Xin Li, Jiahui Zhang, Kathrin Rousk, Yinghua Zhang, Yi Jiao, Pu Yan, Nianpeng He
{"title":"Leaf multi-dimensional stoichiometry as a robust predictor of productivity on the Tibetan Plateau","authors":"Xin Li, Jiahui Zhang, Kathrin Rousk, Yinghua Zhang, Yi Jiao, Pu Yan, Nianpeng He","doi":"10.1111/jipb.13960","DOIUrl":"10.1111/jipb.13960","url":null,"abstract":"<div>\u0000 \u0000 <p>Accurately predicting gross primary productivity (GPP) is crucial for understanding carbon cycling; however, most studies have predominantly investigated GPP using only environmental metrics, overlooking the pivotal role of functional traits as intermediaries between the environment and GPP and the predictive potential of GPP. Therefore, this study developed a three-dimensional “engine” framework to predict GPP and tested it by leveraging functional traits from 2,040 plant communities on the Tibetan Plateau, incorporating environmental factors and the length of the plant-growing season. Our results highlight that while the environment exerts a dominant direct influence on GPP dynamics, the contribution of leaf density traits to GPP prediction should not be overlooked. The proposed framework achieved a prediction accuracy close to 0.92, underscoring its feasibility in GPP prediction. However, incorporating the nitrogen-to-phosphorus ratio into the framework diminished the model's predictive accuracy. Within the stoichiometric dimension alone, the prediction accuracy significantly increased with the number of input traits, indicating a substantial potential for enhancing predictive capability. In the dimension of environmental factors, incorporating more environmental factors does not significantly enhance the model's predictive ability. Our research facilitates the dynamic, continuous, and relatively accurate monitoring of GPP, contributing to a better understanding of carbon cycle dynamics and supporting informed ecosystem planning and management.</p></div>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 9","pages":"2416-2429"},"PeriodicalIF":9.3,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504261","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":"OsDNR1 as a key regulator of rice resistance to 4-hydroxyphenylpyruvate dioxygenase-inhibiting herbicides","authors":"Yang Li, Xitie Ling, Wenting Zhang, Dongshu Guo, Jinyan Wang, Zeyu Qiu, Yuanda Lv, Yuwen Yang, Qing Liu, Xiaodong Hou, Baolong Zhang","doi":"10.1111/jipb.13962","DOIUrl":"10.1111/jipb.13962","url":null,"abstract":"<p><i>DULL NITROGEN RESPONSE 1</i> (<i>OsDNR1</i>) is a key gene in rice resistance to herbicides that target 4-hydroxyphenylpyruvate dioxygenase, which are phytotoxic due to their effects on homogentisic acid levels. Knocking out <i>OsDNR1</i> leads to hydroxyphenylpyruvic acid accumulation in rice plants, thereby increasing homogentisic acid levels and conferring herbicide resistance.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 9","pages":"2262-2264"},"PeriodicalIF":9.3,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13962","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504262","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":"GmGASA12 coordinates hormonal dynamics to enhance soybean water-soluble protein accumulation and seed size","authors":"Yuming Yang, Lina Zhang, Huifang Zuo, Yifei Yang, Dandan Hu, Shanshan Zhang, Wenjie Yuan, Xuhao Zhai, Mengshi He, Mengjun Xu, Jinshe Wang, Weiguo Lu, Dezhou Hu, Deyue Yu, Fang Huang, Dan Zhang","doi":"10.1111/jipb.13952","DOIUrl":"10.1111/jipb.13952","url":null,"abstract":"<div>\u0000 \u0000 <p>Water-soluble protein (WSP) content determines soybean nutritional value and processing efficiency, yet its genetic and molecular regulation remains poorly understood. Here, we identified <i>Glycine max gibberellic acid-stimulated Arabidopsis 12</i> (<i>GmGASA12</i>), encoding a gibberellin-regulated protein, as a major quantitative trait locus (QTL) governing WSP, through genome-wide association studies across five environments. Knockout of <i>GmGASA12</i> resulted in 28.7% higher WSP content, 27.6% enlarged seed cells, and 20% yield increase, while overexpression suppressed these traits. Hormonal profiling revealed that <i>GmGASA12</i> knockout elevates gibberellin, auxin, and abscisic acid but reduces cytokinin, driving cell expansion and protein body accumulation. GmGASA12 cooperatively regulates the biosynthesis of β-conglycinin and glycinin, the core storage proteins in soybean seeds, through its interaction with GmCG-6. Transcriptomics linked <i>GmGASA12</i> to nitrogen metabolism and hormone signaling, with knockout upregulating amino acid transporters (<i>GmAAP3/6/27</i>) and storage protein genes (<i>GmCG-1–6</i>). Evolutionary analyses demonstrated strong selection for elite <i>GmGASA12</i> haplotypes during domestication, with 94% of cultivars harboring favorable alleles. Our findings establish GmGASA12 as a molecular hub integrating hormonal dynamics and protein interaction to enhance soybean quality and yield, offering a pivotal target for breeding nutrient-dense varieties.