Plant Physiology最新文献

{"title":"Genome assembly and DNA methylation variation in an epimutant population of hybrid poplar clone NL895.","authors":"Jie He,Guang-Zheng Diao,Yang-Fan Feng,Hao-Ran Liao,Ying Guo,Li-Na Mei,Fang-Fang Fu,Tongming Yin,Fuliang Cao,Liang-Jiao Xue","doi":"10.1093/plphys/kiaf415","DOIUrl":"https://doi.org/10.1093/plphys/kiaf415","url":null,"abstract":"Epimutant populations represent important genetic resources for plant breeding and selection. However, the variation and dynamics of epigenomic modifications among epimutants are still elusive. In this study, we analyzed DNA methylation patterns at both whole-genome and allelic levels in an epimutant population of a model hybrid poplar NL895 (Populus deltoides × P. euramericana cv. 'Nanlin895'). Epimutants were generated through the application of 5-Azacytidine (5-Aza) during tissue culture. A haplotype-resolved assembly of NL895 was constructed to serve as a reference for epigenomic analysis. Compared to control plants, averaged DNA methylation levels across the entire genome were reduced in epimutants. The methylation patterns of epimutants exhibited high diversity in several aspects, including the number of differentially methylated regions (DMRs), distribution of DMRs in sequence contexts, and genomic features. The observed epigenomic diversity suggests stochastic effects resulting from 5-Aza treatment. At the gene level, non-expressed genes consistently displayed higher rates of methylation across all examined epimutants. Among allele-specific expressed genes (ASEGs), fold changes between parental alleles were more pronounced in allele pairs exhibiting greater disparities in DNA methylation rates. For allele-specific methylation regions (ASMRs), the differences in methylation levels were notably elevated in ASMRs overlapped with genomic structural variations (SVs). Our results provide valuable germplasm resources characterized by phenotypic variations for poplar breeding, and the dynamics of DNA methylation in hybrid poplar epimutants highlights potential clues for application of hybrid vigor.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"89 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145117049","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":"Glycosylated sterols enhance cold tolerance in tomato via membrane stabilization and jasmonate signaling.","authors":"Cuiyun Deng,Antoni Garcia-Molina,Aurelio Gómez-Cadenas,Vicente Vives-Peris,Rubén Alcázar,Albert Ferrer,Teresa Altabella","doi":"10.1093/plphys/kiaf420","DOIUrl":"https://doi.org/10.1093/plphys/kiaf420","url":null,"abstract":"Free and glycosylated sterols play a central role in maintaining the structural integrity and proper functioning of the plasma membrane, which serves as the primary sensor of cold and initiates signaling cascades to mitigate chilling-induced damage. Here, we characterize the cold response of tomato (Solanum lycopersicum cv. Micro-Tom) mutants with higher and lower ratios of glycosylated to free sterols than wild type plants, resulting from the overexpression and silencing of the STEROL GLYCOSYLTRANSFERASES 1 and 2 (SlSGT2 and SlSGT1), respectively. The SlSGT2 overexpressing mutants show increased cold tolerance, membrane stability and oxidative stress responses, while silencing of the SlSGT1 gene causes the opposite phenotypes. Furthermore, changes in the glycosylated to free sterols ratio activate distinct transcriptional programs that establish a preconditioned stress-responsive state under basal conditions and trigger a more efficient response to cold in the SlSGT2 overexpressing mutants, as well as compromise the capacity to withstand the effects of cold stress in the SlSGT1-silenced mutants. The SlSGT2 overexpressing mutants also contain higher levels of jasmonates under basal conditions and display enhanced biosynthesis of these hormones under cold stress compared to SlSGT1-silenced and control plants. The facilitating effect of elevated glycosylated to free sterols ratio on JA biosynthesis and signaling leads to the activation of cold-responsive genes, including those of the CBF-COR pathway, antioxidant defenses, and polyamine biosynthesis. Our findings provide key insights into the mechanisms by which glycosylated sterols help improve cold tolerance in tomato.