Molecular Plant最新文献

{"title":"Evolution and functional characterization of a biosynthetic gene cluster for saponin biosynthesis in Sapindaceae.","authors":"Yingxiao Mai, Huimin Hu, Wenjuan Ji, Yaxuan Xiao, Hong Zhou, Zaohai Zeng, Wenshu Lv, Xingling Su, Jiakun Zheng, Jing Xu, Yanwei Hao, Zhenhua Liu, Rui Xia","doi":"10.1016/j.molp.2025.04.013","DOIUrl":"10.1016/j.molp.2025.04.013","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143971771","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":"DNA damage: Driver of methylome reshaping?","authors":"Jean Molinier","doi":"10.1016/j.molp.2025.02.005","DOIUrl":"10.1016/j.molp.2025.02.005","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"557-559"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143523944","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 large-scale integrated transcriptomic atlas for soybean organ development.","authors":"Jingwei Fan, Yanting Shen, Chuan Chen, Xi Chen, Xiaoyue Yang, Haixia Liu, Ruiying Chen, Shulin Liu, Bohan Zhang, Min Zhang, Guoan Zhou, Yu Wang, Haixi Sun, Yuqiang Jiang, Xiaofeng Wei, Tao Yang, Yucheng Liu, Dongmei Tian, Ziqing Deng, Xun Xu, Xin Liu, Zhixi Tian","doi":"10.1016/j.molp.2025.02.003","DOIUrl":"10.1016/j.molp.2025.02.003","url":null,"abstract":"<p><p>Soybean is one of the most important crops globally, and its production must be significantly increased to meet increasing demand. Elucidating the genetic regulatory networks underlying soybean organ development is essential for breeding elite and resilient varieties to ensure increased soybean production under climate change. An integrated transcriptomic atlas that leverages multiple types of transcriptomics data can facilitate the characterization of temporal-spatial expression patterns of most organ development-related genes and thereby help us to understand organ developmental processes. Here, we constructed a comprehensive, integrated transcriptomic atlas for soybeans, integrating bulk RNA sequencing (RNA-seq) datasets from 314 samples across the soybean life cycle, along with single-nucleus RNA-seq and spatially enhanced resolution omics sequencing datasets from five organs: root, nodule, shoot apex, leaf, and stem. Investigating genes related to organ specificity, blade development, and nodule formation, we demonstrate that the atlas has robust power for exploring key genes involved in organ formation. In addition, we developed a user-friendly panoramic database for the transcriptomic atlas, enabling easy access and queries, which will serve as a valuable resource to significantly advance future soybean functional studies.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"669-689"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458699","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":"Large-scale metabolomic landscape of edible maize reveals convergent changes in metabolite differentiation and facilitates its breeding improvement.","authors":"Chunhui Li, Zhiyong Li, Baishan Lu, Yaxing Shi, Senlin Xiao, Hui Dong, Ruyang Zhang, Hui Liu, Yanyan Jiao, Li Xu, Aiguo Su, Xiaqing Wang, Yanxin Zhao, Shuai Wang, Yanli Fan, Meijie Luo, Shengli Xi, Ainian Yu, Fengge Wang, Jianrong Ge, Hongli Tian, Hongmei Yi, Yuanda Lv, Huihui Li, Ronghuan Wang, Wei Song, Jiuran Zhao","doi":"10.1016/j.molp.2025.02.007","DOIUrl":"10.1016/j.molp.2025.02.007","url":null,"abstract":"<p><p>Edible maize is an important food crop that provides energy and nutrients to meet human health and nutritional requirements. However, how environmental pressures and human activity have shaped the metabolome of edible maize remains unclear. In this study, we collected 452 diverse edible maize accessions worldwide, including waxy, sweet, and field maize. A total of 3020 non-redundant metabolites, including 802 annotated metabolites, were identified using a two-step optimized approach, which generated the most comprehensive annotated metabolite dataset in plants to date. Although specific metabolite differentiation was detected between field and sweet maize and between field and waxy maize, convergent metabolite differentiation was the dominant pattern. We identified hub genes in all metabolite classes by hotspot analysis in a metabolite genome-wide association study. Seventeen and 15 hub genes were selected as the key differentiation genes for flavonoids and lipids, respectively. Surprisingly, almost all of these genes were under diversifying selection, suggesting that diversifying selection was the main genetic mechanism of convergent metabolic differentiation. Further genetic and molecular studies revealed the roles and genetic diversifying selection mechanisms of ZmGPAT11 in convergent metabolite differentiation in the lipid pathway. On the basis of our research, we established the first edible maize metabolome database, EMMDB (https://www.maizemdb.site/home/). We successfully used EMMDB for precision improvement of nutritional and flavor traits and bred the elite inbred line 6644_2, with greatly increased contents of flavonoids, lysophosphatidylcholines, lysophosphatidylethanolamines, and vitamins. Collectively, our study sheds light on the genetic mechanisms of metabolite differentiation in edible maize and provides a database for breeding improvement of flavor and nutritional traits in edible maize by metabolome precision design.