Shifa Shaffique, Muhammad Farooq, Arjun Adhikari, Muhammad Aaqil Khan, Sang-Mo Kang, In-Jung Lee
{"title":"Genomic and Functional Insights Into Bacillus cereus SH-10 for Mitigating Lead Stress in Soybean.","authors":"Shifa Shaffique, Muhammad Farooq, Arjun Adhikari, Muhammad Aaqil Khan, Sang-Mo Kang, In-Jung Lee","doi":"10.1111/pce.70052","DOIUrl":"https://doi.org/10.1111/pce.70052","url":null,"abstract":"<p><p>Beneficial microbes serve as powerful biological tools for enhancing stress tolerance in crops. This study aimed to isolate stress-tolerant, plant growth-promoting bacterium, characterise it using high-throughput next-generation sequencing and expression profiling and assess its potential in improving soybean (Glycine max (L.) Merr.) growth and development under lead (Pb) stress. We identified Bacillus cereus SH-10 as a metal-resistant rhizobacterium capable of tolerating Pb concentrations exceeding 75 mg/kg. When inoculated into soybean plants under Pb stress, SH-10 significantly improved phosphorus and calcium uptake and reduced Pb accumulation. This reduction was associated with increased expression of the stress signalling protein GmCYP82A3. SH-10 also modulated the phytohormone balance by lowering abscisic acid (ABA) levels in shoots and enhancing salicylic acid (SA) biosynthesis. These hormonal shifts corresponded with the downregulation of ABA biosynthesis-related genes (GmNCED1, NCED3, GmbZIP) and the upregulation of the SA biosynthesis gene GmPAL1. Furthermore, SH-10 significantly mitigated oxidative stress in Pb-exposed plants, while enhancing antioxidant activities. The study also identified two phytohormone biosynthesis pathways in rhizobacteria: (1) Terpenes → β-carotene → Xanthoxin → ABA, and (2) Terpenes → Geranylgeranyl diphosphate → gibberellic acid. These findings highlight Bacillus cereus SH-10 as a promising biofertiliser that alleviates Pb toxicity in crops.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551538","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}
Pietro Zocca, Eva van Doore, Alwin J.M. Roovers, Joris J. Glas, Maarten Uittenbogaard, Maarten G. Verlaan, Zeger van Herwijnen, Michel A. Haring, Robert C. Schuurink
{"title":"Glandless, a tomato HD-ZIP transcription factor, is important for the gland formation of type VI trichomes","authors":"Pietro Zocca, Eva van Doore, Alwin J.M. Roovers, Joris J. Glas, Maarten Uittenbogaard, Maarten G. Verlaan, Zeger van Herwijnen, Michel A. Haring, Robert C. Schuurink","doi":"10.1111/tpj.70308","DOIUrl":"https://doi.org/10.1111/tpj.70308","url":null,"abstract":"<p>Tomato (<i>Solanum lycopersicum</i>) is a model plant to study glandular trichome development and their specialized metabolism, and several transcription factors (TF) regulating these intertwined traits and their network have been functionally characterized. Among them are members of the homeodomain leucine zipper subfamily IV (HD-ZIP IV). Here, we study a tomato EMS-mutant line, <i>glandless</i>, presenting mutant, glandless type VI trichomes with a consequential reduction in volatile terpene levels. This mutant trichome also has some morphological characteristics of a type IV trichome. The <i>glandless</i> mutant has altered trichome densities, and acylsugar biosynthesis is slightly increased. As verified via virus-induced gene silencing (VIGS), the gene underlying this phenotype is SlHDZ38, the first member of HD-ZIP subfamily I found to regulate the development and specialized metabolism of glandular trichomes. Additionally, we show that the expression of an intricate network of known trichome-related regulatory TFs and biosynthetic enzymes is affected by the <i>glandless</i> mutation. Overall, our results contribute to the elucidation of the network of TFs controlling tomato trichomes.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70308","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144536796","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}
Li Cheng, Xinyi Liu, Tianzhi Rao, Weijia Xiang, Shuangshuang Dou, Ke Mao, Changhai Liu, Chao Li, Fengwang Ma, Xiaoqing Gong