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"10 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145127147","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 CANNOT RESPOND TO DMBQ 1–GLUTAREDOXIN C1 module regulates Arabidopsis root growth via quinone-induced oxidation","authors":"Liang Zhang, Long Wang, Xiaonan Qiang, Ke Chen, Jingyi Xue, Zhixuan Liu, Longqin Sun, Zhenghong Zhao, Lianyang Bai, Feng Yu, Lifeng Wang","doi":"10.1093/plphys/kiaf419","DOIUrl":"https://doi.org/10.1093/plphys/kiaf419","url":null,"abstract":"Quinones are secondary metabolites widely produced by plants. They are sensed by the leucine-rich receptor kinase CANNOT RESPOND TO DMBQ 1 (CARD1) and play important roles in immunity and growth in nonparasitic plants. Quinone perception typically involves the posttranslational modification of proteins, particularly through cysteine oxidation. However, the relationship between quinone-induced cysteine modifications and the quinone–CARD1 signaling pathway remains unclear. Here, we performed a redox proteomics analysis to determine the extent of CARD1-mediated cysteine oxidation of proteins in Arabidopsis (Arabidopsis thaliana) seedlings following treatment with a quinone, 2,6-dimethoxy-1,4-benzoquinone (DMBQ). We found that GLUTAREDOXIN C1 (GRXC1) is a substrate protein of CARD1, whose oxidation is induced by DMBQ treatment. GRXC1 interacts with and is phosphorylated by CARD1, mediating Arabidopsis primary root growth. This work provides a molecular basis for understanding the DMBQ-induced redox signaling pathway and the DMBQ–CARD1–GRXC1 signaling pathway in response to redox alterations in Arabidopsis.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"14 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133505","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":"Interactions of separately conserved α-(1→6) glucosidases that participate in maize endosperm starch biosynthesis.","authors":"Susan K Boehlein,Tracie A Hennen-Bierwagen,Stacie L Shuler,William F Tracy,L Curtis Hannah,Marcio F R Resende,Alan M Myers","doi":"10.1093/plphys/kiaf417","DOIUrl":"https://doi.org/10.1093/plphys/kiaf417","url":null,"abstract":"Chloroplast-containing species possess two α-(1→6)-glucosidases that share a common ancestor but were independently acquired by horizontal gene transfer from separate eubacterial donors. The pullulanase-type enzyme (CAZy subfamily GH13_13) and the isoamylase-type enzyme (CAZy subfamily GH13_11) both hydrolyze branch linkages in α-polyglucans. Thus, both enzyme types function as debranching enzymes (DBE) in starch metabolism. As both enzyme types are conserved, distinct selectable functions are expected. This study describes the functional interactions between maize (Zea mays L.) pullulanase1 (ZPU1) and the isoamylase-type enzyme complex comprising the paralogous proteins isoamylase1 (ISA1) and isoamylase2 (ISA2). Mutation of ISA1 or ISA2 caused reduced ZPU1 activity in developing endosperm extracts, and the addition of ISA1 to ZPU1-expressing yeast (Saccharomyces cerevisiae) cells caused increased ZPU1 activity. Specific amino acid substitutions in ISA1 resulted in altered ZPU1 mobility in SDS-PAGE. In vivo protein-protein interaction tests and co-immunoprecipitation revealed that ZPU1 and ISA1 interact in multi-subunit complexes. Maize lines harboring ISA1 mutations, exhibiting a classical low-starch, high-phytoglycogen-accumulation phenotype, were altered by recurrent selection so that kernel appearance reverted to near normal. Extragenic suppression indicated the requirement for ISA1/ISA2 activity had been bypassed. These results are consistent with a functional overlap between the GH13_11 and GH13_13 DBE types and raise the possibility that multiple GH13 proteins, namely ZPU1, ISA1 and ISA2, act together to physically coordinate their hydrolytic activities on precursor α-polyglucans.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"10 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145117048","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 Trichoderma microRNA-like RNA suppresses a chitinase gene in Solanum lycopersicum to escape host immunity during early root colonization.","authors":"Ming Xue,Rui Wang,Jumei Hou,Raja Asad Ali Khan,Jie Chen,Runmao Lin,Lin Wang,Hongwei Zhao,Golam Jalal Ahammed,Tong Liu","doi":"10.1093/plphys/kiaf413","DOIUrl":"https://doi.org/10.1093/plphys/kiaf413","url":null,"abstract":"MicroRNAs play crucial roles in biological processes, but the function of microRNA-like RNAs (milRNAs) from Trichoderma remains elusive. In this study, we report that Tra-milR1 is transferred from Trichoderma to ‌Solanum lycopersicum via extracellular vesicles (EVs). Tra-milR1 associates with Solanum lycopersicum Argonaute protein SlyAGO1 to suppress the expression of SlyChit4, a key immunity-related chitinase gene. Overexpression of Tra-milR1 in Trichoderma accelerated the colonization process. SlyChit4 loss of function enhanced susceptibility to Botrytis cinerea and facilitated Trichoderma colonization, while SlyChit4 overexpression had the reverse effect. Furthermore, recombinant SlyChit4 protein inhibited Trichoderma spore germination, blocked hyphal growth, and disrupted the fungal cell wall. Moreover, Tra-milR1 enabled Trichoderma DQ-1 to evade host immunity at the early stage of colonization (0-24 hours post-inoculation (hpi)), while its elicitors stimulated the host plant's immunity at the late stage of colonization (24-96 hpi). These results highlight the mechanisms by which Trichoderma exerts precise temporal regulation of the immune response in tomato.