Journal of Integrative Plant Biology最新文献

{"title":"MaizeGP: An open graph-based maize pangenome platform for integrative multi-scale exploration of structural variation.","authors":"Nianhua Jia, Xianyan Kuang, Yueli Wang, Wei Song, Yan Du, Yuhang Guo, Yuanhao Guo, Chungen Yi, Zeyang Ma, Shaojiang Chen, Junjie Fu, Wenxin Liu","doi":"10.1111/jipb.70439","DOIUrl":"https://doi.org/10.1111/jipb.70439","url":null,"abstract":"<p><p>MaizeGP, an interactive graph-based pangenome platform, integrates structural variation from 48 diverse maize genomes with functional annotations and visualization tools. MaizeGP enables multi-scale exploration of genomic variation across individual loci, gene families, and trait associations. This accessible resource supports future investigation of maize genome diversity and its biological implications.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149340016","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":"PbAGO4-dependent hypermethylation of the PbNAC71 promoter regulates anthocyanin synthesis in pear.","authors":"Yansong Zhu, Xinyu Li, Chen Yang, Wenjun Liu, Qi Zou, Lei Yu, Nan Wang, Xuesen Chen, Zongying Zhang","doi":"10.1111/jipb.70430","DOIUrl":"https://doi.org/10.1111/jipb.70430","url":null,"abstract":"<p><p>Bud mutations in perennial fruit trees often involve epigenetic variation, but the underlying mechanisms remain unclear. We identified a spontaneous green bud mutant of the red-skinned pear \"Aohong No. 1\" that fails to accumulate anthocyanins under light. Integrated methylome and transcriptome analyses revealed that in the mutant, hypermethylation of a 148-bp light-responsive enhancer in the PbNAC71 promoter, maintained by PbAGO4, represses PbNAC71 expression. In the wild type, this enhancer remains hypomethylated, whereas in the mutant, it is hypermethylated; this differential methylation is detectable at the young fruit stage and stably maintained at the post-harvest stages examined, representing a pre-set epigenetic state. Silencing of PbNAC71 downregulated PbMYB10 and PbCHI1, and attenuated PbMYB10-mediated activation of PbCHS1 and PbDFR3, thereby suppressing anthocyanin accumulation. Both PbAGO4 knockout in callus and PbAGO4 silencing in fruit peel reduced enhancer methylation, and increased PbNAC71 expression and anthocyanin accumulation. Together, these results reveal a mechanism by which PbAGO4-dependent methylation of a light-responsive enhancer establishes a stable pre-set state that controls how environmental light signals regulate anthocyanin synthesis.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149340017","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":"SlMED2 regulates locule number through the SlTPL-SlKNU floral meristem module.","authors":"Sufu Gan, Yong Kang, Can Luo, Ying Li, Ying Gao, Jianghua Cai, Leilei Zhou, Mondher Bouzayen, Baowen Huang, Yulin Cheng, Zhengguo Li","doi":"10.1111/jipb.70437","DOIUrl":"https://doi.org/10.1111/jipb.70437","url":null,"abstract":"<p><p>The Mediator complex subunit SlMED2 controls carpel number in tomato through promoter-proximal and long-range genomic interactions with the SlTPL-SlKNU floral meristem module, which represses SlWUS and SlCLV3, resulting in termination of stem cell activity.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149331859","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":"Temporal control of root system architecture under osmotic stress: ABA-SnRK2 signaling and adaptive plasticity.","authors":"Yupeng Zhang, Ruirui Xu, Yue Wang, Chengchao Zheng, Guodong Yang, Shizhong Zhang","doi":"10.1111/jipb.70432","DOIUrl":"https://doi.org/10.1111/jipb.70432","url":null,"abstract":"<p><p>Drought and salt stress impose osmotic and ionic challenges on plant roots, with drought reducing soil water potential and salt imposing additional ionic toxicity beyond osmotic stress, driving the plastic remodeling of root system architecture (RSA). Abscisic acid (ABA) is a central hormone regulating root adaptability, and its signaling coordinates adaptive responses of roots across multiple time scales through the SNF1-related protein kinase 2 (SnRK2) family kinases. This review systematically summarizes the temporal coding mechanisms of the ABA-SnRK2 signaling network underlying root adaptation to osmotic stress. We propose that plant roots achieve a dynamic balance between short-term defense and long-term adaptation through the coordinated activities of different SnRK2 subgroups along the temporal axis. This proposed \"balance point\" of temporal coding is shaped by multiple temporal readouts. We also review how crosstalk between ABA and other hormones such as auxin fine-tunes root plasticity. Based on this framework, we propose a \"balance point engineering\" strategy that provides a theoretical blueprint for designing stress-tolerant crops with tunable durations of stress responses.