Plant Biotechnology Journal最新文献

{"title":"A system genetics analysis uncovers the regulatory variants controlling drought response in wheat","authors":"Bin Chen, Yuling Liu, Yanyan Yang, Qiannan Wang, Shumin Li, Fangfang Li, Linying Du, Peiyin Zhang, Xuemin Wang, Shuangxing Zhang, Xiaoke Zhang, Zhensheng Kang, Xiaojie Wang, Hude Mao","doi":"10.1111/pbi.14605","DOIUrl":"https://doi.org/10.1111/pbi.14605","url":null,"abstract":"Plants activate a variable response to drought stress by modulating transcription of key genes. However, our knowledge of genetic variations governing gene expression in response to drought stress remains limited in natural germplasm. Here, we performed a comprehensive analysis of the transcriptional variability of 200 wheat accessions in response to drought stress by using a systems genetics approach integrating pan-transcriptome, co-expression networks, transcriptome-wide association study (TWAS), and expression quantitative trait loci (eQTLs) mapping. We identified 1621 genes and eight co-expression modules significantly correlated with wheat drought tolerance. We also defined 620 664 and 654 798 independent eQTLs associated with the expression of 17 429 and 18 080 eGenes under normal and drought stress conditions. Focusing on dynamic regulatory variants, we further identified 572 eQTL hotspots and constructed transcription factors governed drought-responsive network by the XGBoost model. Subsequently, by combining with genome-wide association study (GWAS), we uncovered a 369-bp insertion variant in the <i>TaKCS3</i> promoter containing multiple <i>cis</i>-regulatory elements recognized by eQTL hotspot-associated transcription factors that enhance its transcription. Further functional analysis indicated that elevating <i>TaKCS3</i> expression affects cuticular wax composition to reduce water loss during drought stress, and thereby increase drought tolerance. This study sheds light on the genome-wide genetic variants that influence dynamic transcriptional changes during drought stress and provides a valuable resource for the mining of drought-tolerant genes in the future.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"2 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462434","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":"Lysine deacetylase TaSRT1 mediates wheat drought tolerance by deacetylating TaDT-A to reduce its protein stability and transcriptional activity","authors":"Shumin Chang, Qun Yang, Wei Chu, Xingbei Liu, Jinpeng Li, Zehui Liu, Jingchen Lin, Debiao Liu, Danyang Zhao, Xiao Peng, Mingming Xin, Yingyin Yao, Xiaodong Xie, Huiru Peng, Zhongfu Ni, Qixin Sun, Zhaorong Hu","doi":"10.1111/pbi.14613","DOIUrl":"https://doi.org/10.1111/pbi.14613","url":null,"abstract":"Drought is one of the major environmental stresses limiting crop growth and yield. Epigenetic regulations play crucial roles in plant adaptation to environmental changes, whereas the epigenetic mechanism of drought resistance in crops remains largely elusive. Here, we report that the nicotinamide adenine dinucleotide (NAD⁺)-dependent deacetylase TaSRT1 negatively regulates drought tolerance in wheat. Compared with the wild type, the <i>tasrt1</i> mutant had higher relative water contents, along with a smaller stomatal aperture and improved water use efficiency under drought conditions, whereas <i>TaSRT1</i> overexpression plants exhibited opposite phenotypes. TaSRT1 directly interacted with the drought-resistant pivotal factor TaDT-A to regulate its protein stability and transcriptional activity through lysine deacetylation. Furthermore, the key lysine residue of TaDT-A was identified as a deacetylation/acetylation site that plays an important role in regulating its stability. In addition, genetic analysis indicated TaDT-A functions downstream of TaSRT1 to modulate drought resistance. These findings uncover how the functional interplay between epigenetic regulator and transcription factors regulates drought resistance in plants, and illustrate a mechanism by which lysine deacetylase affects gene transcription via influencing non-histone protein acetylation and regulating their function.