Pub Date : 2024-08-12Epub Date: 2024-06-06DOI: 10.1016/j.xplc.2024.100984
Sergio Alan Cervantes-Pérez, Prince Zogli, Sahand Amini, Sandra Thibivilliers, Sutton Tennant, Md Sabbir Hossain, Hengping Xu, Ian Meyer, Akash Nooka, Pengchong Ma, Qiuming Yao, Michael J Naldrett, Andrew Farmer, Olivier Martin, Samik Bhattacharya, Jasper Kläver, Marc Libault
The soybean root system is complex. In addition to being composed of various cell types, the soybean root system includes the primary root, the lateral roots, and the nodule, an organ in which mutualistic symbiosis with N-fixing rhizobia occurs. A mature soybean root nodule is characterized by a central infection zone where atmospheric nitrogen is fixed and assimilated by the symbiont, resulting from the close cooperation between the plant cell and the bacteria. To date, the transcriptome of individual cells isolated from developing soybean nodules has been established, but the transcriptomic signatures of cells from the mature soybean nodule have not yet been characterized. Using single-nucleus RNA-seq and Molecular Cartography technologies, we precisely characterized the transcriptomic signature of soybean root and mature nodule cell types and revealed the co-existence of different sub-populations of B. diazoefficiens-infected cells in the mature soybean nodule, including those actively involved in nitrogen fixation and those engaged in senescence. Mining of the single-cell-resolution nodule transcriptome atlas and the associated gene co-expression network confirmed the role of known nodulation-related genes and identified new genes that control the nodulation process. For instance, we functionally characterized the role of GmFWL3, a plasma membrane microdomain-associated protein that controls rhizobial infection. Our study reveals the unique cellular complexity of the mature soybean nodule and helps redefine the concept of cell types when considering the infection zone of the soybean nodule.
{"title":"Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process.","authors":"Sergio Alan Cervantes-Pérez, Prince Zogli, Sahand Amini, Sandra Thibivilliers, Sutton Tennant, Md Sabbir Hossain, Hengping Xu, Ian Meyer, Akash Nooka, Pengchong Ma, Qiuming Yao, Michael J Naldrett, Andrew Farmer, Olivier Martin, Samik Bhattacharya, Jasper Kläver, Marc Libault","doi":"10.1016/j.xplc.2024.100984","DOIUrl":"10.1016/j.xplc.2024.100984","url":null,"abstract":"<p><p>The soybean root system is complex. In addition to being composed of various cell types, the soybean root system includes the primary root, the lateral roots, and the nodule, an organ in which mutualistic symbiosis with N-fixing rhizobia occurs. A mature soybean root nodule is characterized by a central infection zone where atmospheric nitrogen is fixed and assimilated by the symbiont, resulting from the close cooperation between the plant cell and the bacteria. To date, the transcriptome of individual cells isolated from developing soybean nodules has been established, but the transcriptomic signatures of cells from the mature soybean nodule have not yet been characterized. Using single-nucleus RNA-seq and Molecular Cartography technologies, we precisely characterized the transcriptomic signature of soybean root and mature nodule cell types and revealed the co-existence of different sub-populations of B. diazoefficiens-infected cells in the mature soybean nodule, including those actively involved in nitrogen fixation and those engaged in senescence. Mining of the single-cell-resolution nodule transcriptome atlas and the associated gene co-expression network confirmed the role of known nodulation-related genes and identified new genes that control the nodulation process. For instance, we functionally characterized the role of GmFWL3, a plasma membrane microdomain-associated protein that controls rhizobial infection. Our study reveals the unique cellular complexity of the mature soybean nodule and helps redefine the concept of cell types when considering the infection zone of the soybean nodule.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369782/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285385","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}
Pub Date : 2024-08-12Epub Date: 2024-04-30DOI: 10.1016/j.xplc.2024.100931
Daniele Del Corpo, Daniele Coculo, Marco Greco, Giulia De Lorenzo, Vincenzo Lionetti
The apoplast is one of the first cellular compartments outside the plasma membrane encountered by phytopathogenic microbes in the early stages of plant tissue invasion. Plants have developed sophisticated surveillance mechanisms to sense danger events at the cell surface and promptly activate immunity. However, a fine tuning of the activation of immune pathways is necessary to mount a robust and effective defense response. Several endogenous proteins and enzymes are synthesized as inactive precursors, and their post-translational processing has emerged as a critical mechanism for triggering alarms in the apoplast. In this review, we focus on the precursors of phytocytokines, cell wall remodeling enzymes, and proteases. The physiological events that convert inactive precursors into immunomodulatory active peptides or enzymes are described. This review also explores the functional synergies among phytocytokines, cell wall damage-associated molecular patterns, and remodeling, highlighting their roles in boosting extracellular immunity and reinforcing defenses against pests.
