Plant Physiology最新文献

{"title":"Digital PCR enables direct root biomass quantification and species profiling in soil samples.","authors":"Nurbanu Shynggyskyzy,Claus K Madsen,Per L Gregersen,Jim Rasmussen,Uffe Jørgensen,Henrik Brinch-Pedersen","doi":"10.1093/plphys/kiaf276","DOIUrl":"https://doi.org/10.1093/plphys/kiaf276","url":null,"abstract":"Roots support plant growth and resilience and are a major route for carbon sequestration. Thus, the study of roots in agricultural and natural systems is essential to develop strategies to mitigate and adjust to climate change. Methods to quantify root biomass in mono- and mixed crop systems are therefore in high demand. A promising approach is to exploit the correlation between root biomass and nuclear DNA. The use of qPCR for the quantitative analysis of root samples has been reported. Here, we show how digital PCR can be used to quantify root DNA from soil samples harboring single species or species mixtures. This molecular method has several advantages over more time-consuming methods, including enhanced sensitivity and absolute quantification of target DNA, increased accuracy and reliability, and the ability to quantify roots directly from soil in different species mixtures. We developed a DNA-based digital droplet PCR (ddPCR) method for root species profiling and biomass quantification directly from soil samples under semi-field conditions. Our findings suggest that implementing this ddPCR method can substantially simplify and improve root quantification of specific species, even in crop mixtures. This method offers a more time- and labor-efficient alternative to traditional techniques (e.g., root separation or C13 labeling). The complement of primer-probe sets presented here can be continuously expanded to include additional plant species, thus broadening the scope of this DNA-based ddPCR method.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"93 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478924","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":"Functions of Arabidopsis CTP:phosphocholine cytidylyltransferase 1 in phosphatidylcholine biosynthesis and root growth.","authors":"Qiong Xiao,Daniel Bustos,Kristian M Caldo,Luis Morales-Quintana,Tao Huan,Guanqun Chen","doi":"10.1093/plphys/kiaf272","DOIUrl":"https://doi.org/10.1093/plphys/kiaf272","url":null,"abstract":"Phosphatidylcholine (PC) is a crucial membrane phospholipid involved in both cellular processes and stress responses. CTP:phosphocholine cytidylyltransferase 1 (CCT1) is considered to catalyze a key regulatory step in primary PC de novo biosynthesis, but its functions and regulation are yet to be well elucidated. This study explored the physiological functions of CCT1 in Arabidopsis (Arabidopsis thaliana) (AthCCT1) in PC biosynthesis under normal growth conditions and in root development under osmotic stress, as well as its regulation by phosphorylation. Arabidopsis cct1 knockdown cct2 knockout lines exhibited significantly decreased PC intensities under normal growth conditions and impaired root growth under osmotic stress, which was rescued by AthCCT1 overexpression. Moreover, based on our previous findings that AthCCT1 is phosphorylated at Serine 187 (S187), we further investigated how this phosphorylation affects its biochemical and biological functions. The S187D phosphomimetic protein mutant of AthCCT1 exhibited reduced lipid-induced conformational changes and decreased enzymatic activity compared to the native protein. Molecular dynamics simulations of the S187D protein mutant revealed that the auto-inhibitory region, a conserved regulatory domain across CCT enzymes, remained closer to the αE helix, maintaining a constrained interaction between them. Consistent with the results of the in vitro analyses, overexpression of AthCCT1-S187D did not rescue stress-induced short root phenotypes in cct1 knockdown cct2 knockout Arabidopsis lines. Taken together, the results revealed that AthCCT1 regulates PC biosynthesis under normal conditions and root development under osmotic stress, with its phosphorylation state at S187 playing an important role in modulating its enzymatic activity and physiological functions.