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"25 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462433","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":"Generation of suspension cell cultures with high syringin content and anti‐inflammatory activity through overexpressing glycotransferase SiUGT72BZ2 in Saussurea involucrata","authors":"Yue Xu, Yingping Cao, Fangfang Tie, Xiuya Kong, Yuchen Liu, Yaru Zhang, Wenna Guan, Na Hu, Honglun Wang, Xiaochun Qin, Zhenying Wu, Chunxiang Fu","doi":"10.1111/pbi.70001","DOIUrl":"https://doi.org/10.1111/pbi.70001","url":null,"abstract":"SummaryThe snow lotus species <jats:italic>Saussurea involucrata</jats:italic> (Kar. &amp; Kir.) Sch.Bip., an endangered traditional Chinese herb, belongs to a genus of the Asteraceae family. Syringin present in <jats:styled-content style=\"fixed-case\"><jats:italic>S. involucrata</jats:italic></jats:styled-content> stands as one of the predominant bioactive compounds. However, the biosynthetic pathway of syringin remains largely elusive. Here, <jats:styled-content style=\"fixed-case\"><jats:italic>S. involucrata</jats:italic></jats:styled-content> suspension cell culture was subjected to methyl jasmonate (MeJA) treatment, which stimulated the synthesis of syringin, increasing its content by up to 3.9‐fold. Comparative transcriptome analysis revealed that genes involved in syringin biosynthesis were generally upregulated in response to MeJA. Furthermore, two candidate UDP‐glycosyltransferase genes, <jats:italic>SiUGT72BZ2</jats:italic> and <jats:italic>SiUGT72CY1</jats:italic>, were identified through phylogenetic tree and expression profiling analyses. Overexpression of <jats:italic>SiUGT72BZ2</jats:italic> (BZ2_OE) and <jats:italic>SiUGT72CY1</jats:italic> (CY1_OE) in <jats:styled-content style=\"fixed-case\"><jats:italic>S. involucrata</jats:italic></jats:styled-content> suspension cell cultures led to 15.2‐ and 5.9‐fold higher syringin levels than empty vector control cultures, respectively. Notably, upregulation of <jats:italic>SiUGT72BZ2</jats:italic> enhanced the biosynthesis of coniferin as well. In contrast, only trace amounts of coniferin were present in control and CY1_OE cell cultures. Subsequent anti‐inflammatory assays using lipopolysaccharide (LPS)‐stimulated RAW264.7 cells demonstrated that the extracts from these cell cultures possessed remarkable anti‐inflammatory properties. Most strikingly, the BZ2_OE cultures exhibited superior anti‐inflammatory effects compared to the control and CY1_OE. In conclusion, our research has not only identified the key enzymes in syringin synthesis but also, through genetic engineering, has generated novel cell culture resources enriched with syringin and coniferin, and enhanced anti‐inflammatory activities, highlighting the potential of <jats:styled-content style=\"fixed-case\"><jats:italic>S. involucrata</jats:italic></jats:styled-content> cell culture as an alternative for wild snow lotus resources.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"377 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443221","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":"Expression of endochitinase and exochitinase in lettuce chloroplasts increases plant biomass and kills fungal pathogen Candida albicans","authors":"Iqra Fatima, Geetanjali Wakade, Niaz Ahmad, Henry Daniell","doi":"10.1111/pbi.14596","DOIUrl":"https://doi.org/10.1111/pbi.14596","url":null,"abstract":"SummaryLettuce (<jats:italic>Lactuca sativa</jats:italic>) is a popular leafy vegetable with global production of ~28 million Mt, cultivated &gt;1 million hectares, with a market value of US$ 4 billion in 2022. However, lettuce is highly susceptible to fungal pathogens that drastically reduce biomass and quality due to spoilage/rot. Therefore, in this study, we investigated the expression of chitinase genes via the lettuce chloroplast genome to enhance biomass and disease resistance. Site‐specific integration of the expression cassette into chloroplast genomes was confirmed using two sets of PCR primers. Homoplasmy in transplastomic lines was confirmed in Southern blots by the absence of untransformed genomes. Maternal inheritance of transgenes was confirmed by the lack of segregation when seedlings were germinated in the selection medium. Chitinases expressed in chloroplasts are active in a broad range of pH (5–9) and temperatures (20–50 °C). Exochitinase expression significantly increased the number of leaves, root or shoot length and biomass throughout the growth cycle. Endochitinase expression reduced root/shoot biomass at early stages but recovered in older plants. Plant extracts expressing endochitinase/exochitinase showed activities as high as purified commercial enzymes. Antifungal activity in <jats:italic>Candida albicans</jats:italic> cultures inhibited growth up to 87%. A novel Carbotrace 680™ Optotracer binding to the ß‐1,4 linkages of chitin, evaluated for the first time in plant systems, is highly sensitive to measure chitinase activity. To the best of our knowledge, this is the first report of chitinase expression via the chloroplast genomes of an edible plant, to confer desired agronomic traits or for biomedical applications.