Nature Plants最新文献_第4页

Enhancing local meiotic crossovers in Arabidopsis and maize through juxtaposition of heterozygous and homozygous regions 通过杂合区和纯合区并置增强拟南芥和玉米的局部减数分裂杂交

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-09-02 DOI: 10.1038/s41477-025-02085-8

Mikhail E. Mikhailov, Franz Boideau, Maja Szymanska-Lejman, Vasile Botnari, Piotr A. Ziolkowski

{"title":"Enhancing local meiotic crossovers in Arabidopsis and maize through juxtaposition of heterozygous and homozygous regions","authors":"Mikhail E. Mikhailov, Franz Boideau, Maja Szymanska-Lejman, Vasile Botnari, Piotr A. Ziolkowski","doi":"10.1038/s41477-025-02085-8","DOIUrl":"10.1038/s41477-025-02085-8","url":null,"abstract":"Meiotic crossovers, which exchange DNA between homologous chromosomes, are vital for accurate segregation and generate genetic diversity. In plant breeding, they help create new haplotypes by combining beneficial alleles. In Arabidopsis, heterozygous regions in an otherwise homozygous background attract more crossovers than in full F1 hybrids—a phenomenon so far observed only in this self-fertilizing species. Here we report a similar effect in outcrossing maize: local crossover rates increase up to threefold in regions where polymorphism is spatially confined compared to full hybrids. This stimulation occurs in both male and female meiosis and is strongest when heterozygous regions fully span the measured area, likely due to crossover redistribution. As Arabidopsis and maize represent distantly related plant lineages (eudicots and monocots), this shared phenomenon suggests a conserved mechanism. Importantly, it provides a tool for breeding, offering a way to boost recombination and accelerate the introgression of desired traits using interhomologue polymorphism. This study discovered that locally confined DNA differences boost crossover rates in both Arabidopsis and maize, revealing a conserved mechanism that can accelerate plant breeding and trait introgression.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 9","pages":"1769-1784"},"PeriodicalIF":13.6,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41477-025-02085-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144928359","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}

引用次数: 0

Diversity favoured: heterozygosity attracts crossovers 多样性有利：杂合性吸引杂交

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-09-02 DOI: 10.1038/s41477-025-02066-x

Maria Cuacos, Stefan Heckmann

引用次数: 0

Genome analyses and breeding of polyploid crops 多倍体作物基因组分析与选育

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-08-28 DOI: 10.1038/s41477-025-02088-5

Lin Cheng, Zhigui Bao, Qianqian Kong, Ludivine Lassois, Nils Stein, Sanwen Huang, Qian Zhou

{"title":"Genome analyses and breeding of polyploid crops","authors":"Lin Cheng, Zhigui Bao, Qianqian Kong, Ludivine Lassois, Nils Stein, Sanwen Huang, Qian Zhou","doi":"10.1038/s41477-025-02088-5","DOIUrl":"10.1038/s41477-025-02088-5","url":null,"abstract":"Polyploidization is a common and important evolutionary process in the plant kingdom. Compared with diploid plant species, the intricate genome architecture of polyploid plant species presents substantial challenges in applying multi-omics approaches for crop breeding improvement. In this Review, we summarize the current techniques for analysing polyploid genomes, including constructing reference genomes and pan-genomes, and detecting variants. We also assess findings related to polyploid genome architecture, population genetics and breeding programmes, highlighting advanced techniques in the breeding of polyploid crops. Finally, we explore the challenges and demands posed by polyploid genome complexity during analysis with available biotechnological tools. This Review emphasizes the importance of a comprehensive understanding of polyploid genomic features for the further genetic improvement of polyploid crops. This Review highlights recent advances in polyploid genome analysis and breeding, emphasizing methodological innovations and the importance of deciphering genome complexity to accelerate genetic improvement in polyploid crops.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 9","pages":"1714-1728"},"PeriodicalIF":13.6,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144910706","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}

引用次数: 0

Reticulata weaves the metabolic net 网状植物编织代谢之网

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-08-25 DOI: 10.1038/s41477-025-02100-y