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"619-638"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537444","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":"FERONIA signaling maintains cell wall integrity during brassinosteroid-induced cell expansion in Arabidopsis.","authors":"Ajeet Chaudhary, Yu-Chun Hsiao, Fang-Ling Jessica Yeh, Milan Župunski, Hongliang Zhang, Yalikunjiang Aizezi, Andrey Malkovskiy, Guido Grossmann, Hen-Ming Wu, Alice Y Cheung, Shou-Ling Xu, Zhi-Yong Wang","doi":"10.1016/j.molp.2025.02.001","DOIUrl":"10.1016/j.molp.2025.02.001","url":null,"abstract":"<p><p>Plant cell expansion is regulated by hormones and driven by turgor pressure, which stretches the cell wall and can potentially cause wall damage or rupture. How plant cells avoid cell wall rupture during hormone-induced rapid cell expansion remains poorly understood. Here, we show that the wall-sensing receptor kinase FERONIA (FER) plays an essential role in maintaining cell wall integrity during brassinosteroid (BR)-induced cell elongation. Compared with the wild type, the BR-treated fer mutants display an increased initial acceleration of cell elongation, increased cell wall damage and rupture, reduced production of reactive oxygen species (ROS), and enhanced cell wall acidification. Long-term treatments of fer with high concentrations of BR cause stress responses and reduce growth, whereas osmolytes, reducing turgor, alleviate the defects. These results show that BR-induced cell elongation causes damage to cell walls and the release of cell wall fragments that activate FER, which promotes ROS production, attenuates apoplastic acidification, and slows cell elongation, thereby preventing further cell wall damage and rupture. Furthermore, we show that BR signaling promotes FER accumulation at the plasma membrane (PM). When the BR level is low, the GSK3-like kinase BIN2 phosphorylates FER to reduce FER accumulation and translocation from the endoplasmic reticulum to PM. BR-induced inactivation of BIN2 leads to dephosphorylation and PM accumulation of FER. Thus, BR signaling enhances FER-mediated cell wall integrity surveillance while promoting cell expansion, whereas FER acts as a brake to maintain a safe cell elongation rate. Collectively, our study reveals a vital signaling circuit that coordinates hormone signaling with mechanical sensing to prevent cell rupture during hormone-induced cell expansion.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"603-618"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11981838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143365275","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":"Sensing H₂O₂ for defense in plants.","authors":"Yan Bi, Leeza Tariq, Hui Wang, Fengming Song","doi":"10.1016/j.molp.2025.03.004","DOIUrl":"10.1016/j.molp.2025.03.004","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"563-565"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567746","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":"Gene editing produces CoQ₁₀ rice.","authors":"Jie Luo","doi":"10.1016/j.molp.2025.02.004","DOIUrl":"10.1016/j.molp.2025.02.004","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"555-556"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476089","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":"Large-scale genomic and phenomic analyses of modern cultivars empower future rice breeding design.","authors":"Xiaoding Ma, Hao Wang, Shen Yan, Chuanqing Zhou, Kunneng Zhou, Qiang Zhang, Maomao Li, Yaolong Yang, Danting Li, Peng Song, Cuifeng Tang, Leiyue Geng, Jianchang Sun, Zhiyuan Ji, Xianjun Sun, Yongli Zhou, Peng Zhou, Di Cui, Bing Han, Xin Jing, Qiang He, Wei Fang, Longzhi Han","doi":"10.1016/j.molp.2025.03.007","DOIUrl":"10.1016/j.molp.2025.03.007","url":null,"abstract":"<p><p>Modern cultivated rice plays a pivotal role in global food security. China accounts for nearly 30% of the world's rice production and has developed numerous cultivated varieties over the past decades that are well adapted to diverse growing regions. However, the genomic bases underlying the phenotypes of these modern cultivars remain poorly characterized, limiting the exploitation of this vast resource for breeding specialized, regionally adapted cultivars. In this study, we constructed a comprehensive genetic variation map of modern rice using resequencing datasets from 6044 representative cultivars from five major rice-growing regions in China. Our genomic and phenotypic analyses of this diversity panel revealed regional preferences for specific genomic backgrounds and traits, such as heading date, biotic/abiotic stress resistance, and grain shape, which are crucial for adaptation to local conditions and consumer preferences. We identified 3131 quantitative trait loci associated with 53 phenotypes across 212 datasets under various environmental conditions through genome-wide association studies. Notably, we cloned and functionally verified a novel gene related to grain length, OsGL3.6. By integrating multiple datasets, we developed RiceAtlas, a versatile multi-scale toolkit for rice breeding design. We successfully utilized the RiceAtlas breeding design function to rapidly improve the grain shape of the Suigeng4 cultivar. These valuable resources enhance our understanding of the adaptability and breeding requirements of modern rice and can facilitate advances in future rice-breeding initiatives.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"651-668"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625475","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":"Mobilizing Triticeae diversity from gene banks to farmer's field.","authors":"Awais Rasheed, Jindong Liu, Rudi Appels, Zhonghu He","doi":"10.1016/j.molp.2025.03.006","DOIUrl":"10.1016/j.molp.2025.03.006","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"566-569"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586359","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 near-complete genome assembly of pickling cucumber and its mutation library illuminate cucumber functional genomics and genetic improvement.","authors":"Yao Tian, Kui Li, Tonghui Li, Wudi Gai, Jie Zhou, Xing Wang Deng, Yan Xue, Yun Deng, Hang He, Xingping Zhang","doi":"10.1016/j.molp.2025.03.001","DOIUrl":"10.1016/j.molp.2025.03.001","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"551-554"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567751","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}