Journal of Experimental Botany最新文献

{"title":"Transcriptional and epigenomic changes in response to polyethylene glycol-triggered osmotic stress in Brassica napus L.","authors":"Melvin Prasad, Prateek Shetty, Avik Kumar Pal, Gábor Rigó, Kamal Kant, Laura Zsigmond, István Nagy, Padubidri V Shivaprasad, László Szabados","doi":"10.1093/jxb/eraf123","DOIUrl":"10.1093/jxb/eraf123","url":null,"abstract":"<p><p>Drought hinders growth, development, and productivity of higher plants. While the physiological and molecular background of plant responses to drought has been extensively studied, the role of post-translational modifications of histones or DNA methylation in response to dehydration remains largely elusive. In this study, we deciphered genome-wide changes in transcriptome and histone modifications in response to dehydration in rapeseed (Brassica napus L.). High-throughput transcript profiling (RNA-seq) and ChIP followed by sequencing (ChIP-seq) of polyethylene glycol (PEG)-treated rapeseed plants revealed genome-scale changes in transcription and histone methylation patterns, specifically in histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 tri-methylated lysine 27 (H3K27me3) sites. We have identified gene sets with altered transcript profiles as well as histone methylation marks in response to osmotic stress. Several proline biosynthesis regulatory genes coding for Delta 1-Pyrroline-5-Carboxylate Synthetases (P5CS) displayed changes in H3K4me3 and/or H3K36me3 enrichment post-PEG treatment. Targeted bisulfite sequencing further identified stress-dependent gene body DNA methylation in one of the BnP5CSA gene copies that correlates with its stress-induced activation. By integrating physiological, transcriptional, and epigenomic data, our study contributes to a better understanding of the drought response control in crop plants.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"2535-2556"},"PeriodicalIF":5.6,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of RNA polymerase II transcript elongation factors in plant stress responses.","authors":"Klaus D Grasser","doi":"10.1093/jxb/erae472","DOIUrl":"10.1093/jxb/erae472","url":null,"abstract":"<p><p>The elongation phase is a dynamic and highly regulated step of the RNA polymerase II (RNAPII) transcription cycle. A variety of transcript elongation factors (TEFs) comprising regulators of RNAPII activity, histone chaperones, and modulators of histone modifications assist transcription through chromatin. Thereby, TEFs substantially contribute to establish gene expression patterns during plant growth and development. Beyond that, recent research indicates that TEFs and RNAPII transcriptional elongation also play a key role in plant responses to environmental cues. Thus, certain TEFs (i.e. PAF1C, FACT, and TFIIS) were found to mediate transcriptional reprogramming by different mechanisms to establish plant tolerance to abiotic conditions such as heat stress and elevated salt concentrations. Hence, TEFs govern RNAPII elongation to generate the transcriptional output adequate for distinct environments. It is to be expected that future research in this developing field will reveal that TEFs are involved in a growing number of plant responses to changing environmental conditions.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"2447-2454"},"PeriodicalIF":5.6,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of mobile DNA elements in the dynamics of plant genome plasticity.","authors":"Robyn Emmerson, Marco Catoni","doi":"10.1093/jxb/erae523","DOIUrl":"10.1093/jxb/erae523","url":null,"abstract":"<p><p>Plants host a range of DNA elements capable of self-replication. These molecules, usually associated with the activity of transposable elements or viruses, are found integrated in the genome or in the form of extrachromosomal DNA. The activity of these elements can impact genome plasticity by a variety of mechanisms, including the generation of structural variants, the shuffling of regulatory or coding DNA sequences across the genome, and DNA endoduplication. This plasticity can dynamically alter gene expression and genome stability, ultimately affecting plant development or the response to environmental changes. While the activation of these elements is often considered deleterious to the genome, their role in creating variation is important in adaptation and evolution. Moreover, the mechanisms by which mobile DNA proliferates have been exploited for plant engineering, or contributed to understand how desirable traits can be generated in crops. In this review, we discuss the origins and the roles of mobile DNA element activity on genome plasticity and plant biology, as well as their potential function and current application in plant biotechnology.