</p></div>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 9","pages":"2401-2415"},"PeriodicalIF":9.3,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473565","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}
Judit Dobránszki, Valya Vassileva, Dolores R. Agius, Panagiotis Nikolaou Moschou, Philippe Gallusci, Margot M.J. Berger, Dóra Farkas, Marcos Fernando Basso, Federico Martinelli
{"title":"Gaining insights into epigenetic memories through artificial intelligence and omics science in plants","authors":"Judit Dobránszki, Valya Vassileva, Dolores R. Agius, Panagiotis Nikolaou Moschou, Philippe Gallusci, Margot M.J. Berger, Dóra Farkas, Marcos Fernando Basso, Federico Martinelli","doi":"10.1111/jipb.13953","DOIUrl":"10.1111/jipb.13953","url":null,"abstract":"<p>Plants exhibit remarkable abilities to learn, communicate, memorize, and develop stimulus-dependent decision-making circuits. Unlike animals, plant memory is uniquely rooted in cellular, molecular, and biochemical networks, lacking specialized organs for these functions. Consequently, plants can effectively learn and respond to diverse challenges, becoming used to recurring signals. Artificial intelligence (AI) and machine learning (ML) represent the new frontiers of biological sciences, offering the potential to predict crop behavior under environmental stresses associated with climate change. Epigenetic mechanisms, serving as the foundational blueprints of plant memory, are crucial in regulating plant adaptation to environmental stimuli. They achieve this adaptation by modulating chromatin structure and accessibility, which contribute to gene expression regulation and allow plants to adapt dynamically to changing environmental conditions. In this review, we describe novel methods and approaches in AI and ML to elucidate how plant memory occurs in response to environmental stimuli and priming mechanisms. Furthermore, we explore innovative strategies exploiting transgenerational memory for plant breeding to develop crops resilient to multiple stresses. In this context, AI and ML can aid in integrating and analyzing epigenetic data of plant stress responses to optimize the training of the parental plants.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 9","pages":"2320-2349"},"PeriodicalIF":9.3,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13953","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473564","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":"Reciprocal regulation between AtFH5-labeled secretory vesicles and PI(4,5)P2 oscillation at the plasma membrane directs pollen germination","authors":"Yuwan Zhao, Zijing Huang, Ting Wang, Yi Zhang, Zhufeng Chen, Yihao Li, Haiyun Ren","doi":"10.1111/jipb.13945","DOIUrl":"10.1111/jipb.13945","url":null,"abstract":"<p>Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P<sub>2</sub>) is known to be an instrumental anionic phospholipid in governing pollen germination and pollen tube growth. However, the precise functions and regulatory mechanisms of PI(4,5)P<sub>2</sub> in pollen polarity establishment and germination remain poorly understood. Our previous studies demonstrated the pivotal involvement of <i>Arabidopsis</i> formin homology 5 (AtFH5)-dependent vesicle trafficking in polarity establishment of pollen. Here, we observed that PI(4,5)P<sub>2</sub> accumulated and oscillated at the prospective germination site, a process closely associated with the rotational movement of AtFH5-labeled vesicles. Disruption of the mobility of AtFH5-labeled vesicles, either through AtFH5 mutation or pharmacological treatment, significantly perturbed the accumulation of PI(4,5)P<sub>2</sub> at the plasma membrane. Subcellular localization and genetic analysis revealed that two phosphatidylinositol 4-phosphate 5-kinases, AtPIP5K1 and AtPIP5K4, are essential for PI(4,5)P<sub>2</sub> oscillation at the germination site prior to pollen germination. Furthermore, we found that the dynamics of AtPIP5K4 depended on the mobility of AtFH5-labeled vesicles and reduced PI(4,5)P<sub>2</sub> in turn disturbed the attachment of AtFH5-labeled secretory vesicles to the plasma membrane. In conclusion, these findings collectively highlight the reciprocal regulation of AtFH5-labeled secretory vesicles and PI(4,5)P<sub>2</sub> oscillations at the plasma membrane, providing critical insights into the molecular mechanism underlying polarity establishment during pollen germination.