Katrin Philippar

引用次数: 0

Apoplastic metabolomics reveals sugars as mesophyll messengers regulating guard cell ion transport under red light 外质体代谢组学揭示糖作为叶肉信使在红光下调节保护细胞离子运输

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-08-25 DOI: 10.1038/s41477-025-02078-7

Yotam Zait, Mengmeng Zhu, Eigo Ando, Yunqing Zhou, Adi Yaaran, Sunheng Yon, Mami Okamoto, Yuki Hayashi, Masami Y. Hirai, Timothy Jegla, Toshinori Kinoshita, Sixue Chen, Sarah M. Assmann

{"title":"Apoplastic metabolomics reveals sugars as mesophyll messengers regulating guard cell ion transport under red light","authors":"Yotam Zait, Mengmeng Zhu, Eigo Ando, Yunqing Zhou, Adi Yaaran, Sunheng Yon, Mami Okamoto, Yuki Hayashi, Masami Y. Hirai, Timothy Jegla, Toshinori Kinoshita, Sixue Chen, Sarah M. Assmann","doi":"10.1038/s41477-025-02078-7","DOIUrl":"10.1038/s41477-025-02078-7","url":null,"abstract":"Guard cell pairs in the leaf epidermis enclose stomata, microscopic pores mediating CO2 uptake and water loss. Historical data suggest that signals from interior mesophyll tissue may modulate guard-cell regulation of stomatal apertures, but the molecular identity of any metabolite-based signals has remained elusive. We discovered that extracellular (apoplastic) fluid from Arabidopsis thaliana and Vicia faba enhances red-light-induced stomatal opening. Our extensive metabolomics analyses identified 448 apoplastic metabolites; among these, both sugars (photosynthetic products) and maleic acid increased under red light and caused enhanced stomatal opening. Immunohistochemical assays demonstrated sucrose upregulation of H+-ATPase phosphorylation, indicating increased ATPase activity. Patch clamp assays revealed that sucrose inhibits slow anion currents, thus opposing anion efflux. These impacts occurred at sucrose concentrations matching those present endogenously under red light. These regulatory influences promote guard-cell solute import and retention, which drive stomatal opening. Our research thus addresses the decades-long question concerning the existence, identity and mechanistic impact of mesophyll messengers that coordinate photosynthesis with stomatal response. Guard cells define microscopic stomatal pores for CO2 uptake and water loss. Characterization of the extracellular metabolome revealed sugars as ‘mesophyll messengers’ from the leaf interior that enhance stomatal opening via regulation of the guard-cell H+-ATPase and anion channels.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 9","pages":"1847-1862"},"PeriodicalIF":13.6,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41477-025-02078-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900208","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}

引用次数: 0

RETICULATA1 is a plastid-localized basic amino acid transporter RETICULATA1是一种定位于质体的碱性氨基酸转运蛋白

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-08-22 DOI: 10.1038/s41477-025-02080-z

Franziska Kuhnert, Philipp Westhoff, Vanessa Valencia, Stephan Krüger, Karolina Vogel, Peter K. Lundquist, Christian Rosar, Tatjana Goss, Andreas P. M. Weber

{"title":"RETICULATA1 is a plastid-localized basic amino acid transporter","authors":"Franziska Kuhnert, Philipp Westhoff, Vanessa Valencia, Stephan Krüger, Karolina Vogel, Peter K. Lundquist, Christian Rosar, Tatjana Goss, Andreas P. M. Weber","doi":"10.1038/s41477-025-02080-z","DOIUrl":"10.1038/s41477-025-02080-z","url":null,"abstract":"Plants have a crucial role in providing essential amino acids for human nutrition. Nine of the 20 proteinogenic amino acids are exclusively synthesized de novo in plastids, yet transporters mediating their exchange across the plastid inner envelope remain unknown. Here we identify RETICULATA1 (RE1) as a plastid-localized transporter for basic amino acids—including Arg, Citr, Orn and Lys—in Arabidopsis thaliana. Loss-of-function mutants display a reticulate leaf phenotype, contain lower amounts of basic amino acids and are impaired in amino acid homeostasis. RE1 belongs to a novel class of membrane transport proteins that contain a domain of unknown function 3411 and are found exclusively in plastid-containing organisms. Our results indicate functional overlap with its closest homologue RER1, as the double mutant is lethal. Isotope labelling reveals that loss of RE1 reduces basic amino acid biosynthesis and affects the equilibration of plastidic and cytosolic amino acid pools. These findings uncover a critical role for plastidial amino acid transporters in coordinating primary metabolism, development and nutrient allocation in plants. RETICULATA1 is a plastid membrane transporter in Arabidopsis that enables basic amino acid exchange across the plastid inner envelope. Loss-of-function mutants reveal its essential role in amino acid homeostasis, plant development and seed production.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 9","pages":"1890-1902"},"PeriodicalIF":13.6,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41477-025-02080-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900242","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}