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"270 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144488031","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 miR156k-SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE2 module regulates the abscisic acid receptor PYL2 during citrus fruit ripening.","authors":"Li Zhang,Chenyu Xu,Yanhui Xu,Zhenmei Cai,Zhenmei Zhao,Hanyuan Cheng,Minqiang Yin,Haijian Yang,Xianming Li,Hualin Yi,Juxun Wu","doi":"10.1093/plphys/kiaf278","DOIUrl":"https://doi.org/10.1093/plphys/kiaf278","url":null,"abstract":"Members of the microRNA156 (miR156) family play essential roles in various biological processes, yet their involvement in regulating fruit ripening in citrus remains poorly understood. In this study, we determined that the miR156k- SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 2 (SPL2) module plays an important role in regulating citrus fruit ripening. Heterologous expression of csi-miR156k in Mini-Citrus Hongkong kumquat (Fortunella hindsii) significantly promoted fruit ripening, with the same phenotype observed when SPL2 was transiently silenced. Phenotypic analysis of F. hindsii transgenic lines revealed that SPL2 is the key target gene through which miR156k regulates fruit ripening in citrus. We used DNA affinity purification sequencing (DAP-Seq) and interaction assays to identify PYRABACTIN RESISTANCE LIKE 2 (PYL2) as the downstream target gene of SPL2, showing that PYL2 is negatively regulated by SPL2. Transient expression or repression of PYL2 in F. hindsii fruit greatly altered the duration of fruit color break. Moreover, screening of a yeast two-hybrid library revealed that caffeoyl CoA methyltransferase 7 (CCoAOMT7) directly interacts with SPL2. CCoAOMT7 recruits S-adenosyl-L-homocysteine hydrolase1 (SAHH1), leading to alterations in the DNA and histone methylation levels of the PYL2 promoter. Overall, this study reveals a previously uncharacterized mechanism by which the miR156k-SPL2 module regulates citrus fruit ripening by modulating PYL2 through epigenetic regulation.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"34 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478642","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 ERF5-WOX4 transcription factor regulatory module controls mannan biosynthesis in the orchid Dendrobium officinale.","authors":"Danqi Zeng,Hongyu Shi,Jing Chen,Can Si,Jun Duan,Zhong-Jian Liu,Chunmei He","doi":"10.1093/plphys/kiaf273","DOIUrl":"https://doi.org/10.1093/plphys/kiaf273","url":null,"abstract":"Plants produce mannans, which compose a class of polysaccharides with considerable potential for health-related applications. GDP-mannose pyrophosphorylase (GMP) plays a pivotal role in mannan biosynthesis by facilitating the formation of GDP-mannose. In this study, we identified the WUSCHEL (WUS)-related homeobox (WOX) transcription factor DoWOX4 as a candidate protein that interacts with the DoGMP1 promoter in Dendrobium officinale through yeast one-hybrid library screening. We demonstrated that DoWOX4 directly binds to the DoGMP1 promoter and activates its expression. DoWOX4 overexpression significantly enhanced mannan biosynthesis, whereas silencing DoWOX4 inhibited this process. Furthermore, we found that the ethylene response factor 5 (DoERF5) binds to the DoWOX4 promoter in vitro. Subsequent analyses revealed that DoERF5 negatively regulates DoWOX4 and mannan biosynthesis. This study deepens our understanding of the regulatory mechanisms governing mannan biosynthesis in plants and provides valuable genetic resources for plant bio-breeding initiatives.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"26 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144488030","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":"Divergent pathways across vascular plant lineages drive reduced nighttime transpiration during drought.","authors":"Talitha S Pereira,Anju Manandhar,Amanda A Cardoso,Samuel C V Martins,Scott A M McAdam","doi":"10.1093/plphys/kiaf274","DOIUrl":"https://doi.org/10.1093/plphys/kiaf274","url":null,"abstract":"Stomatal closure in response to water deficit is crucial for maintaining plant water balance. While the mechanisms driving daytime stomatal closure under drought are well studied, the mechanism driving progressive declines in nighttime transpiration (Enight) during drought remains less understood. To investigate whether either abscisic acid (ABA) or declining leaf water status drives progressive declines in nighttime transpiration during drought in vascular plants, we conducted experiments using representative fern, gymnosperm, and angiosperm species, including a severe ABA-deficient mutant and tree species. These species span a spectrum of stomatal control by ABA, ranging from insensitive to endogenous ABA in the fern to reliance on ABA for stomatal closure in the herbaceous angiosperm. We found that reductions in Enight during drought are driven by hydropassive stomatal closure in ferns and gymnosperms, transitioning to ABA regulation in gymnosperms under severe stress, and are triggered by ABA in herbaceous angiosperms. In all species, the proportion of total transpiration occurring at night increased as stomata closed during the drought. The reduction of nighttime transpiration during drought appears to be a convergent stomatal response across vascular land plants but is driven by diverse regulatory mechanisms linked to evolutionary history and ecological strategy.