aBIOTECH最新文献_第6页

Establishment of a genome‐editing system to create fragrant germplasm in sweet sorghum 甜高粱芳香种质基因组编辑系统的建立

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-09-27 DOI: 10.1007/s42994-024-00180-6

Zixiang Cheng, Ke Li, Hongxiu Liu, Xingen Wei, Tao Yin, Xin Xing, Lida Han, Yi Sui

{"title":"Establishment of a genome‐editing system to create fragrant germplasm in sweet sorghum","authors":"Zixiang Cheng, Ke Li, Hongxiu Liu, Xingen Wei, Tao Yin, Xin Xing, Lida Han, Yi Sui","doi":"10.1007/s42994-024-00180-6","DOIUrl":"10.1007/s42994-024-00180-6","url":null,"abstract":"<div>Sorghum, the fifth largest global cereal crop, comprises various types, such as grain, sweet, forage, and biomass sorghum, delineated by their designated end uses. Among these, sweet sorghum (Sorghum bicolor (L.) Moench) stands out for its unique versatility, exceptional abiotic stress tolerance and large biomass serving the multi-purpose of high-sugar forage, syrup, and biofuel production. Despite its significance, functional genomic research and biotechnological breeding in sweet sorghum are still in nascent stages, necessitating more efficient genetic transformation and genome-editing techniques. This study unveils Gaoliangzhe (GZ), an elite sweet sorghum variety for heightened resistance to salinity and drought. Through the establishment of an Agrobacterium tumefaciens‐mediated genetic transformation and CRISPR/Cas9-based genome-editing system in GZ, a breakthrough is achieved. Using genome-editing technology, we first produced a fragrant sweet sorghum line by targeting the BETAINE ALDEHYDE DEHYDROGENASE 2 (SbBADH2) gene. Our results establish a strong foundation for further functional genomic research and biotechnological breeding of sweet-sorghum varieties.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 4","pages":"502 - 506"},"PeriodicalIF":4.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00180-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Prime editing enables precise genome modification of a Populus hybrid 引体编辑可以对杨树杂交品种进行精确的基因组修饰

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-09-06 DOI: 10.1007/s42994-024-00177-1

Jinpeng Zou, Yuhong Li, Kejian Wang, Chun Wang, Renying Zhuo

{"title":"Prime editing enables precise genome modification of a Populus hybrid","authors":"Jinpeng Zou, Yuhong Li, Kejian Wang, Chun Wang, Renying Zhuo","doi":"10.1007/s42994-024-00177-1","DOIUrl":"10.1007/s42994-024-00177-1","url":null,"abstract":"<div>CRISPR/Cas-based genome editing has been extensively employed in the breeding and genetic improvement of trees, yet precise editing remains challenging in these species. Prime editing (PE), a revolutionary technology for precise editing, allows for arbitrary base substitutions and the insertion/deletion of small fragments. In this study, we focused on the model tree poplar 84K (Populus alba × P. glandulosa). We used the 2 × 35S promoter to express a fusion protein of spCas9 nickase (nCas9) and engineered Moloney murine leukemia virus (MMLV), and the Arabidopsis thaliana AtU6 promoter to express an engineered PE guide RNA (epegRNA) and Nick gRNA, pioneering the establishment of the Prime Editor 3 (PE3) system in dicot poplar. Single-base substitutions, multiple-base substitutions, and small-fragment insertions/deletions were edited into three endogenous target genes. The desired edits were identified in hygromycin-resistant (transformed) calli at seven out of nine target sites, with an average editing efficiency ranging from 0.1 to 3.6%. Furthermore, stable T0 plants contained the desired edits at four out of nine targets, with editing efficiencies ranging from 3.6 to 22.2%. Establishment of the PE3 system provides a powerful tool for the precise modification of the poplar genome.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 4","pages":"497 - 501"},"PeriodicalIF":4.6,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00177-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction: Characterization and functional analysis of gerbera plant defensin (PDF) genes reveal the role of GhPDF2.4 in defense against the root rot pathogen Phytophthora cryptogea 更正：非洲菊植物防御素（PDF）基因的鉴定和功能分析揭示了GhPDF2.4在抵御根腐病病原隐疫霉（Phytophthora cryptoa）中的作用

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-08-26 DOI: 10.1007/s42994-024-00179-z

Chunzhen Cheng, Huan Wu, Yongyan Zhang

引用次数: 0

Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2 数据库选择和置信度对Kraken2分类性能的影响

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-07-31 DOI: 10.1007/s42994-024-00178-0

