New Phytologist最新文献

{"title":"PGCopilot : an AI ‐assisted research agent for plant functional genomics","authors":"Chenyu He, Lin Liu, Zhenglin Du, Yu Xiu, Jianbo Xie","doi":"10.1111/nph.71738","DOIUrl":"https://doi.org/10.1111/nph.71738","url":null,"abstract":"Summary <jats:list list-type=\"bullet\"> <jats:list-item> The exponential expansion of multi‐omic data presents a major bottleneck for researchers seeking to derive biological insights from heterogeneous genomic resources. Although large language models (LLMs) enable natural language interaction with scientific knowledge, general‐purpose LLMs are not designed to reason over plant‐specific biological issues and frequently produce hallucinated or oversimplified outputs. </jats:list-item> <jats:list-item> We developed PGCopilot, an AI‐assisted research agent tailored for plant functional genomics. It integrated task planning, identifier disambiguation, and tool orchestration to actively retrieve and synthesize evidence across heterogeneous biological databases using the Model Context Protocol. Built on a knowledge base of 1.83 million records, together with online access to PubMed titles and available abstracts covering over 33 million indexed articles and STRING protein–protein interaction data, it could plan retrieval strategies and integrate evidence into grounded responses, reducing unsupported outputs and addressing data fragmentation and identifier discrepancies. </jats:list-item> <jats:list-item> In expert‐guided benchmarking, PGCopilot achieved higher performance than the evaluated baseline LLMs, demonstrating advantages in task relevance, evidence integration, hallucination control, and research utility, and providing more verifiable citations and explicit reporting of cross‐database inconsistencies. As an autonomous agent supporting multiturn tool interaction, it streamlined cross‐database evidence integration from labor‐intensive search‐and‐retrieval to automated analysis‐and‐synthesis. </jats:list-item> <jats:list-item> This approach streamlines cross‐database navigation and evidence integration, allowing researchers to focus more on hypothesis formulation, experimental design, and critical interpretation of comprehensive evidence. </jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"6 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149367685","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":"Chlorophagy targets chloroplasts irreversibly damaged by photoinhibition","authors":"Sakuya Nakamura, Daisuke Takagi, Shuhei Kusano, Kazuya Kodama, Mayumi Wakazaki, Mayuko Sato, Kiminori Toyooka, Shigeichi Kumazaki, Toshiharu Shikanai, Hiroyuki Ishida, Shinya Hagihara, Masanori Izumi","doi":"10.1111/nph.71688","DOIUrl":"https://doi.org/10.1111/nph.71688","url":null,"abstract":"Summary <jats:list list-type=\"bullet\"> <jats:list-item> Chlorophagy removes photodamaged chloroplasts in plants, while individual chloroplasts are also protected by mechanisms that limit damage to the photosynthetic apparatus caused by excess light energy, known as photoinhibition. How chlorophagy is functionally coupled with chloroplast‐level protective mechanisms during acclimation to photoinhibition remains unclear. </jats:list-item> <jats:list-item> We investigated acclimatory responses to photoinhibition at the intracellular level in <jats:italic>Arabidopsis thaliana</jats:italic> through an integrative analysis combining Chl fluorescence measurements, microscopy imaging, and genetic analyses using mutants defective in nonphotochemical quenching (NPQ) or the chloroplast avoidance response. The functionality of individual chloroplasts was further assessed by Chl fluorescence lifetime imaging and probe‐based visualization of singlet oxygen and starch. </jats:list-item> <jats:list-item> Severe photoinhibition of photosystem II precedes the appearance of abnormally swollen chloroplasts, which are subsequently recognized by the autophagy machinery for degradation. The swollen chloroplasts represent irreversibly damaged chloroplasts that accumulate reactive oxygen species and lose photosynthetic function. The formation of these nonfunctional chloroplasts was enhanced in mutants defective in NPQ or the chloroplast avoidance response, and hyperaccumulation of nonfunctional