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"2433-2446"},"PeriodicalIF":5.6,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Induction of flowering under long-day photoperiod requires DNA hypermethylation in orchardgrass.","authors":"Zhongfu Yang, Haidong Yan, Gang Nie, Jiajing Xiao, Jianping Wang, Guangyan Feng, Dandan Li, Linkai Huang, Xinquan Zhang","doi":"10.1093/jxb/eraf015","DOIUrl":"10.1093/jxb/eraf015","url":null,"abstract":"<p><p>Flowering, a pivotal plant life cycle event, is intricately regulated by environmental and endogenous signals via genetic and epigenetic mechanisms. Photoperiod is a crucial environmental cue that induces flowering by activating integrators through genetic and epigenetic pathways. However, the specific role of DNA methylation, a conserved epigenetic marker, in photoperiodic flowering remains unclear. This study integrated methylome, transcriptome, and gene expression analyses in orchardgrass (Dactylis glomerata) to elucidate the molecular mechanisms underlying long-day (LD) flowering. We found that LD treatment led to CHH hypermethylation, which was associated with the increased expression of RNA-dependent DNA methylation pathway components. LD-induced CHH hypermethylation in promoters correlated with up-regulated photoperiod pathway genes and down-regulated miRNAs. The suppression of DNA methylation under LD conditions delays flowering, highlighting the critical role of hypermethylation. Additionally, a novel miR1736-3p was identified as a negative regulator of FLOWERING LOCUS T (DgFT). These findings elucidate the promotion of flowering through LD-induced CHH hypermethylation and provide insights into using epigenetic techniques to control plant flowering time.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"2557-2572"},"PeriodicalIF":5.6,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Iron retention coupled with trade-offs in localized symbiotic effects confers tolerance to combined iron deficiency and drought in soybean.","authors":"Md Rokibul Hasan, Asha Thapa, Ahmad H Kabir","doi":"10.1093/jxb/eraf263","DOIUrl":"https://doi.org/10.1093/jxb/eraf263","url":null,"abstract":"<p><p>Iron (Fe) and water availability are closely interlinked, with deficiencies in both adversely affecting soybean growth. However, the strategies employed by soybean to tolerate such conditions remain poorly understood. This study elucidates the interactions of host factors, and microbial associations using multi-omics approaches in Clark (tolerant) and Arisoy (sensitive) genotypes exposed to Fe deficiency and drought. Clark exhibited resilience to stress through sustained osmotic regulation, nutrient uptake, and photosynthetic activity, in contrast to Arisoy. Particularly, Fe retention in Clark, accompanied by the upregulation of ferritin-like proteins, may mitigate oxidative stress by reducing Fenton reactions. Furthermore, higher jasmonic and salicylic acid levels in Clark may contribute to its enhanced stress adaptation compared to Arisoy. RNA-seq analysis revealed 818 and 500 upregulated, along with 931 and 361 downregulated genes, in the roots of Clark and Arisoy, respectively, under stress. We observed the upregulation of symbiotic genes, such as Chalcone-flavonone isomerase 1 and SWEET10, accompanied by increased rhizosphere siderophore and root flavonoid in Clark. This indicates a significant role of microbes in mediating differential stress tolerance in soybean. Particularly, the combined stress led to distinct root and nodule microbiome dynamics, with Clark recruiting beneficial microbes such as Variovorax and Paecilomyces, whereas Arisoy exhibited the opposite pattern. In addition, Clark maintained nodule Bradyrhizobium and tissue nitrogen status, supported by ammonium retention and induction of Ammonium transporter 1 in the roots. Furthermore, in vitro compatibility between V. paradoxus and P. lilacinus suggests a synergistic interaction, with their localized signals benefiting Clark. Remarkably, enriched microbiomes significantly improved growth parameters, accompanied by elevated rhizosphere siderophore in sensitive genotypes under stress. This study is the first to uncover mechanisms of dual stress tolerance in soybean that may offer promising targets for breeding programs and microbiome-based biofertilizer strategies to improve combined stress tolerance in soybean and other legumes.