLM·Rice (SeedLLM), a 7-billion-parameter model trained using 1.4 million rice-related publications, which represent nearly 98.24% of global rice research. Additionally, we present a novel human evaluation framework designed to assess LLM performance in rice biology tasks. Initial evaluations of rice-specific tasks demonstrate that SeedLLM outperforms general-purpose models such as OpenAI GPT-4o1 and DeepSeek-R1, achieving win rates ranging from 57% to 88%. Furthermore, SeedLLM is integrated with the rice biological knowledge graph (RBKG), which consolidates genome annotations for Nipponbare and large-scale synthesis of transcriptomic and proteomic information from over 1,800 studies. This integration enhances the ability of SeedLLM to address complex research questions requiring the fusion of textual and multiomics data. To facilitate global collaboration, we provide free access to SeedLLM and the RBKG via an interactive web portal (https://seedllm.org.cn/). SeedLLM represents a transformative tool for rice biology research, facilitating unprecedented discoveries in crop improvement and climate adaptation through its advanced reasoning capabilities and comprehensive data integration.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181225","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 top HAT: A maize mutant hypersusceptible to Agrobacterium transformation.","authors":"Catherine M Doorly, Wout Vandeputte, Inge De Clercq, Laurens Pauwels","doi":"10.1016/j.molp.2025.05.012","DOIUrl":"10.1016/j.molp.2025.05.012","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151344","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":"Potatome: Harnessing natural variation of potatoes.","authors":"Delphine Van Inghelandt, Benjamin Stich","doi":"10.1016/j.molp.2025.05.008","DOIUrl":"10.1016/j.molp.2025.05.008","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136379","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":"Balancing growth with integrity: The tangle between brassinosteroid and FERONIA.","authors":"Yosapol Harnvanichvech, Yuchen Long","doi":"10.1016/j.molp.2025.05.009","DOIUrl":"10.1016/j.molp.2025.05.009","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136376","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 novel NF-Ys-QT12-IRE1 module controlling grain quality and yield thermotolerance in rice.","authors":"Bowen Yang, Yongyao Xie, Yaoguang Liu","doi":"10.1016/j.molp.2025.05.007","DOIUrl":"10.1016/j.molp.2025.05.007","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079144","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":"Phosphorylation/dephosphorylation-mediated regulation of ABI1/2 activity and stability for fine-tuning ABA signaling.","authors":"Mar Bono, Maria Rivera-Moreno, Armando Albert, Pedro L Rodriguez","doi":"10.1016/j.molp.2025.05.006","DOIUrl":"10.1016/j.molp.2025.05.006","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079152","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}