{"title":"Pull the fuzes: Processing protein precursors to generate apoplastic danger signals for triggering plant immunity.","authors":"Daniele Del Corpo, Daniele Coculo, Marco Greco, Giulia De Lorenzo, Vincenzo Lionetti","doi":"10.1016/j.xplc.2024.100931","DOIUrl":"10.1016/j.xplc.2024.100931","url":null,"abstract":"<p><p>The apoplast is one of the first cellular compartments outside the plasma membrane encountered by phytopathogenic microbes in the early stages of plant tissue invasion. Plants have developed sophisticated surveillance mechanisms to sense danger events at the cell surface and promptly activate immunity. However, a fine tuning of the activation of immune pathways is necessary to mount a robust and effective defense response. Several endogenous proteins and enzymes are synthesized as inactive precursors, and their post-translational processing has emerged as a critical mechanism for triggering alarms in the apoplast. In this review, we focus on the precursors of phytocytokines, cell wall remodeling enzymes, and proteases. The physiological events that convert inactive precursors into immunomodulatory active peptides or enzymes are described. This review also explores the functional synergies among phytocytokines, cell wall damage-associated molecular patterns, and remodeling, highlighting their roles in boosting extracellular immunity and reinforcing defenses against pests.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140858985","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}
Pub Date : 2024-08-12Epub Date: 2024-05-08DOI: 10.1016/j.xplc.2024.100926
Man Yu, Yongjie Kuang, Chenyang Wang, Xuemei Wu, Shaofang Li, Dawei Zhang, Wenxian Sun, Xueping Zhou, Bin Ren, Huanbin Zhou
CRISPR-mediated base editors have been widely used to correct defective alleles and create novel alleles by artificial evolution for the rapid genetic improvement of crops. The editing capabilities of base editors strictly rely on the performance of various nucleotide modification enzymes. Compared with the well-developed adenine base editors (ABEs), cytosine base editors (CBEs) and dual base editors suffer from unstable editing efficiency and patterns at different genomic loci in rice, significantly limiting their application. Here, we comprehensively examined the base editing activities of multiple evolved TadA8e variants in rice. We found that both TadA-CDd and TadA-E27R/N46L achieved more robust C-to-T editing than previously reported hyperactive hAID∗Δ, and TadA-CDd outperformed TadA-E27R/N46L. A C-to-G base editor (CGBE) engineered with TadA-CDd and OsUNG performed highly efficient C-to-G editing in rice compared with that of TadA-N46P. In addition, a dual base editor constructed with a single protein, TadDE, enabled simultaneous, highly efficient C-to-T and A-to-G editing in rice. Collectively, our results demonstrate that TadA8e derivatives improve both CBEs and dual base editors in rice, providing a powerful way to induce diverse nucleotide substitutions for plant genome editing.