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"187 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478644","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":"Root-derived cytokinin regulates Arabidopsis flowering time through components of the age pathway.","authors":"Isabel Bartrina,Sören Werner,Andreas Schenke,Debora Gasperini,Tomáš Werner,Thomas Schmülling","doi":"10.1093/plphys/kiaf204","DOIUrl":"https://doi.org/10.1093/plphys/kiaf204","url":null,"abstract":"The transition to flowering is governed by different pathways integrating endogenous and exogenous signals. Here, we evaluated the role of the phytohormone cytokinin (CK) in regulating Arabidopsis thaliana flowering time. By analyzing key mutants in CK metabolism, transport and signalling, we found that the hormone promotes flowering under both long-day (LD) and short-day (SD) conditions, with a stronger impact on flowering under SDs. Genetic analyses indicated that both trans- and cis-zeatin regulate the floral transition, while isopentenyladenine plays a minor role. Blocking CK export from roots and reciprocal grafting experiments revealed that root-derived CK is an important flowering signal. Perception and transmission of the CK flowering signal depended on distinct CK receptors, phosphotransmitter proteins and several B-type response regulators. Further, CK functioned through floral integrators such as OVEREXPRESSION OF CONSTANS1 (SOC1) and components of the age pathway. The CK status of plants affected the levels of the age pathway microRNAs miR156 and miR172. Cytokinin-promoted flowering required the miR156-target SQUAMOSA PROMOTER BINDING PROTEIN-LIKE15 (SPL15) and miR172, and the late-flowering phenotype of LD-grown CK-deficient plants depended on miR172-targeted APETALA2 (AP2)-like genes encoding floral repressors. Collectively, this study shows that CK regulates flowering time through the two-component signaling system and components of the age pathway, providing a genetic framework for future investigations.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"241 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478645","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 computer vision-based approach for high-throughput automated analysis of Arabidopsis seedling phenotypes.","authors":"Zhongxiang Wan,Weiji Kong,Yan Tang,Feixiang Ma,Yusi Ji,Yang Peng,Ziqiang Zhu","doi":"10.1093/plphys/kiaf275","DOIUrl":"https://doi.org/10.1093/plphys/kiaf275","url":null,"abstract":"Phenotype observations are common methodologies in plant biology studies, ranging from recording growth parameters to flowering dates. Identifying mutants or varieties with different phenotypes greatly advances our understanding of regulatory mechanisms in plant growth and development. Over the past two decades, naked-eye-based observations and manual measurements using ImageJ software have been leading approaches for recording phenotypes. However, these low-efficiency and error-prone methods have met difficulties in large-scale pipelines. Although some high-throughput imaging platforms have been commercialized, it remains challenging to efficiently, conveniently, accurately, and automatically analyze data generated by these platforms. To address this issue, we designed an automatic phenotype analysis tool. We trained a YOLOv11 (You Only Look Once version 11) model to locate Arabidopsis thaliana seedlings grown on petri dishes and developed a high-accuracy semantic segmentation model based on Swin Transformer and kernel update head, achieving a segmentation accuracy of 83.56% mIoU. By post-processing the segmentation masks, we automated the analysis of five representative seedling phenotypes: hypocotyl length, root length, root gravitropic bending angle, petiole length, and cotyledon opening rate. Compared with manual recording, our tool demonstrated high accuracy across all five phenotypes, offering a reliable and efficient solution for phenotypic analysis in plant research. Our automatic tool enables high-throughput phenotyping and will shift the traditional paradigm of phenotype recording.