chloroplasts led to necrotic cell death. </jats:list-item> <jats:list-item> Together, our findings illustrate how multilayered responses coordinate acclimation to photoinhibition: Chloroplast protective mechanisms minimize the formation of nonfunctional chloroplasts while chlorophagy removes them when they arise. </jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"15 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149367686","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":"C2H2 zinc‐finger transcription factor FveJAG cooperates with SIMPLE LEAF1 to regulate compound leaf morphogenesis in strawberry","authors":"Zhenying Zhu, Mengting Pi, Zeying Huang, Jianglan Zhu, Wanglong Zhao, Shaoqiang Hu, Ruhan Zhong, Chunying Kang","doi":"10.1111/nph.71733","DOIUrl":"https://doi.org/10.1111/nph.71733","url":null,"abstract":"Summary <jats:list list-type=\"bullet\"> <jats:list-item> Leaves play a vital role in photosynthesis, respiration, and transpiration, significantly impacting a plant's adaptability and crop yield. Strawberry plants develop trifoliate compound leaves, the molecular regulatory pathways of which are not well‐understood. </jats:list-item> <jats:list-item> Here, we identified a woodland strawberry ( <jats:italic>Fragaria vesca</jats:italic> ) mutant, designated <jats:italic>simple leaf 2</jats:italic> ( <jats:italic>sl2</jats:italic> ), which exhibits the complete suppression of the two lateral leaflets. The causal gene encodes a C2H2 zinc‐finger transcription factor that is homologous to JAGGED and is named <jats:italic>FveJAG</jats:italic> . A point mutation located within the intron triggers alternative splicing and generates a premature stop codon. </jats:list-item> <jats:list-item> The prior key transcriptional regulator of leaflet initiation, SIMPLE LEAF1 (SL1), directly targets the promoter of <jats:italic>FveJAG</jats:italic> to activate its transcription. The synergistic interaction between <jats:italic>sl1</jats:italic> and <jats:italic>sl2</jats:italic> indicates that <jats:italic>SL1</jats:italic> and <jats:italic>FveJAG</jats:italic> function within the same regulatory pathway. Genetic and expression analyses suggest that <jats:italic>FveJAG</jats:italic> also acts downstream of <jats:italic>FveMYB117a</jats:italic> during leaflet initiation. </jats:list-item> <jats:list-item> Taken together, our results uncover a direct SL1 target gene and elucidate a complex regulatory network involving <jats:italic>SL1</jats:italic> , <jats:italic>FveJAG</jats:italic> , and <jats:italic>FveMYB117a</jats:italic> in strawberry compound leaf morphogenesis, offering further mechanistic insights into the genetic regulation of leaf complexity. </jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"24 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149367688","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":"Rethinking the soil core microbiome","authors":"Jaejin Lee,&nbsp;Bolívar Aponte Rolón,&nbsp;Phillip de Lorimier,&nbsp;Jean-Michel Ané,&nbsp;Gian Maria Niccolò Benucci,&nbsp;Alyssa A. Carrell,&nbsp;Yen Ning Chai,&nbsp;Janith Chandrasoma,&nbsp;Nicole Geerdes,&nbsp;Valentina Infante,&nbsp;Brandon Kristy,&nbsp;Stanton Martin,&nbsp;Imani Pascoe,&nbsp;Rounak Patra,&nbsp;Lorien Radmer,&nbsp;Tomás Allen Rush,&nbsp;Ndenum Suzzy Shita,&nbsp;Andie Suratt,&nbsp;Patrick F. Suthers,&nbsp;Melissa A. Cregger,&nbsp;Adina Howe,&nbsp;Sarah Lebeis,&nbsp;Henrik Vibe Scheller","doi":"10.1111/nph.71509","DOIUrl":"10.1111/nph.71509","url":null,"abstract":"<p>The concept of a core microbiome emerged from host-associated research to describe microbial members or functions conserved across clearly defined spatial, temporal, and biological boundaries. In soil- and plant-associated microbiome research, however, the term has increasingly shifted toward analytically defined subsets selected using study-specific thresholds or criteria. Synthesizing recent literature and cross-site analyses of bioenergy crop field soils, we show that the original biological meaning of the core microbiome has been blurred by dataset-specific analytical criteria. Taxa designated as ‘core’ were highly sensitive to methodological choices and often reflected explanatory value rather than conserved biological membership. Moreover, many studies