CRISPR 介导的碱基编辑器已被广泛用于纠正有缺陷的等位基因,并通过人工进化创造出新的等位基因,从而实现农作物的快速遗传改良。碱基编辑器的编辑能力严格依赖于各种核苷酸修饰酶的性能。与成熟的腺嘌呤碱基编辑器(ABE)相比,胞嘧啶碱基编辑器(CBE)和双碱基编辑器在水稻不同基因组位点的编辑效率和模式不稳定,大大限制了它们的应用。在这里,我们全面考察了水稻中多个进化的 TadA8e 变体在碱基编辑中的活性。我们发现,TadA-CDd和TadA-E27R/N46L都能实现比以前报道的超活性hAID*Δ更强大的C-to-T编辑,而TadA-CDd的表现优于TadA-E27R/N46L。此外,与 TadA-N46P 相比,用 TadA-CDd 和 OsUNG 在水稻中设计的 C-G 碱基编辑器(CGBE)能进行高效的 C-G 编辑。此外,用单个蛋白 TadDE 构建的双碱基编辑器也能在水稻中同时高效编辑 C 到 T 和 A 到 G。总之,我们的研究表明,TadA8e 衍生物改进了水稻中的 CBE 和双碱基编辑器,为诱导植物基因组编辑中的多种核苷酸替换提供了有力的途径。
{"title":"Diverse nucleotide substitutions in rice base editing mediated by novel TadA variants.","authors":"Man Yu, Yongjie Kuang, Chenyang Wang, Xuemei Wu, Shaofang Li, Dawei Zhang, Wenxian Sun, Xueping Zhou, Bin Ren, Huanbin Zhou","doi":"10.1016/j.xplc.2024.100926","DOIUrl":"10.1016/j.xplc.2024.100926","url":null,"abstract":"<p><p>CRISPR-mediated base editors have been widely used to correct defective alleles and create novel alleles by artificial evolution for the rapid genetic improvement of crops. The editing capabilities of base editors strictly rely on the performance of various nucleotide modification enzymes. Compared with the well-developed adenine base editors (ABEs), cytosine base editors (CBEs) and dual base editors suffer from unstable editing efficiency and patterns at different genomic loci in rice, significantly limiting their application. Here, we comprehensively examined the base editing activities of multiple evolved TadA8e variants in rice. We found that both TadA-CDd and TadA-E27R/N46L achieved more robust C-to-T editing than previously reported hyperactive hAID∗Δ, and TadA-CDd outperformed TadA-E27R/N46L. A C-to-G base editor (CGBE) engineered with TadA-CDd and OsUNG performed highly efficient C-to-G editing in rice compared with that of TadA-N46P. In addition, a dual base editor constructed with a single protein, TadDE, enabled simultaneous, highly efficient C-to-T and A-to-G editing in rice. Collectively, our results demonstrate that TadA8e derivatives improve both CBEs and dual base editors in rice, providing a powerful way to induce diverse nucleotide substitutions for plant genome editing.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900063","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}
Pub Date : 2024-08-12Epub Date: 2024-05-07DOI: 10.1016/j.xplc.2024.100941
Ruilian Yin, Ruiying Chen, Keke Xia, Xun Xu
The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement. This developmental process incorporates a series of cell fate transitions and reprogramming. However, our understanding of cell heterogeneity and mechanisms of cell fate transition during callus induction remains quite limited. Here, we report a time-series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0, 1, and 4 days, and the construction of a detailed single-cell transcriptional atlas of the callus induction process. We identify the cell types responsible for initiating the early callus: lateral root primordium-initiating (LRPI)-like cells and quiescent center (QC)-like cells. LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia. We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells. QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration. We also identify the transcription factors that regulate QC-like cells and the gene expression signatures that are related to cell fate decisions. Overall, our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transitions during callus formation, significantly improving our understanding of callus formation.