{"title":"MdATG10 Is Targeted by MdbHLH155 and Delays Leaf Senescence in Apple Plants by Activating Autophagy.","authors":"Li Cheng, Xinyi Liu, Tianzhi Rao, Weijia Xiang, Shuangshuang Dou, Ke Mao, Changhai Liu, Chao Li, Fengwang Ma, Xiaoqing Gong","doi":"10.1111/pce.70053","DOIUrl":"https://doi.org/10.1111/pce.70053","url":null,"abstract":"<p><p>Leaf senescence is a type of programmed cell death characterised by irreversible physiological and biochemical changes. Autophagy, a cellular degradation pathway, plays a crucial role in regulating plant development, senescence, and resistance to environmental stresses. However, how this pathway affects leaf senescence remains incompletely understood. We showed that MdATG10 plays a negative role in leaf senescence. Following the induction of leaf senescence via dark treatment, the expression of MdATG10 was upregulated, and overexpression of MdATG10 mitigated the yellowing of leaves during the dark-induced senescence process. The opposite patterns were observed in MdATG10-silenced apple plants. Additional studies revealed that a bHLH transcription factor, MdbHLH155, can bind to the promoter of MdATG10 and activate its expression, and MdbHLH155 further accelerated the expression of MdATG10 under dark treatment. MdbHLH155 was also induced by dark-induced leaf senescence before the expression of MdATG10. Silencing of MdbHLH155 in apple plants accelerated dark-induced leaf senescence and suppressed the expression of MdATG10 and autophagy activity. In sum, our findings suggest that MdATG10 delayed leaf senescence by elevating autophagy activity, and this was positively controlled by the upstream regulator MdbHLH155, which negatively regulates dark-induced leaf senescence in apple plants.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551539","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}
Tianci Zhao, Stefanie N Vink, Xiu Jia, Alexander Erban, Stephanie Schaarschmidt, Joachim Kopka, Ellen Zuther, Krzysztof Treder, Dorota Michałowska, Rémy Guyoneaud, J Theo M Elzenga, Eléonore Attard, Joana Falcão Salles
{"title":"Unveiling Potato Cultivars With Microbiome Interactive Traits for Sustainable Agricultural Production.","authors":"Tianci Zhao, Stefanie N Vink, Xiu Jia, Alexander Erban, Stephanie Schaarschmidt, Joachim Kopka, Ellen Zuther, Krzysztof Treder, Dorota Michałowska, Rémy Guyoneaud, J Theo M Elzenga, Eléonore Attard, Joana Falcão Salles","doi":"10.1111/pce.70019","DOIUrl":"https://doi.org/10.1111/pce.70019","url":null,"abstract":"<p><p>Root traits significantly shape rhizosphere microbiomes, yet their interaction with microbes is often overlooked in plant breeding programs. Here, we propose that selecting modern cultivars based on microbiome interactive trait (MIT), such as root biomass, exudate patterns and the rhizosphere microbiome, can enhance agricultural sustainability by interacting effectively with soil microbiomes, which in turn, promotes plant growth and resistance to stress, thereby reducing reliance on synthetic crop protectants. Through a stepwise selection process (in silico and in vitro) that started with approximately 1000 potato genotypes, we chose 51 potato cultivars based on known phenotypical properties and distinct root exudate patterns. We conducted a greenhouse experiment to evaluate their capacity to interact with the soil microbiome and to assess their MIT scores. Our findings revealed that cultivars significantly influence plant growth, metabolite profiles, and rhizosphere fungal community composition. Moreover, we observed a positive correlation between microbial community diversity and root biomass. Additionally, leaf metabolites were correlated with rhizosphere bacterial composition, supporting the plant holobiont framework. Utilising z-scores, we aggregated all data related to plant growth, metabolomes, and microbiomes, creating a classification of 51 cultivars based on a gradient of MIT scores. By examining the distribution of low, intermediate, and high MIT, we identified a group of 11 potato cultivars suitable for further studies to assess their resilience and productivity under low-input production systems. This study provides an in-depth correlation between microbiome and several plant traits across 51 cultivars, offering tools to facilitate and expedite the incorporation of microbiome traits into breeding goals to support sustainable agriculture.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537600","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}