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149331860","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":"Local auxin biosynthesis links cell wall remodeling to lateral root emergence.","authors":"Lei Li, Xinfang Zhu, Zhaojun Ding, Cuiling Li, Xiangpei Kong","doi":"10.1111/jipb.70442","DOIUrl":"https://doi.org/10.1111/jipb.70442","url":null,"abstract":"<p><p>Auxin promotes lateral root emergence by remodeling surrounding root tissues. Cell wall modifications, including altered lignin deposition, are associated with successful root emergence, revealing a mechanism by which plants establish branched root systems to sustain growth and survival.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149331858","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":"ZmSGT1-mediated competitive protection of ZmBBI1 enhances maize resistance to Rhizoctonia solani.","authors":"Yuanyuan Sun, Le Wang, Xiaofei He, Bingding Zhu, Zhijin Ma, Kun Wan, Ning Li","doi":"10.1111/jipb.70441","DOIUrl":"https://doi.org/10.1111/jipb.70441","url":null,"abstract":"<p><p>Banded leaf and sheath blight (BLSB), incited by the necrotrophic basidiomycete Rhizoctonia solani, is a devastating soil-borne disease that severely constrains global maize (Zea mays) production. Bowman-Birk inhibitors (BBIs) constitute a critical class of protease inhibitors in plant innate immunity; yet, their biological functions and upstream regulatory circuits in maize defense against necrotrophic pathogens remain largely uncharacterized. Here, we show that ZmBBI1, a BBI family member transcriptionally upregulated upon R. solani infection, positively modulates BLSB resistance. Its defense activity is strictly dependent on trypsin-inhibitory function, mediated by the evolutionarily conserved Thr52 and Arg53 residues in its canonical reactive loop. We identify Rs03254, a secreted virulence effector from R. solani, that directly engages ZmBBI1 and biochemically inactivates its protease-inhibitory activity to promote fungal colonization. We further demonstrate that the conserved immune co-chaperone ZmSGT1 physically interacts with ZmBBI1 and is genetically required for its full defense function. Mechanistically, ZmSGT1 competes with Rs03254 for binding to ZmBBI1, displacing the pathogen effector and restoring ZmBBI1's trypsin-inhibitory activity. Our work defines a tripartite molecular arms race module in the maize-R. solani pathosystem and uncovers a noncanonical role for SGT1 as a molecular bodyguard that protects host defense factors from effector-mediated suppression, providing actionable targets for engineering durable BLSB resistance in maize.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149331861","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":"Chemical cues and cognitive models: Integrating metabolomics and AI for plant stress resilience.","authors":"Aiswarya Girija, Veda Krishnan, Julia von Steimker, Alisdair R Fernie","doi":"10.1111/jipb.70434","DOIUrl":"10.1111/jipb.70434","url":null,"abstract":"<p><p>Plants make thousands of different chemicals that reveal how they cope with changing climates. This view explains how evolving artificial intelligence approaches can combine these chemical fingerprints with genetics and environment to build a digital twin of a plant, helping breeders predict performance and develop climate-resilient crops much faster.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149316496","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":"Engineering AP/Exo-Cas12 as an efficient toolbox for rice genome editing via integrated repair and exonuclease modules.","authors":"Nan Chai, Ruixiang Zhang, Guangzhou Li, Liying Su, Jun Wen, Shirui Huo, Xudong Yuan, Ruyue Chang, Xinglei Zheng, Zhiye Zheng, Taoli Liu, Dongchang Zeng, Qiupeng Lin, Yao-Guang Liu, Xianrong Xie, Jiantao Tan, Qinlong Zhu","doi":"10.1111/jipb.70440","DOIUrl":"https://doi.org/10.1111/jipb.70440","url":null,"abstract":"<p><p>A modular apurinic/apyrimidinic (AP)/Exo-Cas12 toolbox integrates cell selection enrichment with AP-repair pathways or exonucleases for plant editing. It achieves efficient multiplex genome editing and easily detectable large DNA deletions in rice, providing a robust platform for multigene knockouts and crop improvement.