{"title":"A single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis.","authors":"Ruilian Yin, Ruiying Chen, Keke Xia, Xun Xu","doi":"10.1016/j.xplc.2024.100941","DOIUrl":"10.1016/j.xplc.2024.100941","url":null,"abstract":"<p><p>The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement. This developmental process incorporates a series of cell fate transitions and reprogramming. However, our understanding of cell heterogeneity and mechanisms of cell fate transition during callus induction remains quite limited. Here, we report a time-series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0, 1, and 4 days, and the construction of a detailed single-cell transcriptional atlas of the callus induction process. We identify the cell types responsible for initiating the early callus: lateral root primordium-initiating (LRPI)-like cells and quiescent center (QC)-like cells. LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia. We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells. QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration. We also identify the transcription factors that regulate QC-like cells and the gene expression signatures that are related to cell fate decisions. Overall, our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transitions during callus formation, significantly improving our understanding of callus formation.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140892819","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}
Plants can shape their root microbiome to promote growth and nutrient uptake. PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) is a central regulator of phosphate signaling in rice, but whether OsPHR2 can shape the root microbiome to promote phosphorus uptake is unclear. Here, we investigate the role of OsPHR2 in recruiting microbiota for phosphorus uptake using high-throughput sequencing and metabolite analysis. OsPHR2-overexpressing (OsPHR2 OE) rice showed 69.8% greater shoot P uptake in natural soil compared with sterilized soil under high-phosphorus (HP) conditions, but there was only a 54.8% increase in the wild-type (WT). The abundance of the family Pseudomonadaceae was significantly enriched in OsPHR2 OE roots relative to those of WT rice. Compared with the WT, OsPHR2 OE rice had a relatively higher abundance of succinic acid and methylmalonic acid, which could stimulate the growth of Pseudomonas sp. (P6). After inoculation with P6, phosphorus uptake in WT and OsPHR2 OE rice was higher than that in uninoculated rice under low-phosphorus (LP) conditions. Taken together, our results suggest that OsPHR2 can increase phosphorus use in rice through root exudate-mediated recruitment of Pseudomonas. This finding reveals a cooperative contribution of the OsPHR2-modulated root microbiome, which is important for improving phosphorus use in agriculture.
{"title":"OsPHR2-mediated recruitment of Pseudomonadaceae enhances rice phosphorus uptake.","authors":"Jianping Liu, Weifeng Xu, Qian Zhang, Wencheng Liao, Liang Li, Shu Chen, Jinyong Yang, Zhengrui Wang, Feiyun Xu","doi":"10.1016/j.xplc.2024.100930","DOIUrl":"10.1016/j.xplc.2024.100930","url":null,"abstract":"<p><p>Plants can shape their root microbiome to promote growth and nutrient uptake. PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) is a central regulator of phosphate signaling in rice, but whether OsPHR2 can shape the root microbiome to promote phosphorus uptake is unclear. Here, we investigate the role of OsPHR2 in recruiting microbiota for phosphorus uptake using high-throughput sequencing and metabolite analysis. OsPHR2-overexpressing (OsPHR2 OE) rice showed 69.8% greater shoot P uptake in natural soil compared with sterilized soil under high-phosphorus (HP) conditions, but there was only a 54.8% increase in the wild-type (WT). The abundance of the family Pseudomonadaceae was significantly enriched in OsPHR2 OE roots relative to those of WT rice. Compared with the WT, OsPHR2 OE rice had a relatively higher abundance of succinic acid and methylmalonic acid, which could stimulate the growth of Pseudomonas sp. (P6). After inoculation with P6, phosphorus uptake in WT and OsPHR2 OE rice was higher than that in uninoculated rice under low-phosphorus (LP) conditions. Taken together, our results suggest that OsPHR2 can increase phosphorus use in rice through root exudate-mediated recruitment of Pseudomonas. This finding reveals a cooperative contribution of the OsPHR2-modulated root microbiome, which is important for improving phosphorus use in agriculture.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140867562","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}