that identify taxonomic ‘core’ members interpret their significance in functional terms, suggesting that functional conservation may be the biological interest. Taxonomic conservation may not be the most biologically meaningful target in highly heterogeneous soil and rhizosphere systems, where functional conservation may persist despite taxonomic turnover. Accordingly, ‘core microbiome’ should be reserved for microbial components explicitly demonstrated to be conserved across defined spatial, temporal, and environmental dimensions and linked to conserved ecological functions, while taxa selected for explanatory value are better described as ‘explanatory subsets of taxa’. Greater terminological precision will improve cross-study comparability and strengthen ecological inference in plant–soil microbiome research.</p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"252 5","pages":"1750-1758"},"PeriodicalIF":8.7,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.71509","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148754677","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":"Unraveling the genome of NC292: a maize inbred line conferring resistance to multiple foliar diseases","authors":"Yapeng Wang,&nbsp;Yaqi Zhao,&nbsp;Ruiyu Zhang,&nbsp;Yanzhuo Dong,&nbsp;Ting Li,&nbsp;Qiang Zhang,&nbsp;Qin Yang","doi":"10.1111/nph.71569","DOIUrl":"10.1111/nph.71569","url":null,"abstract":"<p>A high-quality genome assembly of the multiple disease-resistant maize inbred NC292.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"252 5","pages":"1711-1718"},"PeriodicalIF":8.7,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.71569","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148946743","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":"Genetic and molecular networks mediating potato tuber development","authors":"Divyanshu Sinha,&nbsp;दिव्यांशु सिन्हा,&nbsp;Roshan Singh Patel,&nbsp;रोशन सिंह पटेल,&nbsp;Varsha Gupta,&nbsp;वर्षा गुप्ता,&nbsp;Jay Prakash Maurya,&nbsp;जय प्रकाश मौर्य","doi":"10.1111/nph.71599","DOIUrl":"10.1111/nph.71599","url":null,"abstract":"<p>Potato, the world's third most important food crop, is cultivated world-wide for its tubers that store high-energy photoassimilates, which are predominantly induced under short photoperiods with cooler night temperatures. The stored photoassimilates ensure plant survival by vegetative propagation and to support subsequent shoot growth. The leaf-generated main tuberigen signal, StSP6A, upon its transport to stolon, forms tuber-inducing Tuberigen Activation Complex (TAC). Misregulation or redirection of StSP6A transport toward lateral buds contributes to aerial tuber formation, thereby adversely affecting underground tuber yield. The activity of TAC is inhibited by antituberigens, such as StAST1 and StTFL1, which compete with StSP6A and constitute anti-TAC. In this review, we provide a comprehensive overview of the genetic and molecular mechanisms underlying underground and aerial tuber formation, their regulation by antituberigen factors, key genes controlling stolon-to-tuber transitions, the role of StSWEET-StSUT transporters in establishing the source–sink relationship essential for tuber development, and the evolution and global dissemination of modern potato cultivars. Collectively, insights from potato provide a valuable framework for understanding the conserved and divergent mechanisms governing storage organ development in other economically important crops.</p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"252 5","pages":"1768-1786"},"PeriodicalIF":8.7,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.71599","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149077640","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":"Ten rules for robust taxonomy in ecological datasets","authors":"Renato A. Ferreira de Lima,&nbsp;Guilherme S. Grittz,&nbsp;Moabe F. Fernandes,&nbsp;Hans ter Steege,&nbsp;Kyle G. Dexter,&nbsp;Oliver Phillips,&nbsp;Marli P. Morim,&nbsp;Jérôme Chave,&nbsp;Géraldine Derroire,&nbsp;Filipe M. França,&nbsp;Tamara Heartsill-Scalley,&nbsp;Ricardo A. Segovia,&nbsp;Caroline E. R. Lehmann,&nbsp;Luis Cayuela,&nbsp;Karina Banda,&nbsp;Cecilia Blundo,&nbsp;Jesús Aguirre-Gutiérrez,&nbsp;André L. de Gasper,&nbsp;R. Toby