Yunlong Liu, Morteza H. Ghaffari, Tao Ma, Yan Tu

{"title":"Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2","authors":"Yunlong Liu, Morteza H. Ghaffari, Tao Ma, Yan Tu","doi":"10.1007/s42994-024-00178-0","DOIUrl":"10.1007/s42994-024-00178-0","url":null,"abstract":"<div>Accurate taxonomic classification is essential to understanding microbial diversity and function through metagenomic sequencing. However, this task is complicated by the vast variety of microbial genomes and the computational limitations of bioinformatics tools. The aim of this study was to evaluate the impact of reference database selection and confidence score (CS) settings on the performance of Kraken2, a widely used k-mer-based metagenomic classifier. In this study, we generated simulated metagenomic datasets to systematically evaluate how the choice of reference databases, from the compact Minikraken v1 to the expansive nt- and GTDB r202, and different CS (from 0 to 1.0) affect the key performance metrics of Kraken2. These metrics include classification rate, precision, recall, F1 score, and accuracy of true versus calculated bacterial abundance estimation. Our results show that higher CS, which increases the rigor of taxonomic classification by requiring greater k-mer agreement, generally decreases the classification rate. This effect is particularly pronounced for smaller databases such as Minikraken and Standard-16, where no reads could be classified when the CS was above 0.4. In contrast, for larger databases such as Standard, nt and GTDB r202, precision and F1 scores improved significantly with increasing CS, highlighting their robustness to stringent conditions. Recovery rates were mostly stable, indicating consistent detection of species under different CS settings. Crucially, the results show that a comprehensive reference database combined with a moderate CS (0.2 or 0.4) significantly improves classification accuracy and sensitivity. This finding underscores the need for careful selection of database and CS parameters tailored to specific scientific questions and available computational resources to optimize the results of metagenomic analyses.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 4","pages":"465 - 475"},"PeriodicalIF":4.6,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00178-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A simple, highly efficient Agrobacterium tumefaciens‐mediated moss transformation system with broad applications 简单、高效、应用广泛的农杆菌介导苔藓转化系统

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-07-19 DOI: 10.1007/s42994-024-00174-4

Ping Zhou, Xiujin Liu, Yuqing Liang, Yan Zhang, Xiaoshuang Li, Daoyuan Zhang

{"title":"A simple, highly efficient Agrobacterium tumefaciens‐mediated moss transformation system with broad applications","authors":"Ping Zhou, Xiujin Liu, Yuqing Liang, Yan Zhang, Xiaoshuang Li, Daoyuan Zhang","doi":"10.1007/s42994-024-00174-4","DOIUrl":"10.1007/s42994-024-00174-4","url":null,"abstract":"<div>Mosses, particularly desiccation-tolerant (DT) species, are important model organisms for studying genes involved in plant development and stress resistance. The lack of a simple and efficient stable moss transformation system has hindered progress in deciphering the genetic mechanisms underlying traits of interest in these organisms. Here, we present an Agrobacterium tumefaciens-mediated transformation system for DT mosses that uses Agrobacterium strain EHA105 harboring the binary vector pCAMBIA1301-GUS. This system achieved transformation efficiencies of 74% and 81% in Physcomitrium patens and Bryum argenteum protonemata, respectively, without the need for culture and callus formation prior to regeneration. We detected GUS enzyme activity in the regenerated transgenic moss via histochemical staining. Southern blot, PCR, and RT-qPCR analyses confirmed the presence of the GUS gene. In addition, we successfully used this system to transform wild DT Syntrichia caninervis. Furthermore, P. patens and B. argenteum transformed using this system with the stress resistance gene EsDREB from the desert plant Eremosparton songoricum (Litv.) exhibited improved salt tolerance. We thus present an efficient tool for the genetic analysis of DT moss species, paving the way for the development of stress-resistant crop cultivars.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 4","pages":"476 - 487"},"PeriodicalIF":4.6,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00174-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141822289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza 拟南芥和旱生植物组织特异性调控子的推断和优先排序

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-07-16 DOI: 10.1007/s42994-024-00176-2

Honggang Dai, Yaxin Fan, Yichao Mei, Ling-Ling Chen, Junxiang Gao

{"title":"Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza","authors":"Honggang Dai, Yaxin Fan, Yichao Mei, Ling-Ling Chen, Junxiang Gao","doi":"10.1007/s42994-024-00176-2","DOIUrl":"10.1007/s42994-024-00176-2","url":null,"abstract":"<div>A regulon refers to a group of genes regulated by a transcription factor binding to regulatory motifs to achieve specific biological functions. To infer tissue-specific gene regulons in Arabidopsis, we developed a novel pipeline named InferReg. InferReg utilizes a gene expression matrix that includes 3400 Arabidopsis transcriptomes to make initial predictions about the regulatory relationships between transcription factors (TFs) and target genes (TGs) using co-expression patterns. It further improves these anticipated interactions by integrating TF binding site enrichment analysis to eliminate false positives that are only supported by expression data. InferReg further trained a graph convolutional network with 133 transcription factors, supported by ChIP-seq, as positive samples, to learn the regulatory logic between TFs and TGs to improve the accuracy of the regulatory network. To evaluate the functionality of InferReg, we utilized it to discover tissue-specific regulons in 5 Arabidopsis tissues: flower, leaf, root, seed, and seedling. We ranked the activities of regulons for each tissue based on reliability using Borda ranking and compared them with existing databases. The results demonstrated that InferReg not only identified known tissue-specific regulons but also discovered new ones. By applying InferReg to rice expression data, we were able to identify rice tissue-specific regulons, showing that our approach can be applied more broadly. We used InferReg to successfully identify important regulons in various tissues of Arabidopsis and Oryza, which has improved our understanding of tissue-specific regulations and the roles of regulons in tissue differentiation and development.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 3","pages":"309 - 324"},"PeriodicalIF":4.6,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141643629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The acyl-CoA-binding protein VdAcb1 is essential for carbon starvation response and contributes to virulence in Verticillium dahliae 酰基-CoA 结合蛋白 VdAcb1 对于大丽轮枝菌的碳饥饿反应至关重要，并有助于提高其毒力

