Na Li, Hailan Wang, Jiayin Wen, Xiangling Liu, Meng Zhang
{"title":"A method for maintaining the release of co-suppression and maximally restoring the RDR6 expression.","authors":"Na Li, Hailan Wang, Jiayin Wen, Xiangling Liu, Meng Zhang","doi":"10.1007/s00299-025-03508-8","DOIUrl":"10.1007/s00299-025-03508-8","url":null,"abstract":"<p><strong>Key message: </strong>Tissue-specific RDR6 compensation rescues Arabidopsis defects while maintaining seed polyunsaturated fatty acid accumulation, balancing co-suppression relief and key trait retention for modular engineering. The transgene-induced co-suppression of fatty acid desaturase 2 (FAD2) can be effectively released in rdr6 mutant, enabling a significant increase in polyunsaturated fatty acid (PUFA) content in seeds. However, the global suppression of RNA-dependent RNA polymerase 6 (RDR6) compromises plant growth and disease resistance. To address this limitation, we developed a spatiotemporal compensation strategy by restoring RDR6 expression in non-seed tissues using tissue-specific promoters while maintaining its low expression during seed maturation. To implement this goal, we identified P<sub>BnTC06</sub>, a Brassica napus promoter, through transcriptomic data mining and functional characterization. GUS staining revealed that the P<sub>BnTC06</sub> promoter drives strong gene expression in vegetative tissues (e.g., leaves, stems, and flowers) but exhibits negligible activity in mid- to late-stage-developing seeds. We introduced P<sub>BnTC06</sub>::RDR6 into Pha::AtFAD2/rdr6-11, the previously established high- PUFA Arabidopsis line. This intervention rescued the rdr6 mutant phenotype (characterized by gracile, downward-curling leaves) to wild-type morphology and restored RDR6 expression across non-seed tissues, while maintaining minimal expression in middle and late developing seeds. Crucially, FAD2 transcript levels remained at a high level during late seed development, resulting in sustained high PUFA accumulation in mature seeds. This strategy establishes a practical strategy to circumvent transgene co-suppression and proposes a modular framework for precision breeding of complex traits in crops.</p>","PeriodicalId":20204,"journal":{"name":"Plant Cell Reports","volume":"44 6","pages":"118"},"PeriodicalIF":5.3,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042013","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":"Distinct actin microfilament localization during early cell plate formation through deep learning-based image restoration.","authors":"Suzuka Kikuchi, Takumi Kotaka, Yuga Hanaki, Minako Ueda, Takumi Higaki","doi":"10.1007/s00299-025-03498-7","DOIUrl":"10.1007/s00299-025-03498-7","url":null,"abstract":"<p><strong>Key message: </strong>Using deep learning-based image restoration, we achieved high-resolution 4D imaging with minimal photodamage, revealing distinct localization and suggesting Lifeact-RFP-labeled actin microfilaments play a role in initiating cell plate formation. Phragmoplasts are plant-specific intracellular structures composed of microtubules, actin microfilaments (AFs), membranes, and associated proteins. Importantly, they are involved in the formation and the expansion of cell plates that partition daughter cells during cell division. While previous studies have revealed the important role of cytoskeletal dynamics in the proper functioning of the phragmoplast, the localization and the role of AFs in the initial phase of cell plate formation remain controversial. Here, we used deep learning-based image restoration to achieve high-resolution 4D imaging with minimal laser-induced damage, enabling us to investigate the dynamics of AFs during the initial phase of cell plate formation in transgenic tobacco BY-2 cells labeled with Lifeact-RFP or RFP-ABD2 (actin-binding domain 2). This computational approach overcame the limitation of conventional imaging, namely laser-induced photobleaching and phototoxicity. The restored images indicated that RFP-ABD2-labeled AFs were predominantly localized near the daughter nucleus, whereas Lifeact-RFP-labeled AFs were found not only near the daughter nucleus but also around the initial cell plate. These findings, validated by imaging with a long exposure time, highlight distinct localization patterns between the two AF probes and suggest that Lifeact-RFP-labeled AFs play a role in initiating cell plate formation.</p>","PeriodicalId":20204,"journal":{"name":"Plant Cell Reports","volume":"44 6","pages":"115"},"PeriodicalIF":5.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12058911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143980659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fatma Salem, Ahmed ElGamal, Zujian Zhang, Weiwen Kong