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"54 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478883","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":"Coordinated chromatin modifications mediated by AREB and MYB transcription factors sustain drought tolerance in Populus.","authors":"Jinghui Gao,Xiaoqian Wu,Rui Zhai,Huizi Liu,Jinfeng Zhao,Chenguang Zhou,Shuang Li,Wei Li","doi":"10.1093/plphys/kiaf271","DOIUrl":"https://doi.org/10.1093/plphys/kiaf271","url":null,"abstract":"Sustained drought tolerance in plants relies on transcriptional memory through successive stress cycles, yet the chromatin-based mechanisms underlying this memory remain unclear. Previously, we revealed that PtrMYB161 overexpression in Populus trichocarpa results in phenotypes characteristic of drought tolerance. Here, we confirm that such transgenesis instills an epigenetic path to gene transregulation for drought tolerance. PtrMYB161 binds directly to the MYB-core motif in the promoter of PtrNAC120, a drought response/tolerance gene, to recruit the histone acetyltransferase (HAT) dimer GENERAL CONTROL NON-DEREPRESSIBLE5-1-ALTERATION/DEFICIENCY IN ACTIVATION2b-3 (PtrGCN5-1-PtrADA2b-3), forming the ternary protein complex (PtrMYB161-PtrGCN5-1-PtrADA2b-3). This ternary system enables enhanced acetylation of nucleosome histone 3 lysine-9, -14, and -27 (H3K9, H3K14, and H3K27) for enriched RNA Pol II occupancy in the PtrNAC120 promoter to elevate its expression for drought tolerance. Unlike PtrAREB1-2, an important drought-inducible transcription factor that can also mediate PtrNAC120 transactivation for tolerance, PtrMYB161 expression remains unaffected by drought. However, under drought conditions, induced PtrAREB1-2 could form HAT ternary complexes, PtrAREB1-2-PtrGCN5-1-PtrADA2b-3, and bind to PtrAREB1-binding sites (ABREs) in the PtrNAC120 promoter for PtrNAC120's enhanced H3K acetylation, RNA Pol II occupancy, and transactivation for drought tolerance. PtrMYB161-PtrGCN5-1-PtrADA2b-3-mediated PtrNAC120 transactivation was induced following severe, prolonged drought stress (below 40% Relative Soil Water Content) and PtrAREB1-2-induced PtrNAC120 transactivation. Further loss- and gain-of-function transgenesis experiments in whole plants and stem differentiating xylem protoplasts suggest that, under stress, the PtrAREB1-2 regulatory system activates an ancillary regulation mediated by PtrMYB161. Our findings propose coordinated epigenetic regulations mediated by HAT complexes to jointly sustain drought tolerance in Populus.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"45 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144488028","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 trans-long-chain prenyl diphosphate synthase promotes ubiquinone 10 biosynthesis in grape.","authors":"Peipei Wang,TingTing Ren,Ruyue You,Yazheng Cao,Yang Xu,Guo Wei,Yuting Liu,Xinglong Ji,Yiran Ren,Kekun Zhang,Yongfeng Zhou,Lei Sun,Xiangpeng Leng","doi":"10.1093/plphys/kiaf268","DOIUrl":"https://doi.org/10.1093/plphys/kiaf268","url":null,"abstract":"Prenyl diphosphate synthase (PDS) plays indispensable roles in terpene biosynthesis. However, there is an ongoing debate regarding whether grape (Vitis vinifera) geranyl diphosphate synthase (VvGDS, VIT_15s0024g00850) can generate geranyl diphosphate (GPP), the precursor of monoterpene biosynthesis. Here, we demonstrated that VvGDS localizes in mitochondria and is an authentic trans-long-chain prenyl diphosphate synthase (thus, VvGDS was renamed VvPDS), which is essential for ubiquinone (UQ) biosynthesis. This finding is in contrast to the initial association of VvPDS with GDS activity related to monoterpene biosynthesis. VvPDS not only falls within the subgroup comprising mitochondrial trans-long-chain PDSs, which participate in UQ biosynthesis in other eukaryotes, but also exhibits a positive association with UQ10 content in different grape tissues. VvPDS cannot catalyze GPP biosynthesis using isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) as substrates. Furthermore, VvPDS functionally complements the yeast coq1 mutation lacking mitochondrial hexaprenyl diphosphate synthase activity and catalyzes UQ10 and UQ9 biosynthesis. Transient overexpression of VvPDS in grape leaves increased UQ10 accumulation, whereas silencing VvPDS caused an obvious reduction in UQ10 content. Similarly, the stable overexpression of VvPDS enhanced UQ10 accumulation in tobacco (Nicotiana tabacum), and these UQ10-overproducing plants exhibited improved oxidative stress tolerance, primarily through enhanced reactive oxygen species-scavenging capacity. Taken together, these findings provide biochemical and genetic evidence supporting UQ biosynthesis in grape and encourage future research to reevaluate the enzymatic functions and physiological roles of angiosperm PDSs.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"8 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478693","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":"Jasmonic Acid Oxidase (JAO): balancing growth and defense in rice.","authors":"Marcella Alves Teixeira","doi":"10.1093/plphys/kiaf266","DOIUrl":"https://doi.org/10.1093/plphys/kiaf266","url":null,"abstract":"","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512334","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}