Pennington","doi":"10.1111/nph.71658","DOIUrl":"10.1111/nph.71658","url":null,"abstract":"<p>Accurate taxonomy, including species identification and naming, underpins ecological inference, yet taxonomic information in ecological datasets is often inconsistently recorded or weakly standardized. With the increasing integration of ecological datasets across taxa and regions, datasets with poor taxonomic practices can hinder data exchange and propagate errors. We propose 10 rules to improve the storage and management of taxonomic information in ecological datasets. These rules draw on our experiences in plant ecology and taxonomy, but the conclusions may be generalized to other organisms and disciplines. They emphasize aspects from species identification to the permanent storage of verifiable records (e.g. voucher specimens) and include taxonomic standardization, nomenclature, validation, and updating. We also address the treatment of morphotypes and incomplete identifications, the use of automated name-matching tools, and (meta)data standards. Closer collaboration between ecologists and taxonomists is key to ensuring more robust datasets. The application of these rules consumes more time and resources, but they enhance data quality and interoperability, saving time during data integration and improving the reliability and scalability of ecological research.</p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"252 5","pages":"1741-1749"},"PeriodicalIF":8.7,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.71658","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149171787","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":"A novel method based on high-resolution imaging spectroscopy to predict fine-root traits and the economics space of fresh tree roots","authors":"Naoki Makita,&nbsp;Natsuko Tanikawa,&nbsp;Tatsuro Nakaji","doi":"10.1111/nph.71366","DOIUrl":"10.1111/nph.71366","url":null,"abstract":"<p>\u0000 </p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"252 5","pages":"1816-1831"},"PeriodicalIF":8.7,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.71366","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148298998","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":"Seeing the unseen: hyperspectral imaging opens a new window into the root economics space","authors":"Boris Rewald","doi":"10.1111/nph.71527","DOIUrl":"10.1111/nph.71527","url":null,"abstract":"&lt;p&gt;Fine roots – the ‘hidden half’ of plants – regulate water, nutrient uptake and transport, underpin plant resource-use strategies, and influence community and ecosystem processes (Freschet &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2021&lt;/span&gt;). Yet despite their ecological importance, roots remain considerably less studied than leaves and shoots, owing in part to methodological challenges. While advances in imaging technologies have transformed aboveground plant sciences over the past decade, from crop breeding and stress detection to forest monitoring (Fahlgren &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2015&lt;/span&gt;; Bian &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2022&lt;/span&gt;), root research still relies largely on labour-intensive and time-consuming manual measurements. In an article published in this issue of &lt;i&gt;New Phytologist&lt;/i&gt;, Makita &lt;i&gt;et al&lt;/i&gt;. (&lt;span&gt;2026&lt;/span&gt;; pp. 1816–1831) demonstrate how hyperspectral imaging (HSI; Box 1) can be applied to living fine roots to characterize chemical, anatomical, and morphological traits, opening new opportunities for high-throughput and spatially resolved root research.