{"title":"Integrative multi-transcriptomic analysis uncovers core genes and potential defense mechanisms in rice-Magnoporthe oryzae interaction.","authors":"Fatma Salem, Ahmed ElGamal, Zujian Zhang, Weiwen Kong","doi":"10.1007/s00299-025-03490-1","DOIUrl":"10.1007/s00299-025-03490-1","url":null,"abstract":"<p><strong>Key message: </strong>Multiple transcriptomic comprehensive analyses highlight key genes and cast new light on multifaceted pathways that may be important arenas in rice innate immunity against Magnoporthe oryzae blast disease. Magnaporthe oryzae (MOR) poses a significant threat to rice production worldwide. However, defense mechanisms in rice against MOR remain inadequately defined. In this study, a multi-transcriptomic integrative analysis on 441 samples from diverse microarrays and RNA-seq sets was conducted to reveal critical factors in rice defense against MOR infection. A robust pattern of 3534 upregulated genes and 2920 repressed genes was commonly identified across all MOR-infected arrays and RNA-seq profiles. Interestingly, enrichment analysis revealed a consistent triggering of endoplasmic reticulum (ER)-related mechanisms and citric acid cycle (TCA) influx in rice response to MOR infection across all the transcriptome profiles, suggesting their critical role in modulating rice immunity against the pathogen. By contrast, chloroplast and photosynthesis pathways were frequently repressed across all the profiles. Among ER-related mechanisms, the phagosome pathway involved in the activation of NADPH oxidase was highly triggered in early response to MOR infection. Moreover, WGCNA analysis highlighted four key co-expressed gene modules and 80 significant hub genes associated with MOR infection. Among the core genes, Sec61 gene involved in the ER-translocation process was identified along with OsMFP (peroxisomal oxidation gene) and OSAHH gene (involved in cyclic-trans-methylation). Furthermore, MPK6, WRKY24, NUP35, and NPR1 genes were observed as core co-expressed genes, suggesting their significance in regulating rice immunity against MOR. Our findings elucidate key genes and multifaceted mechanisms in rice-MOR interaction, proposing new informative clues that can be exploited to improve rice resistance against blast disease.</p>","PeriodicalId":20204,"journal":{"name":"Plant Cell Reports","volume":"44 6","pages":"114"},"PeriodicalIF":5.3,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040787","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}
Sarah Muniz Nardeli, Ana Luiza Atella de Freitas, Luis Willian Pacheco Arge, Leonardo Lima Pepino Macedo, Marcelo Ribeiro-Alves, Régis Lopes Corrêa, Maria Fatima Grossi-de-Sa, Marcio Alves-Ferreira
{"title":"Blooming resilience: transcriptomic insights into cotton flower responses to boll weevil infestation.","authors":"Sarah Muniz Nardeli, Ana Luiza Atella de Freitas, Luis Willian Pacheco Arge, Leonardo Lima Pepino Macedo, Marcelo Ribeiro-Alves, Régis Lopes Corrêa, Maria Fatima Grossi-de-Sa, Marcio Alves-Ferreira","doi":"10.1007/s00299-025-03503-z","DOIUrl":"10.1007/s00299-025-03503-z","url":null,"abstract":"<p><strong>Key message: </strong>Cotton plants undergo a drastic transcriptional reprogramming after cotton boll weevil infestation, modulating several defense pathways to cope with the damage. The global demand for cotton fiber continues to rise, but pests and pathogens significantly hinder cotton production, causing substantial losses. Among these, the cotton boll weevil (Anthonomus grandis) is