引用次数: 0

A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle 拟南芥生命周期的单细胞空间转录组图谱。

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-08-19 DOI: 10.1038/s41477-025-02072-z

Travis A. Lee, Natanella Illouz-Eliaz, Tatsuya Nobori, Jiaying Xu, Bruce Jow, Joseph R. Nery, Joseph R. Ecker

{"title":"A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle","authors":"Travis A. Lee, Natanella Illouz-Eliaz, Tatsuya Nobori, Jiaying Xu, Bruce Jow, Joseph R. Nery, Joseph R. Ecker","doi":"10.1038/s41477-025-02072-z","DOIUrl":"10.1038/s41477-025-02072-z","url":null,"abstract":"Arabidopsis has been pivotal in uncovering fundamental principles of plant biology, yet a comprehensive, high-resolution understanding of its cellular identities throughout the entire life cycle remains incomplete. Here we present a single-nucleus and spatial transcriptomic atlas spanning ten developmental stages, encompassing over 400,000 nuclei from all organ systems and tissues—from seeds to developing siliques. Leveraging paired single-nucleus and spatial transcriptomic datasets, we annotate 75% of identified cell clusters, revealing striking molecular diversity in cell types and states across development. Our integrated approach identified conserved transcriptional signatures among recurrent cell types, organ-specific heterogeneity and previously uncharacterized cell-type-specific markers validated spatially. Moreover, we uncover dynamic transcriptional programs governing secondary metabolite production and differential growth patterns, exemplified by detailed spatial profiling of the compact yet complex apical hook structure; this profiling revealed transient cellular states linked to developmental progression and hormonal regulation, highlighting the hidden complexity underlying plant morphogenesis. Functional validation of genes uniquely expressed within specific cell contexts confirmed their essential developmental roles, underscoring the predictive power of our atlas. Collectively, this comprehensive resource provides an invaluable foundation for exploring cellular differentiation, environmental responses and genetic perturbations at high resolution, advancing our understanding of plant biology. This study presents an extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents ten distinct developmental time points inclusive of six diverse organs.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 9","pages":"1960-1975"},"PeriodicalIF":13.6,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12416547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883226","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}

引用次数: 0

Still life 仍然生活。

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-08-19 DOI: 10.1038/s41477-025-02101-x

引用次数: 0

Arbuscular mycorrhizal association regulates global root–seed coordination 丛枝菌根联合调节全球根-种子协调。

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-08-19 DOI: 10.1038/s41477-025-02089-4

Qingpei Yang, Binglin Guo, Mingzhen Lu, Yanjie Liu, Paul Kardol, Peter B. Reich, Richard D. Bardgett, Johannes H. C. Cornelissen, Nathan J. B. Kraft, Sandra Díaz, Ian J. Wright, Nianpeng He, J. Aaron Hogan, Yuxin Pei, Qinwen Han, Zhenjiang Li, Zheng Wang, Wanqin Yang, Junxiang Ding, Zhongling Yang, Huifang Wu, Carlos P. Carmona, Oscar J. Valverde-Barrantes, Dezhu Li, Jie Cai, Hui Zeng, Yue Zhang, Weizheng Ren, Yong Zhao, Xitian Yang, Guoqiang Fan, Junjian Wang, Guoyong Li, Deliang Kong