Pub Date : 2024-08-12Epub Date: 2024-04-30DOI: 10.1016/j.xplc.2024.100937
Hu-Jiao Lan, Jie Ran, Wen-Xu Wang, Lei Zhang, Ni-Ni Wu, Ya-Ting Zhao, Min-Jun Huang, Min Ni, Fen Liu, Ninghui Cheng, Paul A Nakata, Jianwei Pan, Steven A Whitham, Barbara J Baker, Jian-Zhong Liu
The crosstalk between clathrin-mediated endocytosis (CME) and the autophagy pathway has been reported in mammals; however, the interconnection of CME with autophagy has not been established in plants. Here, we report that the Arabidopsis CLATHRIN LIGHT CHAIN (CLC) subunit 2 and 3 double mutant, clc2-1 clc3-1, phenocopies Arabidopsis AUTOPHAGY-RELATED GENE (ATG) mutants in both autoimmunity and nutrient sensitivity. Accordingly, the autophagy pathway is significantly compromised in the clc2-1 clc3-1 mutant. Interestingly, multiple assays demonstrate that CLC2 directly interacts with ATG8h/ATG8i in a domain-specific manner. As expected, both GFP-ATG8h/GFP-ATG8i and CLC2-GFP are subjected to autophagic degradation, and degradation of GFP-ATG8h is significantly reduced in the clc2-1 clc3-1 mutant. Notably, simultaneous knockout of ATG8h and ATG8i by CRISPR-Cas9 results in enhanced resistance against Golovinomyces cichoracearum, supporting the functional relevance of the CLC2-ATG8h/8i interactions. In conclusion, our results reveal a link between the function of CLCs and the autophagy pathway in Arabidopsis.
{"title":"Clathrin light chains negatively regulate plant immunity by hijacking the autophagy pathway.","authors":"Hu-Jiao Lan, Jie Ran, Wen-Xu Wang, Lei Zhang, Ni-Ni Wu, Ya-Ting Zhao, Min-Jun Huang, Min Ni, Fen Liu, Ninghui Cheng, Paul A Nakata, Jianwei Pan, Steven A Whitham, Barbara J Baker, Jian-Zhong Liu","doi":"10.1016/j.xplc.2024.100937","DOIUrl":"10.1016/j.xplc.2024.100937","url":null,"abstract":"<p><p>The crosstalk between clathrin-mediated endocytosis (CME) and the autophagy pathway has been reported in mammals; however, the interconnection of CME with autophagy has not been established in plants. Here, we report that the Arabidopsis CLATHRIN LIGHT CHAIN (CLC) subunit 2 and 3 double mutant, clc2-1 clc3-1, phenocopies Arabidopsis AUTOPHAGY-RELATED GENE (ATG) mutants in both autoimmunity and nutrient sensitivity. Accordingly, the autophagy pathway is significantly compromised in the clc2-1 clc3-1 mutant. Interestingly, multiple assays demonstrate that CLC2 directly interacts with ATG8h/ATG8i in a domain-specific manner. As expected, both GFP-ATG8h/GFP-ATG8i and CLC2-GFP are subjected to autophagic degradation, and degradation of GFP-ATG8h is significantly reduced in the clc2-1 clc3-1 mutant. Notably, simultaneous knockout of ATG8h and ATG8i by CRISPR-Cas9 results in enhanced resistance against Golovinomyces cichoracearum, supporting the functional relevance of the CLC2-ATG8h/8i interactions. In conclusion, our results reveal a link between the function of CLCs and the autophagy pathway in Arabidopsis.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140864370","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}
Pub Date : 2024-08-12DOI: 10.1016/j.xplc.2024.101063
Heng Zhong, Changbao Li, Wenjin Yu, Hua-Ping Zhou, Tara Lieber, Xiujuan Su, Wenling Wang, Eric Bumann, Rafaela Miranda Lunny Castro, Yaping Jiang, Wening Gu, Qingli Liu, Brenden Barco, Chengjin Zhang, Liang Shi, Qiudeng Que
Efficient genotype-independent transformation and genome editing is highly desirable for plant biotechnology research and product development efforts. We have developed a novel approach to enable fast, high-throughput and genotype-flexible Agrobacterium-mediated transformation using the important soybean crop as a test system. This new method is called GiFT (Genotype-independent Fast Transformation) and involves only a few simple steps. The method uses germinated seeds as explants and DNA delivery is achieved through Agrobacterium infection of wounded explants as in conventional in vitro-based method. Following infection, the wounded explants are incubated in liquid