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"80 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145127145","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 module involving the cyclin-dependent kinase OsCDKF3 regulates grain size in rice.","authors":"Zhijuan Diao,Ling Lu,Xun Wang,Fanyu Kong,Siyi Wang,Jiahui Sui,Chenyang Qi,Shengping Li","doi":"10.1093/plphys/kiaf418","DOIUrl":"https://doi.org/10.1093/plphys/kiaf418","url":null,"abstract":"Grain size is a key agronomic trait determining grain yields in crops. However, the molecular mechanisms of grain size regulation are still not fully understood. Here, we identified a cyclin-dependent kinase OsCDKF3 that controls grain development in rice (Oryza sativa). Knocking out OsCDKF3 decreased grain size and thousand grain weight. Moreover, we found that OsMPK6 interacts with and phosphorylates OsCDKF3 at Tyr22. Phosphorylation of Tyr22 contributes to the stability and function of OsCDKF3 in grain size regulation. Consistent with this, the phosphomimic OsCDKF3Y22D but not the dephosphomimic OsCDKF3Y22A complemented the grain defects of the oscdkf3 mutant, and knocking down of OsMPK6 also reduced grain size. In addition, OsSCL7, a grain size negative regulator, inhibited the autophosphorylation activity and promoted the degradation of OsCDKF3, as well as suppressed the interaction between OsCDKF3 and OsMPK6. Conversely, OsMPK6 interacted with OsSCL7 to suppress its transcriptional activity. Taken together, our findings revealed the crucial role of the OsMPK6-OsSCL7-OsCDKF3 module in fine regulation of grain size, providing insights into the important function of CDKs in grain development.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"40 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145127112","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":"Guns in Rosettes: The Arabidopsis chemical weapons arsenal.","authors":"Marc Somssich,Daniel J Kliebenstein,Tonni Grube Andersen","doi":"10.1093/plphys/kiaf411","DOIUrl":"https://doi.org/10.1093/plphys/kiaf411","url":null,"abstract":"","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"51 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145127113","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":"Importance of measuring and reporting environmental conditions across plant science subdisciplines.","authors":"Christopher Vincent,Courtney P Leisner,Anna M Locke,Elena Pelech,Stephanie C Schmiege,Thomas D Sharkey,Mauricio Tejera-Nieves,Dorcas Olufunke Alade,Amanda A Cardoso,Ahram Cho,Kithmee De Silva,Nicole Dziedzic,Alison R Gill,Ravneet Kaur,Sarah L Lane,Gillian Zeng Michalczyk,Atinder Singh,Demissew Tesfaye Teshome","doi":"10.1093/plphys/kiaf405","DOIUrl":"https://doi.org/10.1093/plphys/kiaf405","url":null,"abstract":"Understanding plant responses to the environment is based on research performed across several scales and subdisciplines. However, the interpretation and repeatability of experimental results depend on careful reporting of experimental procedures and environmental conditions. These conditions include light intensity and quality, temperature, relative humidity and vapor pressure deficit, soil water potential or volumetric water content, and pot size, which interact upon plant physiological responses across biological and experimental scales regardless of whether they are the focus of the experiment. To ascertain how effectively and consistently these conditions are reported, we reviewed greater than 200 plant science research articles published from 2020 through 2024 on vascular plants. Environmental condition data were often not reported, including cases where the specific environmental variable was the focus of the study. This situation hampers both replicability and interpretability of results and hinders progress in understanding plant physiological responses across subdisciplines. The Environmental and Ecological Plant Physiology section of the American Society of Plant Biologists (ASPB) recommends several best practices to measure and report environmental conditions in plant physiology experiments, such as measuring and reporting actual environmental conditions, especially of control variables, to enable replication and comparative interpretation among experiments. These guidelines can aid authors in experimental design and manuscript preparation and assist reviewers in evaluating submitted manuscripts. Following such guidelines will enhance the dynamic progress of sound plant science within our community by improving replicability and enabling cross-disciplinary interpretation of results.