Liyun Ye, Di Zhang, Qihang Yang, Chengwei Pan, Yudan Xie, Keying Liu, Kemin Wang, Miao Liu
{"title":"Plant Sex Influences Cadmium Detoxification via Mediating Cadmium Transport and Cell Wall Modification Under Different Nitrogen Forms.","authors":"Liyun Ye, Di Zhang, Qihang Yang, Chengwei Pan, Yudan Xie, Keying Liu, Kemin Wang, Miao Liu","doi":"10.1111/pce.70050","DOIUrl":"https://doi.org/10.1111/pce.70050","url":null,"abstract":"<p><p>Although the link between cadmium (Cd) and N availability has been studied, the mechanisms of Cd transport and detoxification in dioecious plants remain underexplored. This study examined sex-specific Cd transport, accumulation, and cell wall detoxification in Populus cathayana using histochemical assays, ecophysiological measures, energy-dispersive X-ray microanalysis, and transcriptomic analyses. Bark accumulated 85% Cd in the shoots of both sexes, while leaf Cd was highest in females under NH<sub>4</sub> <sup>+</sup> supply. Root Cd accumulation was greater with NO<sub>3</sub> <sup>-</sup> than NH<sub>4</sub> <sup>+</sup>, with 40%-60% of Cd sequestrated in cell walls, more so in males. In root cell walls, 60% of Cd was bound to pectin, and 30% was sequestrated in hemicellulose 1. Females sequestrated root Cd by increasing saccharide content, while males enhanced pectin demethylation to bind Cd in cell walls, especially under NO<sub>3</sub> <sup>-</sup> supply. In females under NH<sub>4</sub> <sup>+</sup> supply, endogenous nitric oxide (NO) burst decreased root Cd uptake and cell wall accumulation. In males, endogenous NO upregulated the expression of genes related to Cd transport, detoxification, and cell wall biosynthesis. In conclusion, plant sex adjusted their Cd detoxification strategies in response to the changed soil nutrient availability. Understanding the sex-specific detoxification strategies facilitated to the engineering application to remediate heavy metal-contaminated soils.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537599","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}
Vikas Devkar, Leonidas D'Agostino, Arjun Ojha Kshetry, Yi Chen, Kaushik Ghose, Yong-Villalobos Lenin, Altafhusain B. Nadaf, V. P. Thirumalaikumar, Aleksandra Skirycz, Humira Sonah, Jianxin Ma, Robert M. Stupar, Anthony J. Miller, Luis Herrera-Estrella, Rupesh Deshmukh, Gunvant B. Patil
{"title":"Cell-type-specific response to silicon treatment in soybean leaves revealed by single-nucleus RNA sequencing and targeted gene editing","authors":"Vikas Devkar, Leonidas D'Agostino, Arjun Ojha Kshetry, Yi Chen, Kaushik Ghose, Yong-Villalobos Lenin, Altafhusain B. Nadaf, V. P. Thirumalaikumar, Aleksandra Skirycz, Humira Sonah, Jianxin Ma, Robert M. Stupar, Anthony J. Miller, Luis Herrera-Estrella, Rupesh Deshmukh, Gunvant B. Patil","doi":"10.1111/tpj.70309","DOIUrl":"https://doi.org/10.1111/tpj.70309","url":null,"abstract":"<div>\u0000 \u0000 <p>Mineral nutrient uptake and deposition profoundly influence plant development, stress resilience, and productivity. Silicon (Si), though classified as a non-essential element, significantly influences a plant's physiology, particularly in fortifying defense responses and mitigating stress. While the genetic and molecular mechanisms of Si uptake and transport are well studied in monocots, particularly rice, their role in dicot species, such as soybean, remains unclear at the cellular and molecular levels. In this study, we utilized single-nucleus RNA sequencing (snRNA-seq) to dissect cellular responses to Si accumulation in soybean leaves. We identified distinct cellular populations, including a unique Si-induced or Si-associated cell cluster within vascular cells, suggesting a specialized mechanism of Si distribution. Si treatment notably induced the expression of defense-related genes, with a pronounced enrichment in vascular cells, underscoring their pivotal role in activating plant defense mechanisms. Moreover, Si modulated the expression of genes involved in phytoalexin biosynthesis, salicylic acid, and immune receptor signaling, suggesting transcriptional priming of genes involved in defense responses. Further investigation of Si transporters revealed precise expression of an Si efflux gene in epidermal cells in response to Si treatment. We also validated the role of efflux Si transporters using a <i>Xenopus</i> oocyte assay and CRISPR/Cas9 genome editing of composite soybean plant roots. This study provides critical insights into the biotic stress regulatory networks influenced by Si treatment in soybean leaves at the single-cell level, thus laying the foundation for enhancing stress tolerance through optimized mineral nutrient uptake.