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149316497","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":"An alfalfa MYB71-centered activation-attenuation module fine-tunes redox homeostasis and drought tolerance in Medicago sativa.","authors":"Bingcheng Han, Xueming Dong, Congcong Shi, Pei Mao, Yige Zhang, Qiang Zhou, Longfa Fang, Wenxian Liu, Chunxiang Fu, Jiangqi Wen, Zhipeng Liu","doi":"10.1111/jipb.70436","DOIUrl":"https://doi.org/10.1111/jipb.70436","url":null,"abstract":"<p><p>Drought severely constrains alfalfa (Medicago sativa L.) productivity, yet dissecting drought-response mechanisms in this important perennial forage crop remains challenging because of its highly heterozygous autotetraploid genome, the extended cycle required for stable transformation and regeneration, and the time-consuming evaluation of drought responses in mature plants. Here, we identified MsMYB71, a drought-responsive R2R3-MYB transcription factor, as a positive regulator of drought tolerance in alfalfa. Mechanistically, MsMYB71 directly bound to the promoter of MsPrxQ (peroxiredoxin Q), encoding a chloroplast-associated peroxiredoxin Q, and activated its expression, thereby promoting redox homeostasis under drought stress. In contrast, MsPRL1 (PLEIOTROPIC REGULATORY LOCUS 1, a WD40-repeat protein) and MsCUL4 (Cullin4, a Cullin-family scaffold protein) interacted with MsMYB71 and attenuated its protein accumulation and transcriptional output. To establish the physiological relevance of this regulatory module directly in alfalfa, we generated stable overexpression and RNA interference lines for all four genes. Genetic and physiological analyses showed that MsMYB71 enhanced drought tolerance and restricted excessive reactive oxygen species accumulation. Stable manipulation of MsPrxQ further established its positive role in drought tolerance and antioxidant defense. In contrast, MsPRL1 and MsCUL4 negatively regulated drought tolerance and physically interacted with MsMYB71. Their co-expression reduced MsMYB71 protein accumulation in a proteasome-sensitive manner and attenuated MsMYB71-dependent activation of MsPrxQ, consistent with an MsPRL1/MsCUL4-associated attenuation mechanism. Together, our findings define an MsPRL1/MsCUL4-MsMYB71-MsPrxQ module that couples transcriptional activation with protein-level attenuation to fine-tune redox homeostasis and drought adaptation in alfalfa.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149316495","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 CLE–RLK–LBD signaling module promotes de novo shoot regeneration in plants","authors":"Ziyao Hu,&nbsp;Langrang Zhang,&nbsp;Siwei Bie,&nbsp;Junpeng Niu,&nbsp;Kaiying Chen,&nbsp;Xuan Ji,&nbsp;Jing Wang,&nbsp;Deyan Yang,&nbsp;Yanpeng Zhao,&nbsp;Yonghong Zhang,&nbsp;Chen Li,&nbsp;J. Peter Etchells,&nbsp;Jennifer C. Fletcher,&nbsp;Chao Zhou,&nbsp;Shinichiro Sawa,&nbsp;Guodong Wang","doi":"10.1111/jipb.70300","DOIUrl":"10.1111/jipb.70300","url":null,"abstract":"<div>\u0000 \u0000 <p>Tissue culture recalcitrance limits plant transformation and genome editing for crop improvement. The development of new, generic factors that enhance plant regeneration efficiency could alleviate this bottleneck. Through precursor gene overexpression, exogenous peptide application, and loss-of-function studies, we show here that <i>CLAVATA3/ESR-RELATED 41</i> (<i>CLE41</i>), <i>CLE42</i>, <i>CLE44</i>, and <i>CLE46</i>, collectively referred to as <i>TDIF</i>-related genes, function redundantly to promote <i>de novo</i> shoot regeneration. <i>CLE41</i>, <i>CLE42</i>, and <i>CLE44</i> are abundantly and dynamically expressed in pluripotent callus, whereas <i>CLE46</i> is shoot-induction medium-activated and specifically expressed at explant wound sites. TDIF-related peptides act through PHLOEM INTERCALATED WITH XYLEM/TDIF RECEPTOR (PXY/TDR)-subfamily members to activate <i>WUSCHEL (WUS)-RELATED HOMEOBOX 14</i> (<i>WOX14</i>) and enhance shooting capacity. In addition, we find that <i>LATERAL ORGAN BOUNDARIES DOMAIN4</i> (<i>LBD4</i>) is highly expressed throughout the callus and its expression increases upon TDIF upregulation in a PXY/PXL-dependent manner. Consistently, <i>LBD4</i> overexpression notably improves regeneration efficiency, whereas its loss decreases regeneration. TDIF-enhanced shoot regeneration is significantly suppressed in <i>lbd4</i> mutants, indicating that LBD4 is required for TDIF signaling in shoot regeneration enhancement. Furthermore, WOX14 directly activates <i>LBD4</i> to promote <i>de novo</i> shoot regeneration. Exogenous application of synthetic TDIF-related peptides substantially increases shooting capacity in the recalcitrant crop species <i>Sorghum bicolor</i> L., offering a convenient new avenue to enhance <i>de novo</i> shoot regeneration in crops. In conclusion, we demonstrate that Arabidopsis TDIF-PXY/PXL ligand-receptor pairs markedly boost <i>de novo</i> shoot regeneration through WOX14-potentiated <i>LBD4</i> induction. Our findings elucidate the molecular basis for a novel function of TDIF-related peptides and their receptors in hormone-driven shoot regeneration and demonstrate their practical application in improving adventitious shoot regeneration in a recalcitrant plant species.</p></div>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"68 11","pages":"3929-3946"},"PeriodicalIF":12.5,"publicationDate":"2026-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148012652","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}