one of the most destructive pests. To investigate the molecular responses of cotton (Gossypium hirsutum) to boll weevil infestation, we evaluated the global gene expression of floral buds using mRNA-seq. Additionally, we analyzed the expression of non-coding RNAs, including microRNAs (miRNAs) and long intergenic non-coding RNAs (lincRNAs). Infestation by cotton boll weevil larvae triggered a rapid and drastic transcriptional reprogramming, with 1,656 and 1.698 genes modulated after two and twelve hours, respectively. Gene ontology enrichment analysis revealed significant regulation of defense-related and developmental processes, including photosynthesis, primary metabolism, and cell organization. Transcription factor families such as ERF, WRKY, GRAS, and NAC were strongly affected, highlighting their roles in coordinating defense responses. The jasmonate pathway showed intensive modulation, alongside secondary metabolite pathways like terpenoids and phenylpropanoids, which contribute to plant defense mechanisms. Non-coding RNAs also played a critical role in the response. We identified 921 unique known and novel miRNAs, with 36 modulated by the infestation, and predicted 98,850 putative lincRNAs, several of which were differentially expressed. Understanding the genetic and molecular mechanisms underlying cotton's defense against boll weevil, particularly during early infestation stages, is vital for developing biotechnological strategies to reduce pest damage. Our findings provide critical insights to enhance cotton resilience against herbivores.</p>","PeriodicalId":20204,"journal":{"name":"Plant Cell Reports","volume":"44 6","pages":"113"},"PeriodicalIF":5.3,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144026379","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}
Jing-Jing Yu, Shiling Deng, Jinhui Mo, Han Huang, Zeng-Fu Xu, Yi Wang
{"title":"Functional analysis of the woody oil crop Plukenetia volubilis L. LEC2 homolog PvoB3-69 in promoting regeneration.","authors":"Jing-Jing Yu, Shiling Deng, Jinhui Mo, Han Huang, Zeng-Fu Xu, Yi Wang","doi":"10.1007/s00299-025-03493-y","DOIUrl":"https://doi.org/10.1007/s00299-025-03493-y","url":null,"abstract":"<p><strong>Key message: </strong>Identified a robust regeneration-related genomic sequence of PvoB3-69 from the B3 superfamily in Plukenetia volubilis. gPvoB3-69-assisted transformation of P. volubilis obtained transgenic shoots for the first time. The regenerative capacity of host cells is critical for the genetic transformation efficiency of woody plants. The B3 superfamily is particularly involved in early embryo morphogenesis and late-stage embryo maturation. In this study, 74 PvoB3 members were identified in the genome of P. volubilis, and classified into four subfamilies: LAV, RAV, ARF, and REM. RNA-seq and RT-qPCR analyses revealed that PvoB3-69, a member of the LAV subfamily, has specific expression patterns similar with LEC2. Overexpression of gPvoB3-69 enhanced the bud regeneration capacity of transgenic Nicotiana benthamiana organs during in vitro culture. Additionally, overexpression of gPvoB3-69 significantly improved somatic embryogenesis in transgenic Arabidopsis plants, especially with the aid of 2,4-D. Transcriptome analysis in Arabidopsis thaliana revealed that PvoB3-69 may enhance somatic embryo induction efficiency by activating developmental regulators such as WUS and LEC1, while also modulating salicylic acid, ABA, and ethylene metabolism. Furthermore, overexpression of gPvoB3-69 in the cotyledons of P. volubilis increased the regeneration ability of host cells, and broke the genetic transformation barrier through the Agrobacterium-mediated method, allowing the regenerated transgenic shoots obtained for the first time. This study provides the first systematic analysis of the B3 superfamily in P. volubilis, identifying PvoB3-69 as a key regulator of regeneration. These findings establish a foundation for further comprehensive studies of PvoB3 genes and deepen our understanding of the regulatory mechanism of shoot regeneration in P. volubilis.</p>","PeriodicalId":20204,"journal":{"name":"Plant Cell Reports","volume":"44 5","pages":"112"},"PeriodicalIF":5.3,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144012361","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}