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"8 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103532","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 ethylene response factor ERF1A regulates UV-C-induced delayed ripening in peach fruit.","authors":"Elpida Nasiopoulou,Michail Michailidis,Christina Skodra,Ioannis-Dimosthenis S Adamakis,Martina Samiotaki,Georgia Tanou,Christos Bazakos,Athanasios Dalakouras,Athanassios Molassiotis","doi":"10.1093/plphys/kiaf409","DOIUrl":"https://doi.org/10.1093/plphys/kiaf409","url":null,"abstract":"Ultraviolet-C (UV-C) irradiation delays fruit ripening, yet the underlying mechanisms remain unclear. We investigated tissue-specific responses of peach fruit (Prunus persica L. Batsch) to UV-C by analyzing the peel and flesh separately. UV-C treatment altered central metabolism, promoted anthocyanin accumulation and coloration, and delayed ripening, as evidenced by reduced fruit softening and water loss. However, UV-C enhanced ethylene production and upregulated ethylene-related genes, indicating a reconfiguration of the ethylene response. Among UV-C-responsive genes, the APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor family was most affected, with Ethylene Response Factor 1A (ERF1A) showing the strongest induction in the treated peel, suggesting its role as a key integrator of the UV-C-induced ripening delay. UV-C increased the levels of DNA 5-methylcytosine (5mC) and RNA N6-methyladenosine (m6A) in the peel, without altering cytosine methylation or causing mutations in ERF1A. Silencing ERF1A via RNA interference confirmed that it regulates ethylene production, softening, and ripening-associated metabolites. Immunolocalization revealed changes in the cell wall components of ERF1A-silenced fruit, including arabinogalactan, pectin, and xyloglucan. ERF1A-silenced peels exhibited elevated auxin and salicylic acid levels and reduced abscisic acid content. Additionally, ERF1A suppression altered the biosynthesis of sugars, phenolic compounds, and volatiles. We found extensive proteome reprogramming in ERF1A-silenced peels and identified putative ERF1A target genes that either contain ERF1A-binding sites or are associated with firmness, ethylene signaling, phytohormone metabolism, and color. Notably, Carboxylesterase 11 (PpCXE11), Carboxylesterase 13 (PpCXE13), and Salicylic acid-binding protein 2 (PpSABP2) emerged as potential ERF1A targets. These findings identify ERF1A as a central regulator mediating UV-C-induced ripening delay through modulation of ethylene signaling and downstream ripening pathways.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"1 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103533","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":"OVATE FAMILY PROTEIN 20 regulates fruit shoulder width by modulating auxin distribution in pepper.","authors":"Zhi-Quan Wang,Qing-Yun Shan,Qing Xu,Qi Xu,Ming-Qiu Wu,Qing Li,Ke Fang,Huan He,Yu Duan,Hong-Guan Zhang,Kun Long,Hong-Jie Zhao,Yi Liu,Hui-Yang Yu,Cheng Xiong,Xue-Xiao Zou,Feng Liu,Zhong-Yi Wang,Bo-Wen Hu","doi":"10.1093/plphys/kiaf404","DOIUrl":"https://doi.org/10.1093/plphys/kiaf404","url":null,"abstract":"Fruit shape is a key determinant of pepper (Capsicum annuum L.) fruit commercial value, and the shoulder is a crucial feature of the fruit's proximal end. Despite the fruit shoulder being an important parameter in morphological variation, the genes and regulatory mechanisms underlying fruit shoulder morphology remain elusive. Here, we identified a fruit shoulder (fs) mutant that primarily exhibits a shoulderless fruit phenotype, with an approximately 40% reduction in fruit weight. Our data demonstrated that OVATE family protein 20 (CaOFP20) controls this phenotype. Silencing CaOFP20 in various fruit types consistently led to decreased fruit shoulder width, while fruit length was unaffected. CaOFP20 was mainly expressed in the pericarp, seeds, and placenta, where it regulates organ size by modulating cell division. Loss of CaOFP20 disrupted the expression of auxin pathway genes and the spatial distribution of auxin in fruits. Additionally, we demonstrated that CaOFP20 physically interacts with HECATE1 (CaHEC1), and silencing CaHEC1 in fs resulted in a wider fruit shoulder. Moreover, CaOFP20 and CaHEC1 play distinct yet complementary roles in regulating the expression of auxin pathway genes involved in fruit shoulder development, such as PIN-FORMED1 (CaPIN1), CaPIN3, and Indole-3-Acetic Acid Inducible (CaIAA9), thus finely controlling fruit shoulder development. Taken together, our findings establish CaOFP20 as a central regulator of fruit shoulder development and suggest its potential utility in breeding programs to enhance pepper fruit quality.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"39 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103536","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}