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ruegeria strains promote growth and morphogenesis of the giant coenocytic alga Bryopsis.","authors":"Kanta K Ochiai, Gohta Goshima","doi":"10.1093/jxb/eraf262","DOIUrl":"https://doi.org/10.1093/jxb/eraf262","url":null,"abstract":"<p><p>An evolutionarily intriguing life form among extant organisms is the giant coenocyte, exemplified by green macroalgae in the order Bryopsidales. In these algae, cell separation does not follow nuclear division, resulting in a body composed of a single multinucleated cell. How a single cell grows to over 10 cm and undergoes characteristic morphogenesis without cell division or differentiation remains poorly understood. Macroalgae are known to associate with numerous microbes, and in some cases, these interactions influence algal cell division and differentiation. Here, we show that specific bacterial strains can promote the growth and morphogenesis of the coenocytic macroalga Bryopsis. Among >100 bacterial isolates obtained from Bryopsis, four strains belonging to the genus Ruegeria were found to accelerate the growth of the main axis and induce side-branch formation when co-cultured with the alga. The same effects were observed using conditioned seawater in which Ruegeria had been pre-cultured and subsequently removed. Seasonal microbiome analysis revealed that cultured Bryopsis associates with hundreds of bacterial species, exhibiting seasonal variations in community composition. However, Ruegeria was one of the few bacterial genera consistently associated with the cultured strain, suggesting a symbiotic relationship. Notably, although Ruegeria was not detected in Bryopsis strains isolated from other regions, its effects on growth and morphogenesis were observed in co-culture experiments. These findings suggest that Bryopsis, like multicellular macroalgae, utilises associated bacteria for growth and development without strict specificity.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-parental cross design-based QTL mapping approach dissected the fruit firmness and softening genetic control in European pears (Pyrus communis).","authors":"Federico Grignaffini, Luca Bianco, Erica Di Pierro, Diego Micheletti, Michela Troggio, Lester Brewer, Richard Volz, Francesca Populin, Carolina Font I Forcada, Jordi Giné-Bordonaba, Fabrizio Costa","doi":"10.1093/jxb/eraf258","DOIUrl":"https://doi.org/10.1093/jxb/eraf258","url":null,"abstract":"<p><p>Fruit firmness and softening rate are two key quality parameters defined by the enzymatic disassembly of the polysaccharide architecture of the primary cell wall and middle lamella structure. Technological control of fruit ripening in pear, while extending shelf-life, can negatively affect general fruit quality. Therefore, genetic improvement of these properties can represent a valuable alternative. Two bi-parental populations were employed to dissect the genetic control of static and dynamic firmness parameters, considering fruit firmness assessed at harvest and after storage, as well as the definition of softening and storage index-derived parameters. The integrated QTL analysis was performed through a Multi-Parental Cross Design based on a Pedigree Based Analysis approach. This allowed the identification of specific QTL signatures distinguished by an increasing cumulative percentage of variability expressed from harvest to postharvest stage and highlighted the presence of a major QTL on linkage group 3. The QTL intervals were distinguished by the presence of several classes of genes involved in the degradation of the cell wall, such as expansins, polygalacturonases and pectate lyase. The haploblocks (HBs) derived by single SNPs also elucidated the role of HB-alleles as potential marker tools to assist breeding programs aimed at improving fruit firmness and softening, especially during postharvest.