Qian Xu, Jinxin Gan, Zhikang Zhou, Tao Zhou, Rui Lu, Ningfang Liu, Longxing Hu
{"title":"Dynamic transcriptomics and physiological insights reveal multi-tissue salt adaptation mechanisms in Amaranthus hypochondriacus across stress gradients.","authors":"Qian Xu, Jinxin Gan, Zhikang Zhou, Tao Zhou, Rui Lu, Ningfang Liu, Longxing Hu","doi":"10.1007/s00299-025-03506-w","DOIUrl":"https://doi.org/10.1007/s00299-025-03506-w","url":null,"abstract":"<p><strong>Key message: </strong>Transcriptomic and physiological analyses identified key salt-responsive pathways and genes in Amaranthus hypochondriacus under 100/250 mM NaCl stress. Soil salinization critically threatens crop productivity, necessitating the exploration of salt-tolerant species. Amaranthus hypochondriacus, recognized as a salt-tolerant grain species, exhibits distinct adaptive mechanisms under moderate (100 mM NaCl) and severe (250 mM NaCl) salinity based on the integrated physiological and multi-tissue transcriptomic analyses. Under moderate salt stress, physiological and transcriptomic analyses revealed three key tolerance strategies: rapid ABA signaling activation (e.g., NCED [9-cis-epoxycarotenoid dioxygenase] upregulation within 6 h exposure to salt stress), sustained leaf ion homeostasis (unchanged leaf Na⁺/K⁺ ratio), and tenfold root proline accumulation. Severe stress triggered osmotic imbalance (89% reduced stomatal conductance), ionic toxicity (24-fold elevated leaf Na⁺/K⁺ ratio), and oxidative damage (fivefold elevated leaf relative electrical conductivity) despite upregulated glutathione biosynthesis. Notably, A. hypochondriacus uniquely maintained DNA stability via enriched DNA repair pathways (e.g., homologous recombination) and transcriptional induction of replication-related gene. The WGCNA analysis identified multiple salt tolerance-associated key candidate genes, including the proline biosynthesis genes (P5CS [pyrroline-5-carboxylate synthetase] and P5CR [pyrroline-5-carboxylate reductase]), as well as the ion transporter genes (NHX [Na<sup>+</sup>/K<sup>+</sup> antiporter] for sequestration of Na<sup>+</sup> into vacuoles and SOS1 [Salt Overly Sensitive 1] for extrusion of Na⁺ out of cells). Clustering of 1,578 transcription factors (TFs) identified six expression clusters, with root-specific ERF/MYB activation and leaf-enriched WRKY/C3H induction. This study elucidated the conserved salt tolerance strategies of grain amaranths, emphasizing its dual-phase adaptation: osmotic/ionic homeostasis under moderate stress and DNA stability maintenance under severe stress, orchestrated by lineage-specific TF networks. These findings provide critical insights for improving crop resilience in saline environments.</p>","PeriodicalId":20204,"journal":{"name":"Plant Cell Reports","volume":"44 5","pages":"111"},"PeriodicalIF":5.3,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143976183","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":"MhIDA small peptides modulate the growth and development of roots in Malus hupehensis.","authors":"Ruirui Xu, Shuna Jiang, Hongjuan Ge, Buhang Zhang, Jing Shu, Tianpeng Zhang, Lijun Cao, Shizhong Zhang","doi":"10.1007/s00299-025-03492-z","DOIUrl":"https://doi.org/10.1007/s00299-025-03492-z","url":null,"abstract":"<p><strong>Key message: </strong>MhIDA small peptides promote apple root growth by enhancing auxin synthesis and cell wall remodeling gene expression, revealing a peptide-based strategy to improve root architecture. Although small peptides have been well documented as crucial regulators of plant growth and development, the molecular mechanisms underlying lateral root morphogenesis in Malus hupehensis remain poorly understood. In this research, exogenous application of 1 µM MhIDA-Like family peptides increased primary root (PR) length by 14.31-19.96% and lateral root (LR) number by 124.54-149.08%. MhIDA, predominant expression in the root tip and lateral root primordium, demonstrated