&lt;/p&gt;&lt;p&gt;The study arrives at a pivotal moment in root ecology. Over the past decade, trait-based frameworks have evolved from the one-dimensional root economics spectrum towards the multidimensional root economics space (RES), in which root strategies are structured along at least two independent axes (Bergmann &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;). One axis reflects a conservation trade-off (fast vs slow resource use, e.g. high nitrogen (N) vs high tissue density (RTD)), while the collaboration axis reflects reliance on mycorrhizal partners (thick, cortex-rich roots vs thin ‘do-it-yourself’ roots with high specific root length (SRL)). At the same time, root-order-based analyses have increasingly highlighted the substantial functional differentiation within root systems themselves. Distal, lower-order roots such as tips primarily acquire resources and host mycorrhizal symbionts, whereas higher-order roots increasingly contribute to transport, storage, and structural support. This differentiation can be viewed as an absorptive-to-transport continuum, in which root segments progressively shift from acquisition and symbiotic interaction towards transport and other functions with increasing root order. Different segments of a root system may therefore occupy distinct positions within the RES (McCormack &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2015&lt;/span&gt;; Tawa &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2026&lt;/span&gt;). Together, these conceptual advances highlight the need for approaches capable of characterizing functional variation across multiple biological scales.&lt;/p&gt;&lt;p&gt;Characterizing root strategies across species, environments and branching orders requires the measurement of multiple traits, a process that remains labour-intensive and difficult to scale even when restricted to core traits such as SRL, root diameter (D), root tissue density, and N concentration (Matthus &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2025&lt;/span&gt;). Unlike leaf trait research, which con","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"252 5","pages":"1695-1699"},"PeriodicalIF":8.7,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.71527","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148768124","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":"Disrupting two Arabidopsis thaliana xylosyltransferase genes results in plants deficient in thermomorphogenesis","authors":"Yue Liu,&nbsp;Jie Wang,&nbsp;MeLongying Wangzha,&nbsp;Baoguo Wu,&nbsp;Qianwen Zhang,&nbsp;Chunli Zhang,&nbsp;Yujie Wu,&nbsp;Yizhuo Mu,&nbsp;Keyan Zhang,&nbsp;Junhong Zhang,&nbsp;Zhaojun Liu,&nbsp;Sridevi Sureshkumar,&nbsp;Yubao Lv,&nbsp;Yumeng Yang,&nbsp;Li Lin,&nbsp;Sureshkumar Balasubramanian,&nbsp;Chaowen Xiao,&nbsp;Baocai Zhang,&nbsp;Ruohe Yin","doi":"10.1111/nph.71616","DOIUrl":"10.1111/nph.71616","url":null,"abstract":"<div>\u0000 \u0000 <p>\u0000 </p><ul>\u0000 \u0000 <li>Several cell-wall-modifying enzymes have been implicated in hypocotyl elongation; however, whether cell wall biosynthesis enzymes contribute to this process, particularly under warm temperature, remains largely unknown.</li>\u0000 \u0000 <li>In <i>Arabidopsis</i>, xyloglucan is a major component of the primary cell wall. Xyloglucan xylosyltransferase 1 (XXT1) and XXT2 are the major enzymes required for xyloglucan biosynthesis. Here, we investigated the roles of XXT1/2 in hypocotyl elongation with a focus under warm temperature using genetic, molecular, and transcriptomic approaches.</li>\u0000 \u0000 <li>We show that XXT1/2 are required for warm-temperature-promoted hypocotyl elongation and that the elongation phenotypes of PHYTOCHROME-INTERACTING FACTOR 4 (<i>PIF4</i>) overexpression, Phytochrome B (<i>phyB</i>), and ELONGATED HYPOCOTYL 5 (<i>hy5</i>) depend partly on XXT1/2. PIF4 directly binds to and activates the promoters of <i>XXT1</i> and <i>XXT2</i>, whereas HY5 binds to the same promoter regions and represses their expression. Importantly, the warm-temperature-induced increase in xyloglucan content is antagonistically regulated by PIF4 and HY5. Transcriptomic analyses identified warm-responsive genes whose induction depends on XXT1/2, including <i>expansins</i> (<i>EXPs</i>) and <i>xyloglucan endotransglucosylase/hydrolases</i> (<i>XTHs</i>). Mutants of some <i>EXPs</i> and <i>XTHs</i> showed compromised warm-induced hypocotyl elongation.</li>\u0000 \u0000 <li>Together, our findings identify XXT1/2 as new components of the phyB–PIF4–HY5 growth network, linking environmental signaling to the cell wall biosynthetic machinery required for hypocotyl elongation.</li>\u0000 </ul>\u0000 </div>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"252 5","pages":"1875-1891"},"PeriodicalIF":8.7,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149086835","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}