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 8","pages":"2229-2244"},"PeriodicalIF":9.3,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13945","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332210","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":"Decoding alternative splicing: A key player in plant biotic stress resistance","authors":"Jiayu Zhu, Wenbin Guo, Jianping Chen, Zongtao Sun","doi":"10.1111/jipb.13951","DOIUrl":"10.1111/jipb.13951","url":null,"abstract":"<p>Alternative splicing (AS) is a crucial post-transcriptional mechanism in plants, significantly contributing to the diversification of biological processes and adaptive responses. Distinct splice isoforms are generated by exon skipping (ES), intron retention (IR) and other mechanisms, enabling plants to adapt to a range of biotic stresses, including those posed by bacteria, fungi and viruses. Advances in bioinformatics have greatly improved the detection and characterization of AS events, revealing their critical roles in plant immunity. This review highlights the involvement of AS in regulating RNA interference (RNAi), hormone signaling pathways, and immune responses such as pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). In addition, pathogens exploit AS to produce effectors that subvert plant immunity. Beyond its role in natural immunity, AS also holds promise for pesticide development, offering opportunities to enhance plant disease resistance by targeting pest-associated or immunity-related genes. Future research on AS under biotic stress is expected to uncover novel regulatory mechanisms and provide new strategies for crop improvement and sustainable agriculture.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 9","pages":"2294-2319"},"PeriodicalIF":9.3,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332209","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}
Jie Li, Sophie Mantelin, Miles Armstrong, Amanpreet Kaur, Sonia Gomez, Jiahan Ying, Xiuli Qin, Kathryn M. Wright, Brian Harrower, Paolo Ribeca, Théo Chaumet, Gaynor McKenzie, Huanting Liu, Malcolm F. White, Thomas Adams, Stuart Ronan Fisher, Daolong Dou, Xiaodan Wang, Ingo Hein
{"title":"Solanum bulbocastanum nucleotide-binding leucine-rich repeat receptor evolution reveals functional variants and critical residues in Rpi-blb1/RB","authors":"Jie Li, Sophie Mantelin, Miles Armstrong, Amanpreet Kaur, Sonia Gomez, Jiahan Ying, Xiuli Qin, Kathryn M. Wright, Brian Harrower, Paolo Ribeca, Théo Chaumet, Gaynor McKenzie, Huanting Liu, Malcolm F. White, Thomas Adams, Stuart Ronan Fisher, Daolong Dou, Xiaodan Wang, Ingo Hein","doi":"10.1111/jipb.13950","DOIUrl":"10.1111/jipb.13950","url":null,"abstract":"<p>Host–pathogen co-evolution shapes resistance (<i>R</i>) proteins and their recognition of pathogen avirulence factors. However, little attention has been paid to naturally occurring genetic diversity in <i>R</i> genes. In this study, 12 <i>Solanum bulbocastanum</i> accessions from the Commonwealth Potato Collection were screened for resistance to <i>Phytophthora infestans</i>, identifying 11 resistant and one susceptible accession. Targeted enrichment sequencing of nucleotide-binding leucine-rich repeat (NLR) genes using RenSeq, followed by diagnostic RenSeq (dRenSeq) analysis, revealed that all accessions except 7650 contained <i>Rpi-blb1/RB</i> variants. Variants in accessions 7641 and 7648 were non-functional, while three novel functional variants were identified. Cloning and functional analysis of <i>Rpi-blb1/RB</i> variants assessed their recognition of the avirulence factor IPI-O1. Three variants were functional, conferring resistance to <i>P. infestans</i>. Variants in accessions 7644 and 7647 also recognized IPI-O4, confirmed in transgenic potatoes. Analysis of a non-functional variant in <i>S. bulbocastanum</i> accession 7648 identified amino acid Ser347 in the nucleotide-binding (NB-ARC) domain as critical for cell-death initiation following IPI-O1 recognition. Predictions from the FunFOLD2 protein–ligand interaction model suggested that Ser347 is essential for ATP binding, suggesting potential inhibition on