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"80 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443219","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":"Modified carbon dot-mediated transient transformation for genomic and epigenomic studies in wheat","authors":"Linwei She,&nbsp;Xuejiao Cheng,&nbsp;Peng Jiang,&nbsp;Simin Shen,&nbsp;Fangxiu Dai,&nbsp;Yonghang Run,&nbsp;Mengting Zhu,&nbsp;Mahmoud Tavakoli,&nbsp;Xueming Yang,&nbsp;Xiu-e Wang,&nbsp;Jin Xiao,&nbsp;Caiyan Chen,&nbsp;Zhenhui Kang,&nbsp;Jian Huang,&nbsp;Wenli Zhang","doi":"10.1111/pbi.14573","DOIUrl":"10.1111/pbi.14573","url":null,"abstract":"<p>Genotype restriction poses a significant bottleneck to stable transformation in the vast majority of plant species, thereby severely impeding advancement in plant bioengineering, particularly for crops. Nanoparticles (NPs) can serve as effective carriers for the transient delivery of nucleic acids, facilitating gene overexpression or silencing in plants in a genotype-independent manner. However, the applications of NP-mediated transient systems in comprehensive genomic studies remained underexplored in plants, especially in crops that face challenges in genetic transformation. Consequently, there is an urgent need for efficient NP-mediated delivery systems capable of generating whole plants or seedlings with uniformly transformed nucleic acids. We have developed a straightforward and efficient modified carbon dot (MCD)-mediated transient transformation system for delivering DNA plasmids into the seeds of wheat, which is also applicable to other plant species. This system facilitates the generation of whole seedlings that contain the transferred DNA plasmids. Furthermore, our study demonstrates that this system serves as an excellent platform for conducting functional genomic studies in wheat, including the validation of gene functions, protein interactions and regulation, omics studies, and genome editing. This advancement significantly enhances functional genomic research for any plants or crops that face challenges in stable transformation. Thus, our study provides for the first time evidence of new applications for MCDs in functional genomics and epigenomic studies, and bioengineering potentially leading to the improvement of desirable agronomic traits in crops.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"23 4","pages":"1139-1152"},"PeriodicalIF":10.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.14573","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443218","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":"Global identification and functional characterization of Z-DNA in rice","authors":"Zexue He,&nbsp;Yonghang Run,&nbsp;Yilong Feng,&nbsp;Ying Yang,&nbsp;Mahmoud Tavakoli,&nbsp;Asgar Ahmed,&nbsp;Federico Ariel,&nbsp;Wenli Zhang","doi":"10.1111/pbi.14585","DOIUrl":"10.1111/pbi.14585","url":null,"abstract":"<p>Z-DNA is a left-handed double helix form of DNA that is believed to be involved in various DNA transactions. However, comprehensive investigations aimed at global profiling of Z-DNA landscapes are still missing in both humans and plants. We here report the development of two techniques: anti-Z-DNA antibody-based immunoprecipitation followed by sequencing (ZIP-seq), and cleavage under targets and tagmentation (CUT&amp;TAG) for characterizing Z-DNA in nipponbare rice (<i>Oryza sativa</i> L., Japonica). We found that Z-DNA-IP⁺ (Z-DNA recognized by the antibody) exhibits distinct genomic features as compared to Z-DNA-IP⁻ (Z-DNA not recognized by the antibody). The concomitant presence of G-quadruplexes (G4s) and i-motifs (iMs) may promote Z-DNA formation. DNA modifications such as DNA-6mA/-4acC generally disfavours Z-DNA formation, while modifications like DNA-5mC (CHH) and 8-oxodG promote it, highlighting the