{"title":"Arbuscular mycorrhizal association regulates global root–seed coordination","authors":"Qingpei Yang, Binglin Guo, Mingzhen Lu, Yanjie Liu, Paul Kardol, Peter B. Reich, Richard D. Bardgett, Johannes H. C. Cornelissen, Nathan J. B. Kraft, Sandra Díaz, Ian J. Wright, Nianpeng He, J. Aaron Hogan, Yuxin Pei, Qinwen Han, Zhenjiang Li, Zheng Wang, Wanqin Yang, Junxiang Ding, Zhongling Yang, Huifang Wu, Carlos P. Carmona, Oscar J. Valverde-Barrantes, Dezhu Li, Jie Cai, Hui Zeng, Yue Zhang, Weizheng Ren, Yong Zhao, Xitian Yang, Guoqiang Fan, Junjian Wang, Guoyong Li, Deliang Kong","doi":"10.1038/s41477-025-02089-4","DOIUrl":"10.1038/s41477-025-02089-4","url":null,"abstract":"Terrestrial plants exhibit immense variation in their form and function among species. Coordination between resource acquisition by roots and reproduction through seeds could promote the fitness of plant populations. How root and seed traits covary has remained unclear until our analysis of the largest-ever compiled joint global dataset of root traits and seed mass. Here we demonstrate that seed mass and seed phosphorus mass scale positively with root diameter in arbuscular mycorrhizal (AM) plants, depending on variation in root cortical thickness instead of root vessel size. These findings suggest a dual role of AM association in phosphorus uptake and pathogen resistance which drives the global root–seed coordination, instead of initially expected resource transport via root vessels as the main driver. In contrast, we found no relationship between root traits and seed mass in ectomycorrhizal plants. Overall, our study reveals coordination between roots and seeds in AM plants, which is probably regulated by root–mycorrhizal symbiosis, and may be crucial in shaping global plant diversity and species distributions. In this study, Yang et al. compile a global dataset to uncover the degree to which plants coordinate root and seed traits. They report a global positive correlation between root diameter and seed size, driven by dual roles of arbuscular mycorrhiza in phosphorus uptake and pathogen defence.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 9","pages":"1759-1768"},"PeriodicalIF":13.6,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883227","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}

引用次数: 0

Large-scale pairing identifies a soybean phytocytokine-receptor module conferring disease resistance 大规模配对鉴定大豆植物细胞因子受体模块赋予抗病性。

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-08-19 DOI: 10.1038/s41477-025-02086-7

Liping Yu, Yiwen Gao, Qiujiao Yang, Jing Liu, Tengfei Liu, Weiping Mo, Hangqin Liu, Zhixi Tian, Lei Li

{"title":"Large-scale pairing identifies a soybean phytocytokine-receptor module conferring disease resistance","authors":"Liping Yu, Yiwen Gao, Qiujiao Yang, Jing Liu, Tengfei Liu, Weiping Mo, Hangqin Liu, Zhixi Tian, Lei Li","doi":"10.1038/s41477-025-02086-7","DOIUrl":"10.1038/s41477-025-02086-7","url":null,"abstract":"Plant peptide hormones play essential roles in various physiological processes, including activating defence responses to biotic stress. Membrane-localized pattern recognition receptors (PRRs) typically detect peptide hormones to initiate signalling pathways. Through comprehensive peptide–receptor matching, we identified 63 peptide–receptor pairs in soybeans. Among these, the immunomodulatory phytocytokines GmPEP914 and GmPEP890 trigger robust immune responses that suppress a broad spectrum of pathogen infections, mediated by their identified receptors GmPEP914 and GmPEP890 RECEPTOR1 (GmP98R1) and GmP98R2. Biochemical assays combined with AI-based structural modelling demonstrated that both peptides directly bind GmP98Rs with nanomolar affinity, driven primarily by interactions between the receptors and the C-terminal residue of the peptides. The PEP914-P98R module is conserved across Fabales and Cucurbitales, underscoring its evolutionary importance. Collectively, our study establishes a scalable pipeline for systematic peptide–receptor discovery and elucidates the pivotal role of the PEP914-P98R module in soybean disease resistance. The authors establish a scalable pipeline for systematic peptide–receptor discovery. Applying this approach in soybean, researchers identified a PEP914/890-P98R module that plays a pivotal role in conferring disease resistance.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 9","pages":"1739-1747"},"PeriodicalIF":13.6,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883228","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}

引用次数: 0