medium with sublethal level of selection and then directly transplanted to soil. The transplanted seedlings are then selected with herbicide spray for three weeks. The time required from initiation to fully established healthy T0 transgenic events is about 35 days. The GiFT method requires minimal in vitro manipulation or use of tissue culture media. Since the regeneration is in planta, the GiFT method is thus highly genotype flexible, which we have demonstrated via successful transformation of elite germplasms from diverse genetic backgrounds. We also show that the soybean GiFT method can be applied to both conventional binary vectors and CRISPR-Cas12a vectors for genome editing applications. T1 progeny analyses demonstrated that the events had a high inheritance rate and could be used for genome engineering applications. By minimizing the need for tissue culture, the described novel approach significantly improves operational efficiency while greatly reducing personnel and supply cost. It is the first industry-scale transformation method utilizing in planta selection in a major field crop.
对于植物生物技术研究和产品开发工作来说,不依赖基因型的高效转化和基因组编辑是非常理想的。我们开发了一种新方法,利用重要的大豆作物作为测试系统,实现快速、高通量和基因型灵活的农杆菌介导转化。这种新方法被称为 GiFT(基因型无关的快速转化),只需几个简单的步骤。该方法使用发芽的种子作为外植体,通过农杆菌感染受伤的外植体实现 DNA 的传递,这与传统的体外转化方法相同。感染后,受伤的外植体在具有亚致死选择水平的液体培养基中培养,然后直接移植到土壤中。移栽后的幼苗再喷洒除草剂进行为期三周的筛选。从启动到完全建立健康的 T0 转基因事件大约需要 35 天。GiFT 方法只需极少的体外操作或使用组织培养基。由于再生是在植物体内进行的,因此 GiFT 方法具有高度的基因型灵活性,我们已通过成功转化来自不同遗传背景的优良种质证明了这一点。我们还证明,大豆 GiFT 方法既可应用于传统的二元载体,也可应用于 CRISPR-Cas12a 载体进行基因组编辑。T1后代分析表明,这些事件具有很高的遗传率,可用于基因组工程应用。通过最大限度地减少对组织培养的需求,所述新方法显著提高了操作效率,同时大大降低了人员和供应成本。这是首个在主要大田作物中利用植物体选择的工业规模转化方法。
{"title":"A fast and genotype-independent in planta Agrobacterium-mediated transformation method for soybean.","authors":"Heng Zhong, Changbao Li, Wenjin Yu, Hua-Ping Zhou, Tara Lieber, Xiujuan Su, Wenling Wang, Eric Bumann, Rafaela Miranda Lunny Castro, Yaping Jiang, Wening Gu, Qingli Liu, Brenden Barco, Chengjin Zhang, Liang Shi, Qiudeng Que","doi":"10.1016/j.xplc.2024.101063","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101063","url":null,"abstract":"<p><p>Efficient genotype-independent transformation and genome editing is highly desirable for plant biotechnology research and product development efforts. We have developed a novel approach to enable fast, high-throughput and genotype-flexible Agrobacterium-mediated transformation using the important soybean crop as a test system. This new method is called GiFT (Genotype-independent Fast Transformation) and involves only a few simple steps. The method uses germinated seeds as explants and DNA delivery is achieved through Agrobacterium infection of wounded explants as in conventional in vitro-based method. Following infection, the wounded explants are incubated in liquid medium with sublethal level of selection and then directly transplanted to soil. The transplanted seedlings are then selected with herbicide spray for three weeks. The time required from initiation to fully established healthy T0 transgenic events is about 35 days. The GiFT method requires minimal in vitro manipulation or use of tissue culture media. Since the regeneration is in planta, the GiFT method is thus highly genotype flexible, which we have demonstrated via successful transformation of elite germplasms from diverse genetic backgrounds. We also show that the soybean GiFT method can be applied to both conventional binary vectors and CRISPR-Cas12a vectors for genome editing applications. T1 progeny analyses demonstrated that the events had a high inheritance rate and could be used for genome engineering applications. By minimizing the need for tissue culture, the described novel approach significantly improves operational efficiency while greatly reducing personnel and supply cost. It is the first industry-scale transformation method utilizing in planta selection in a major field crop.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141977168","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}
Pub Date : 2024-08-12Epub Date: 2024-05-08DOI: 10.1016/j.xplc.2024.100942
Zeng-Yuan Wu, Mark A Chapman, Jie Liu, Richard I Milne, Ying Zhao, Ya-Huang Luo, Guang-Fu Zhu, Marc W Cadotte, Ming-Bao Luan, Peng-Zhen Fan, Alex K Monro, Zhi-Peng Li, Richard T Corlett, De-Zhu Li
Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.