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144524647","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":"Expanding the Root Economics Space With Root Nitrogen Reallocation.","authors":"Ying Zhang, Ruzhen Wang, Kaili Xue, Feike A Dijkstra, Jordi Sardans, Heyong Liu, Matthias C Rillig, Josep Peñuelas, Xingguo Han, Yong Jiang","doi":"10.1111/pce.70051","DOIUrl":"https://doi.org/10.1111/pce.70051","url":null,"abstract":"<p><p>Harnessing root nitrogen reallocation (RNR) to enhance plant productivity commences with positioning RNR in the root economics space, about which we still know little. We conducted an inclusive synthesis linking RNR to root traits, combined with a 2-year <sup>15</sup>N-labelling field experiment, to position RNR in the root economics space under acidification. RNR was negatively correlated with specific root length (SRL) and mycorrhizal colonisation in the synthesis, suggesting that RNR is a conservative trait. Sedges, grasses and forbs coordinated root traits (e.g., RD and SRL) from acquisitive to conservative and from low to high RNR reliance (and vice versa for their direct root N uptake) in the <sup>15</sup>N-tracing experiment. Along the collaboration gradient, mycorrhizal symbiosis contributed more to N acquisition in grasses and forbs than in sedges, correlating inversely with SRL but remaining orthogonal to RD and RNR, thus partially reflecting the root economics space. Specifically, sedges and forbs exhibited the lowest and highest RNR that increased and decreased with acidification, respectively. Grasses associated well with mycorrhizal fungi, showing moderate RNR and root traits. Our results demonstrated the significance of RNR in plant growth, and the need to consider RNR as a conservative trait.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525735","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}
Ana Sayago, Raúl González-Domínguez, Ángeles Fernández-Recamales
{"title":"Multi-Elemental Analysis for Geographical Tracing of Chickpeas Produced in Nearby Locations Around a Protected Geographical Indication.","authors":"Ana Sayago, Raúl González-Domínguez, Ángeles Fernández-Recamales","doi":"10.1111/pce.70047","DOIUrl":"https://doi.org/10.1111/pce.70047","url":null,"abstract":"<p><p>The multi-elemental profile has repeatedly been proposed as a reliable indicator of the geographical origin of plant-derived foods, as mineral composition accurately reflects the local soil geochemistry and environmental factors. However, this approach may fail in distinguishing specimens from nearby locations, which are expected to be exposed to similar geoclimatic conditions. Herein, we studied 70 chickpea samples collected in four southwestern Spanish provinces, two located within the Protected Geographical Indication 'Garbanzo de Escacena' (i.e., Huelva and Sevilla), as well as other two boundary areas (i.e., Cádiz and Córdoba). Then, inductively-coupled plasma mass spectrometry was employed to simultaneously determine 31 trace elements and 16 rare-earth elements. Interestingly, we found great similarities in the mineral content of chickpeas cultivated in the regions ascribed to the Protected Geographical Indication, but these could be clearly discriminated from the rest of the samples. Afterward, the application of state-of-the-art machine learning tools provided predictive models with good performance in terms of classification accuracy, sensitivity, and specificity. In conclusion, we have demonstrated that the combination of multi-elemental analysis and advanced chemometrics could be a powerful strategy for food authentication and traceability according to the geographical origin.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525737","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}
Kim-Kristine Mueller, Lukas Pfeifer, Linus Wegner, Katrin Ehlers, Birgit Classen