pentameric resistosome assembly. Western blot analysis revealed that the mutation of Ser347 to Asn markedly compromises the Rpi-blb1/RB protein stability, and co-immunoprecipitation assay further confirmed that this mutation severely disrupts the self-association of CCNB, thereby preventing Rpi-blb1/RB activation. Consistently, substituting Asn347 with serine restored function, underscoring its key role in Rpi-blb1/RB activity. Cell biology experiments demonstrated that Rpi-blb1/RB relocalizes to the plasma membrane in response to IPI-O1. This relocalization depends on Ser347, further supporting the idea that its mutation affects resistosome formation, impairing resistance. This study provides an in-depth functional analysis of natural <i>Rpi-blb1/RB</i> diversity, offering insights into NLR protein evolution and resistance mechanisms in potatoes.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 9","pages":"2491-2509"},"PeriodicalIF":9.3,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13950","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144315664","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":"The targeted metabolomic profile of laticifers in rubber tree.","authors":"Xiaomin Deng, Shuguang Yang, Qiang Gao, Yanling Chen, Xia Zeng, Minjing Shi, Shaohua Wu, Weimin Tian, Xuchu Wang, Jinquan Chao","doi":"10.1111/jipb.13948","DOIUrl":"https://doi.org/10.1111/jipb.13948","url":null,"abstract":"<p><p>Targeted metabolomic profiling of rubber tree (Hevea brasiliensis) laticifers identified metabolites that were reprogramming by domestication, revealed active isoprenoid metabolism in the laticifers, and discovered loci with potential biosynthetic applications, supporting the potential of developing laticifers as bioreactors for production of valuable metabolites in Hevea.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300780","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 CsphyB–CsPIF4–CsBRC1 module regulates ABA biosynthesis and axillary bud outgrowth in cucumber","authors":"Ye Liu, Zhihan Liu, Chuang Li, Min Li, Daixi She, Jiahao Zhang, Huiqi Ren, Xitong Zhong, Yafei Huang, Yuxiang Huang, Yuting He, Yuan Liu, Jiacai Chen, Yan Geng, Xiaoli Li, Kailiang Bo, Yiqun Weng, Xiaolan Zhang, Jianyu Zhao","doi":"10.1111/jipb.13947","DOIUrl":"10.1111/jipb.13947","url":null,"abstract":"<div>\u0000 \u0000 <p>Shoot branching is an important crop agronomic trait that directly affects plant architecture and crop productivity. Although phytochrome B (phyB), <i>BRANCHED1</i> (<i>BRC1</i>), and abscisic acid (ABA) mediate axillary bud outgrowth, it is unknown if there is any integrating factor among them in the Plantae. We report that mutation of <i>CsphyB</i> or inactivation of <i>CsphyB</i> by shade inhibits lateral bud outgrowth in cucumber. Cucumber PHYTOCHROME INTERACTING FACTOR 4 (CsPIF4) interacts with CsphyB and directly binds to the promoter of <i>CsBRC1</i> to activate <i>CsBRC1</i> expression. <i>CsBRC1</i> also directly promotes the expression of ABA biosynthesis gene <i>9</i>-<i>CIS</i>-<i>EPOXICAROTENOID DIOXIGENASE 3</i> (<i>CsNCED3</i>). Functional disruption of <i>CsPIF4</i> decreased expression of <i>CsBRC1</i> and <i>CsNCED3</i>, reduced ABA accumulation, and increased bud outgrowth in cucumber. <i>Csnced3</i> mutants had reduced ABA levels and increased lateral bud outgrowth. These results suggest that a regulatory network involving CsphyB-CsPIF4-<i>CsBRC1</i> exists that integrates light signaling and ABA biosynthesis to modulate bud outgrowth. This provides a strategy to manipulate branch numbers in crop breeding to realize ideal branching characteristics to maximize yield.</p></div>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 10","pages":"2561-2577"},"PeriodicalIF":9.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273794","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":"Cold tolerance acquired through inheritable cold-induced epigenetic variation","authors":"Shuhua Yang, Yijun Qi","doi":"10.1111/jipb.13954","DOIUrl":"10.1111/jipb.13954","url":null,"abstract":"<p>This commentary examines a study by Song et al. (2025) showing that an environmentally induced epiallele at ACQUIRED COLD TOLERANCE 1 mediates the heritable acquisition of an adaptive trait, cold tolerance, in rice.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 9","pages":"2253-2255"},"PeriodicalIF":9.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13954","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273792","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}