the most substantial promoting effects on PR elongation, LR number and density when the treatment concentration reached 1 µM. Furthermore, similar effects were found in MhIDA-overexpression transgenic apple seedlings, with the number and density of transgenic LRs increase by 80.52 and 126.86%, respectively, compared with wild-type seedlings. More importantly, 1 µM MhIDA treatment induced significant hormonal alterations, with the content of auxin, salicylic acid and gibberellic acid increasing by 1.5-fold, 1.4-fold, and 2.1-fold, respectively, compared to control. The qRT-PCR results showed that MhIDA could induce the expression of auxin synthesis genes (MhTAA1 and MhYUCC1) that were up-regulated by about twofold, and the cell wall remodeling-related genes (MhEXP17, MhXTR6, MhPGAZAT and MhPGLR) were upregulated by about 2- to 4-fold after 1 µM MhIDA treatment, thereby regulating LR emergence and formation of Malus hupehensis. Overall, these findings suggested the MhIDA peptide can promote the growth and development of roots, laying the foundation for cultivating apple rootstocks with strong roots and higher resistance to abiotic stress.</p>","PeriodicalId":20204,"journal":{"name":"Plant Cell Reports","volume":"44 5","pages":"110"},"PeriodicalIF":5.3,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144025123","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":"Transcriptomics-proteomics analysis reveals StCOMT1 regulates drought, alkali and combined stresses in potato.","authors":"Ruyan Zhang, Yong Wang, Yichen Kang, Yunyun Du, Xingxing Wang, Shujuan Jiao, Xinyu Yang, Yuhui Liu, Shuhao Qin, Weina Zhang","doi":"10.1007/s00299-025-03496-9","DOIUrl":"https://doi.org/10.1007/s00299-025-03496-9","url":null,"abstract":"<p><strong>Key message: </strong>Transcriptome proteome association analysis screened candidate DEGs, DEPs, and DEGs/DEPs associated with potato response to drought, alkali, and combined stresses. Overexpression of StCOMT1 enhances potato drought and alkali tolerance. Drought and salinity have severely impeded potato (Solanum tuberosum L.) growth and development, significantly reducing global potato production. However, the molecular mechanisms regulating the combined drought and alkali stress process are not fully understood. This study compared the mRNA and protein expression profiles of potato under drought (PEG-6000), alkali (NaHCO<sub>3</sub>), and combined (PEG-6000 + NaHCO<sub>3</sub>) stresses by transcriptome and TMT proteomics sequencing to investigate the common or specific responses of 'Atlantic' potato to single and combined stresses of drought and alkali were preliminarily explored. It was found that 2215 differentially expressed genes (DEGs) and 450 differentially expressed proteins (DEPs) were jointly identified under drought, alkali, and combined stresses. Under drought, alkali, and combined stresses, 234, 185, and 246 DEGs/DEPs were identified, respectively. These DEGs, DEPs, and DEGs/DEPs identified revealed the potential roles of several signaling and metabolic pathways in mediating drought and alkali stress tolerance, including plant hormone signaling, MAPK signaling pathway, phenylpropanoid biosynthesis, and glutathione metabolism. Caffeic acid-O-methyltransferase (COMT) is an essential methylating enzyme in the phenylpropane biosynthetic pathway, which is involved in lignin synthesis and plays an important role in protecting plants from abiotic stresses. In this study, we investigated the changes in physiologic characteristics, such as growth, antioxidant defense, osmotic regulation and lignin accumulation, in overexpressing StCOMT1 (PT0001512/M0ZIL7) transgenic potato after stress. It proved that the gene has the function of adapting to drought and alkali stress, and provided a theoretical basis for further research on the resistance mechanism of the gene in drought and alkali tolerance in potato.</p>","PeriodicalId":20204,"journal":{"name":"Plant Cell Reports","volume":"44 5","pages":"109"},"PeriodicalIF":5.3,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020007","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}