{"title":"New insights into bryophyte arabinogalactan-proteins from a hornwort and a moss model organism","authors":"Kim-Kristine Mueller, Lukas Pfeifer, Linus Wegner, Katrin Ehlers, Birgit Classen","doi":"10.1111/tpj.70312","DOIUrl":"https://doi.org/10.1111/tpj.70312","url":null,"abstract":"<p>Two bryophyte models, the hornwort <i>Anthoceros agrestis</i> (<i>Anthoceros</i>) and the moss <i>Physcomitrium patens</i> (<i>Physcomitrium</i>), were analyzed for the presence of arabinogalactan-proteins (AGPs), as the emergence of these signaling glycoproteins in evolution is still under debate. AGPs of both species had a galactan core structure similar to that of other bryophyte and fern AGPs, but different from angiosperm AGPs, as 1,6-linked pyranosidic galactose was almost absent. In the <i>Physcomitrium</i> AGP, furanosidic arabinose (Ara<i>f</i>) linkages were mainly terminal (10%) or 5-linked (13%), while in <i>Anthoceros</i>, terminal Ara<i>f</i> dominated (26%) and was accompanied by very low amounts of 1,3-Ara<i>f</i> and pyranosidic terminal Ara. Unusual 3-<i>O</i>-methylated pyranosidic rhamnose, which has never been detected in cell walls of angiosperms, occurred in both bryophyte AGPs (5% in <i>Anthoceros</i>, 10% in <i>Physcomitrium</i> AGP). This was comparable to AGPs of other spore-producing land plants. A bioinformatic search in the genomes of 14 bryophyte species revealed that most hornworts lack sequences encoding GPI-anchored classical AGPs. Generally, hornworts contained fewer sequences for AGP protein backbones compared with the liverwort <i>Marchantia polymorpha</i> and the moss <i>P. patens</i>. All of them comprise sequences for chimeric AGPs, and among those, surprisingly xylogen-like AGPs. Homologous sequences encoding glycosyltransferases and other enzymes involved in the synthesis and decoration of the AGP galactan framework were present in all bryophyte genomes. Immunocytochemistry of <i>Anthoceros</i> tissue detected AGPs at the plasma membrane/cell wall interface but also at the tonoplast, suggesting new functions of AGPs in bryophytes.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70312","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144519778","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":"MDR1 DNA glycosylase regulates the expression of genomically imprinted genes and Helitrons","authors":"Kaitlin Higgins, Jonathan Gent, Sarah Anderson","doi":"10.1111/tpj.70304","DOIUrl":"https://doi.org/10.1111/tpj.70304","url":null,"abstract":"<p>Targeted demethylation by DNA glycosylases (DNGs) results in differential methylation between parental alleles in the endosperm, which drives imprinted expression. Here, we performed RNA sequencing on endosperm derived from DNG mutant <i>mdr1</i> and wild-type (WT) endosperm. Consistent with the role of DNA methylation in gene silencing, we find 108 genes and 96 TEs differentially expressed (DE) transcripts that lost expression in the hypermethylated <i>mdr1</i> mutant. Compared with other endosperm transcripts, the <i>mdr1</i> targets are enriched for TEs (particularly Helitrons), and DE genes are depleted for both core genes and GO term assignments, suggesting that the majority of DE transcripts are TEs and pseudo-genes. By comparing DE genes to imprinting calls from prior studies, we find that the majority of DE genes have maternally biased expression, and approximately half of all maternally expressed genes (MEGs) are DE in this study. In contrast, no paternally expressed genes (PEGs) are DE. DNG-dependent imprinted genes are distinguished by maternal demethylation and expression primarily in the endosperm, so we also performed Enzymatic Methyl-seq on hybrids to identify maternal demethylation and utilized a W22 gene expression atlas to identify genes expressed primarily in the endosperm. Overall, approximately ⅔ of all MEGs show evidence of regulation by DNGs. Taken together, this study solidifies the role of MDR1 in the regulation of maternally expressed, imprinted genes and TEs and identifies subsets of genes with DNG-independent imprinting regulation.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70304","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144519806","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}