{"title":"Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop.","authors":"Zeng-Yuan Wu, Mark A Chapman, Jie Liu, Richard I Milne, Ying Zhao, Ya-Huang Luo, Guang-Fu Zhu, Marc W Cadotte, Ming-Bao Luan, Peng-Zhen Fan, Alex K Monro, Zhi-Peng Li, Richard T Corlett, De-Zhu Li","doi":"10.1016/j.xplc.2024.100942","DOIUrl":"10.1016/j.xplc.2024.100942","url":null,"abstract":"<p><p>Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140892823","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}
In angiosperms, the pollen tube enters the receptive synergid cell, where it ruptures to release its cytoplasm along with two sperm cells. This interaction is complex, and the exact signal transducers that trigger the bursting of pollen tubes are not well understood. In this study, we identify three homologous receptor-like cytoplasmic kinases (RLCKs) expressed in pollen tubes of Arabidopsis, Delayed Burst 1/2/3 (DEB1/2/3), which play a crucial role in this process. These genes produce proteins localized on the plasma membrane, and their knockout causes delayed pollen tube burst and entrance of additional pollen tubes into the embryo sac due to fertilization recovery. We show that DEBs interact with the Ca2+ pump ACA9, influencing the dynamics of cytoplasmic Ca2+ in pollen tubes through phosphorylation. These results highlight the importance of DEBs as key signal transducers and the critical function of the DEB-ACA9 axis in timely pollen tube burst in synergids.
{"title":"Pollen-expressed RLCKs control pollen tube burst.","authors":"Yin-Jiao Xu, Ting Luo, Peng-Min Zhou, Wei-Qi Wang, Wei-Cai Yang, Hong-Ju Li","doi":"10.1016/j.xplc.2024.100934","DOIUrl":"10.1016/j.xplc.2024.100934","url":null,"abstract":"<p><p>In angiosperms, the pollen tube enters the receptive synergid cell, where it ruptures to release its cytoplasm along with two sperm cells. This interaction is complex, and the exact signal transducers that trigger the bursting of pollen tubes are not well understood. In this study, we identify three homologous receptor-like cytoplasmic kinases (RLCKs) expressed in pollen tubes of Arabidopsis, Delayed Burst 1/2/3 (DEB1/2/3), which play a crucial role in this process. These genes produce proteins localized on the plasma membrane, and their knockout causes delayed pollen tube burst and entrance of additional pollen tubes into the embryo sac due to fertilization recovery. We show that DEBs interact with the Ca<sup>2+</sup> pump ACA9, influencing the dynamics of cytoplasmic Ca<sup>2+</sup> in pollen tubes through phosphorylation. These results highlight the importance of DEBs as key signal transducers and the critical function of the DEB-ACA9 axis in timely pollen tube burst in synergids.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140867212","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}