distinct roles of DNA base modifications in modulating Z-DNA formation. Importantly, Z-DNA located at transcription start sites (TSSs) enhances gene expression, whereas Z-DNA in genic regions represses it, underscoring its dual roles in regulating the expression of genes involved in fundamental biological functions and responses to salt stress. Furthermore, Z-DNA may play a role in transcriptional initiation and termination rather than in transcriptional elongation. Finally, the presence of Z-DNA in promoters is correlated with the coevolution of overlapping genes, thereby regulating gene domestication. Consequently, our study represents as a pivotal point and a solid foundation for reliably launching genome-wide investigations of Z-DNA, thereby advancing the understanding of Z-DNA biology in both plants and non-plant systems.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"23 4","pages":"1277-1290"},"PeriodicalIF":10.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.14585","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447540","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":"GhMYB102 affects cotton fibre elongation and secondary wall thickening by regulating GhIRX10 in cotton","authors":"Aimin Wu,&nbsp;Tong Shen,&nbsp;Jianhua Lu,&nbsp;Xiaokang Fu,&nbsp;Miaoqian Yang,&nbsp;Mengxi Sun,&nbsp;Liang Ma,&nbsp;Boying Lian,&nbsp;Hongmei Wu,&nbsp;Yiran Li,&nbsp;Shuxun Yu,&nbsp;Hengling Wei,&nbsp;Hantao Wang","doi":"10.1111/pbi.14588","DOIUrl":"10.1111/pbi.14588","url":null,"abstract":"<p>Upland cotton (<i>Gossypium hirsutum</i>) is a principal economic crop and a fundamental raw material for the textile industry. The quality of cotton fibres is significantly influenced by the synthesis of cell wall polysaccharides. This study focuses on <i>GhIRX10</i>, a beta-1,4-xylosyltransferase crucial for xylan backbone synthesis. Overexpression of <i>GhIRX10</i> enhances xylan synthesis, which impacts fibre elongation and secondary cell wall thickening. <i>GhMYB102</i>, identified as a direct regulator of <i>GhIRX10</i> expression, was confirmed through comprehensive validation. Overexpression of <i>GhMYB102</i> resulted in a similar phenotype as OE-<i>GhIRX10</i>: increased cell wall thickness and reduced fibre length. Overexpression of <i>GhMYB102</i> upregulated the expression of key cell wall synthesis-related genes, including <i>GhCESA4/7/8</i>, <i>Gh</i><i>IRXs</i>, <i>GhCESAs</i>, <i>Gh</i><i>GUXs</i>, <i>Gh</i><i>TBLs</i>, <i>Gh</i><i>XTHs</i>, and <i>Gh</i><i>XXTs</i>. Consequently, the cellulose and hemicellulose contents in OE-<i>GhMYB102</i> lines were significantly increased. <i>GhMYB102</i> was also validated as a target gene regulated by <i>GhFSN1</i> and <i>GhMYB7</i>, with the ability to reciprocally regulate <i>GhFSN1</i> expression. In summary, we propose a regulatory model where <i>GhMYB102</i> promotes the expression of <i>GhIRX10</i> and other cell wall-related genes, thereby affecting fibre quality. This study elucidates the regulatory network of secondary cell wall synthesis in cotton and provides potential targets for improving fibre quality through molecular breeding.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"23 4","pages":"1329-1344"},"PeriodicalIF":10.1,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.14588","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447564","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":"OsMAPKKK5 affects brassinosteroid signal transduction via phosphorylating OsBSK1-1 and regulates rice plant architecture and yield.","authors":"Peiwen Yan, Ying Wang, Jinhao Cui, Mingyu Liu, Yu Zhu, Fuying Ma, Yahui Liu, Dengyong Lan, Shiqing Dong, Zejun Hu, Fuan Niu, Yang Liu, Xinwei Zhang, Shicong He, Jian Hu, Xinyu Yuan, Yizhen Li, Jinshui Yang, Liming Cao, Xiaojin Luo","doi":"10.1111/pbi.70008","DOIUrl":"https://doi.org/10.1111/pbi.70008","url":null,"abstract":"<p><p>Improving plant architecture and increasing yields are the main goals of rice breeders. However, yield is a complex trait influenced by many yield-related traits. Identifying and characterizing important genes in the coordinated network regulating complex rice traits and their interactions is conducive to cultivating high-yielding rice varieties. In this study, we determined that the interaction between mitogen-activated protein kinase kinase kinase5 (OsMAPKKK5) and brassinosteroid-signalling kinase1-1 (OsBSK1-1) regulates yield-related traits in rice. Specifically, OsMAPKKK5 phosphorylates OsBSK1-1, which enhances the interaction between these two proteins, but adversely affects the OsBSK1-1-OsBRI1 (BR insensitive1) and OsBSK1-1-OsPPKL1 (protein phosphatase with two Kelch-like domains) interactions. Additionally, OsMAPKKK5 disrupts brassinosteroid signal transduction, which prevents OsBZR1 (brassinazole-resistant1) from efficiently entering the nucleus, thereby negatively modulating its function as a transcription factor regulating downstream effector genes, ultimately adversely affecting plant architecture and yield. This study revealed the relationship between the MAPK cascade and the regulatory effects of brassinosteroid on the rice grain yield involves OsMAPKKK5 and OsBSK1-1. The study data may be important for future investigations on the rice yield-regulating molecular network.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447543","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":"An optimized thymine base editing toolkit with various editing windows enables targeted T-to-G base conversions in rice","authors":"Xinbo Li, Yifu Tian, Rundong Shen, Yongzhen Pang, Kexuan Tang","doi":"10.1111/pbi.14611","DOIUrl":"https://doi.org/10.1111/pbi.14611","url":null,"abstract":"&lt;p&gt;Base editors offer potential for site saturation mutagenesis, yet deaminase-based editors are constrained to adenine and cytosine targets (Li &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023a&lt;/span&gt;). Recently, glycosylase-based base editors (gBEs), which fuse engineered glycosylases with SpCas9 nickase (SpCas9n, D10A) to excise specific guanine or thymine bases, achieve base conversions through DNA repair over abasic sites (He &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;; Tong &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023&lt;/span&gt;; Ye &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;). While glycosylase-based guanine base editors (gGBEs) show efficient guanine conversion in plants (Liu &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;; Tian &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;), thymine base editors (TBEs) remain unexplored (Figure S1).&lt;/p&gt;\u0000&lt;p&gt;Previous studies identified that the Y147A mutation in human uracil DNA glycosylase (hUNG) produces a thymine DNA glycosylase variant (hTDG). Highly active variants, TDG-EK (He &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;) and TDG3 (Ye &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;), were engineered using protein-language-assisted design and directed evolution, respectively, to enhance thymine editing. Cas9-embedding strategy further enhances base editing efficiency in mammalian cells (Figure 1a; He &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;). To engineer efficient TBE tools for plants, we inserted three plant-codon-optimized TDG variants (hTDG, TDG-EK and TDG3; Figure 1b) into SpCas9n at various positions (I1029-G1030, F1046-I1063 and P1249-E1250) with a GGGGS linker.&lt;/p&gt;\u0000&lt;figure&gt;&lt;picture&gt;\u0000&lt;source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/3ae363af-ba10-4c21-b9be-d18282e5a70f/pbi14611-fig-0001-m.jpg\"/&gt;&lt;img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/3ae363af-ba10-4c21-b9be-d18282e5a70f/pbi14611-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/e04c45d8-95ac-4a17-97d7-2ac0d00f2343/pbi14611-fig-0001-m.png\" title=\"Details are in the caption following the image\"/&gt;&lt;/picture&gt;&lt;figcaption&gt;\u0000&lt;div&gt;&lt;strong&gt;Figure 1&lt;span style=\"font-weight:normal\"&gt;&lt;/span&gt;&lt;/strong&gt;&lt;div&gt;Open in figure viewer&lt;i aria-hidden=\"true\"&gt;&lt;/i&gt;&lt;span&gt;PowerPoint&lt;/span&gt;&lt;/div&gt;\u0000&lt;/div&gt;\u0000&lt;div&gt;Engineering an efficient thymine base editing toolkit in rice. (a) Schematic of Cas-embedded base editors. (b) Glycosylase variants used in this study. (c) Dual-luciferase reporter system for assessing thymine editing in rice protoplasts. (d) NLuc restoration activities of different glycosylase base editors. The average relative luminescence units restored by CE&lt;sub&gt;1029&lt;/sub&gt;hTDG are normalized to 1 (&lt;i&gt;n&lt;/i&gt; = 8). (e, f) Indel (e) and thymine base editing (f) efficiencies of CE-TBEs across six targets. Heat maps show ratios of edited