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arginine, a key amino acid for nitrogen nutrition and metabolism of forest trees.","authors":"Concepción Ávila, María Teresa Llebrés, Francisco M Cánovas, Vanessa Castro-Rodríguez","doi":"10.1093/jxb/eraf260","DOIUrl":"https://doi.org/10.1093/jxb/eraf260","url":null,"abstract":"<p><p>Despite the extraordinary significance of forests from an environmental, economic, and social perspectives, our understanding of the mechanisms underlying the growth, development and productivity of forest trees remains limited compared to crop plants mainly due to their perennial growth and recalcitrance to molecular analysis. Amino acids and peptides are key nitrogen (N) sources available in the soil for tree nutrition. Furthermore, when excess N (organic or inorganic) is available, trees can assimilate and store it directly as free arginine, the amino acid with the highest N content, or as a constituent of storage proteins in vegetative and reproductive organs. Arginine is, therefore, of paramount importance in N metabolism, and studying its biosynthesis and metabolic utilization is crucial for understanding N homeostasis in forest trees. This work reviews several aspects of arginine biochemistry and molecular biology in woody plants, including its transport, storage, and mobilization, as well as the enzymes involved in its biosynthesis and their subcellular distribution. Arginine biosynthesis is allosterically controlled by pathway's end-product, and increased glutamine levels act as a signal of N abundance, triggering a response that enhances flux through the pathway, favoring N storage. Additionally, this review discusses the molecular regulation of arginine biosynthesis at both transcriptional and post-transcriptional levels, whit an emphasis on key processes such as embryogenesis and N recycling.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Glandular trichome rupture in tomato plants is an ultra-fast & sensitive defense mechanism against insects.","authors":"Jared Popowski, Lucas Warma, Alicia Abarca Cifuentes, Petra Bleeker, Maziyar Jalaal","doi":"10.1093/jxb/eraf257","DOIUrl":"https://doi.org/10.1093/jxb/eraf257","url":null,"abstract":"<p><p>Trichomes, specialized hair-like structures on the surfaces of many plants, play a crucial role in defense against herbivorous insects. We investigated the biomechanics of type VI glandular trichome rupture in cultivated tomato (Solanum lycopersicum) and a wild relative (Solanum habrochaites). Using micropipette force sensors and high-speed imaging, we uncovered the rupture mechanics underlying gland bursting, highlighting the small forces and short timescales involved in this process. Additionally, we observed larvae of the Western flower thrips (Frankliniella occidentalis), a major pest in tomato cultivation, inadvertently triggering trichome rupture and accumulating glandular secretions on their bodies. We developed a method to directly measure these insect-triggered rupture forces by analyzing the trichome stalk deflections during these interactions, which yielded forces of the same order of magnitude as our micropipette measurements. These findings demonstrate how rapid gland bursting and the fluid dynamics of glandular secretions act as an efficient and swift plant defense mechanism against insect herbivory.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitogen-activated protein kinase 7 phosphorylates transcription factor ZmWRKY104 to enhance salt tolerance in maize.","authors":"Jing Li, Chen Zhang, Yadan Miao, Yang Xiang, Aying Zhang","doi":"10.1093/jxb/eraf253","DOIUrl":"https://doi.org/10.1093/jxb/eraf253","url":null,"abstract":"<p><p>Salt stress is a main environmental factor that severely constrains plant growth, development, and productivity. Our recent study showed that WRKY transcription factor ZmWRKY104 activated ZmSOD4 expression and improved maize salt tolerance. However, the upstream regulator of ZmWRKY104-ZmSOD4 module in salt response is unknown. Here, we identified a mitogen-activated protein kinase ZmMAPK7, as an upstream regulator of ZmWRKY104 in salt stress response, which physically interacts with ZmWRKY104 in vitro and in vivo. ZmMAPK7 enhances the salt tolerance of maize by increasing superoxide dismutase (SOD) activity to reduce the accumulation of superoxide anion (O2·-) generation. Genetic analysis showed that ZmMAPK7 is dependent on ZmWRKY104 in regulating maize salt tolerance. Furthermore, ZmMAPK7 phosphorylates ZmWRKY104 at Ser-142 residue, and ZmMAPK7-mediated phosphorylation of ZmWRKY104 enhances its ability to bind to ZmSOD4 promoter, thereby improving salt tolerance in maize. This study elucidates a novel mechanism by which the ZmMAPK7 functions upstream of ZmWRKY104 to positively regulate salt tolerance in maize.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}