T&lt;sub&gt;0&lt;/sub&gt; plants. (g) Editing types and efficiencies of CE-TDG3 at six endogenous targets. (h–j) Summary of base-edited rice T&lt;sub&gt;0&lt;/sub&gt; plantlets across the protospacers from six endogenous targets edited by CE&lt;sub&gt;1029&lt;/sub&gt;TDG3 (h), CE&lt;sub&gt;1046&lt;/sub&gt;TDG3 (i), and CE&lt;sub&gt;1249&lt;/sub&gt;TDG3 (j). Plants with read proportions ","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"85 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143435509","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":"CRISPR/Cas9-mediated disruption of DA1 enhances both biomass yield and quality in poplar","authors":"Xianfeng Tang, Yi Wang, Junhang Fu, Xiaofei Li, Wei Wang, Yu Liu, Congpeng Wang, Jie Meng, Mengzhu Lu, Shaofeng Li, Dian Wang, Gongke Zhou","doi":"10.1111/pbi.14609","DOIUrl":"https://doi.org/10.1111/pbi.14609","url":null,"abstract":"&lt;p&gt;Biofuels have become important renewable energy alternative to fossil fuels in modern days. The non-food woody lignocellulose biomass drawn more attention to produce biofuel since it is not against the world's food security. Among which, poplar serves as an ideal woody biomass because of its fast growth and inherent secondary cell wall characteristics (Cho &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;). Lignocellulose (secondary cell wall) is mainly composed of lignin, cellulose and hemicellulose. Among which, lignin imparts most significant recalcitrance in deconstruction of the wall materials for saccharification process. Lignin is consist of three monolignols, p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) units, and the relative abundance of H-, G- and S-units, especially the S/G ratio have been proved to be tightly associated with biomass recalcitrance (Zhang &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;). Moreover, lignin-modified plants often exhibit irregular growth which consequently affect biomass production, thus limiting the benefits of lignin modification (Gui &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;). Therefore, searching for the lignin-modified poplar genetic materials with improved both the quantity and quality of wood is critical for the utilization of woody lignocellulosic biomass in the production of biofuel.&lt;/p&gt;\u0000&lt;p&gt;Previous studies revealed that &lt;i&gt;DA1&lt;/i&gt; gene family play a significant role in regulating organ and grain yields across various plant species, including maize, wheat and rice (Gao &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2021&lt;/span&gt;; Liu &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;; Xie &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;). In our previous study, we identified PagDA1 in poplar as a suppressor of vascular cambial development and wood formation (Tang &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2022&lt;/span&gt;). In this study, we further demonstrate &lt;i&gt;da1&lt;/i&gt; mutant created by CRISPR/Cas9 technology possesses great practical application in producing more and better wood biomass. We firstly found that &lt;i&gt;da1&lt;/i&gt; poplars exhibited significantly increased biomass compared with WT in greenhouse conditions, such as plant height, stem diameter and fresh weight (Figure S1a–d). Next, we investigated whether DA1 could impact the secondary wall deposition during wood formation. The expression patterns of &lt;i&gt;PagDA1&lt;/i&gt; genes and RNA in situ hybridization analysis revealed that both &lt;i&gt;PagDA1a&lt;/i&gt; and &lt;i&gt;PagDA1b&lt;/i&gt; showed high expression level in secondary xylem cell (Figure S2), indicating a potential role of &lt;i&gt;PagDA1&lt;/i&gt; in regulating secondary wall formation. Therefore, we analysed the secondary wall components and composition. While no significant difference in xylem fibre thickness between &lt;i&gt;da1&lt;/i&gt; and WT plants, a slight increase of vessel thickness was observed in &lt;i&gt;da1-23&lt;/i&gt; compared to the WT (Figure 1a; Figure S1e,f). We next stained lignin in cross sections of the basal stem xylem with phloroglucinol and it exhibited no significant difference between &lt;i&gt;da1&lt;/i&gt; and WT plants (Figure 1a), which was ","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"13 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143435508","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}