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-07-13 DOI: 10.1007/s42994-024-00175-3

Jing Zhuang, Ya-Duo Zhang, Wei-Xia Sun, Juan Zong, Jun-Jiao Li, Xiao-Feng Dai, Steven J. Klosterman, Jie-Yin Chen, Li Tian, Krishna V. Subbarao, Dan-Dan Zhang

{"title":"The acyl-CoA-binding protein VdAcb1 is essential for carbon starvation response and contributes to virulence in Verticillium dahliae","authors":"Jing Zhuang, Ya-Duo Zhang, Wei-Xia Sun, Juan Zong, Jun-Jiao Li, Xiao-Feng Dai, Steven J. Klosterman, Jie-Yin Chen, Li Tian, Krishna V. Subbarao, Dan-Dan Zhang","doi":"10.1007/s42994-024-00175-3","DOIUrl":"10.1007/s42994-024-00175-3","url":null,"abstract":"<div>In the face of carbon, nitrogen, and phosphorus starvation, microorganisms have evolved adaptive mechanisms to maintain growth. In a previous study, we identified a protein predicted to contain acyl-CoA-binding domains in the plant pathogenic fungus Verticillium dahliae. The predicted protein, designated VdAcb1, possesses an atypical signal peptide. However, the functions of this acyl-CoA-binding protein in V. dahliae are not clear. In this research, in vivo or in vitro assays confirmed that VdAcb1 is secreted extracellularly from V. dahliae, although it does not have the typical signal peptide. Furthermore, the unconventional secretion of VdAcb1 was dependent on VdGRASP, a member of the compartment for unconventional protein secretion (CUPS). The deletion mutant strain of VdAcb1 (ΔVdAcb1) exhibited significant sensitivity to carbon starvation. RNA-seq revealed that the expression of genes related to filamentous growth (MSB2 pathway) and sugar transport were regulated by VdAcb1 under conditions of carbon starvation. Yeast one-hybrid experiments further showed that the expression of VdAcb1 was positively regulated by the transcription factor VdMsn4. The ΔVdAcb1 strain showed significantly reduced virulence on Gossypium hirsutum and Nicotiana benthamiana. We hypothesize that under conditions of carbon starvation, the expression of VdAcb1 is activated by VdMsn4 and VdAcb1 is secreted into the extracellular space. In turn, this activates the downstream MAPK pathway to enhance filamentous growth and virulence of V. dahliae.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 4","pages":"431 - 448"},"PeriodicalIF":4.6,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00175-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141651214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction: Characterization of two constitutive promoters RPS28 and EIF1 for studying soybean growth, development, and symbiotic nodule development 更正：两个组成型启动子 RPS28 和 EIF1 的特性，用于研究大豆的生长、发育和共生结核的发育。

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-06-24 DOI: 10.1007/s42994-024-00171-7

Shengcai Chen, Yaqi Peng, Qi Lv, Jing Liu, Zhihua Wu, Haijiao Wang, Xuelu Wang

引用次数: 0

Simultaneous genetic transformation and genome editing of mixed lines in soybean (Glycine max) and maize (Zea mays) 大豆（Glycine max）和玉米（Zea mays）混合品系的同步遗传转化和基因组编辑。

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-06-18 DOI: 10.1007/s42994-024-00173-5

Michelle Valentine, David Butruille, Frederic Achard, Steven Beach, Brent Brower-Toland, Edward Cargill, Megan Hassebrock, Jennifer Rinehart, Thomas Ream, Yurong Chen

{"title":"Simultaneous genetic transformation and genome editing of mixed lines in soybean (Glycine max) and maize (Zea mays)","authors":"Michelle Valentine, David Butruille, Frederic Achard, Steven Beach, Brent Brower-Toland, Edward Cargill, Megan Hassebrock, Jennifer Rinehart, Thomas Ream, Yurong Chen","doi":"10.1007/s42994-024-00173-5","DOIUrl":"10.1007/s42994-024-00173-5","url":null,"abstract":"<div>Robust genome editing technologies are becoming part of the crop breeding toolbox. Currently, genome editing is usually conducted either at a single locus, or multiple loci, in a variety at one time. Massively parallel genomics platforms, multifaceted genome editing capabilities, and flexible transformation systems enable targeted variation at nearly any locus, across the spectrum of genotypes within a species. We demonstrate here the simultaneous transformation and editing of many genotypes, by targeting mixed seed embryo explants with genome editing machinery, followed by re-identification through genotyping after plant regeneration. Transformation and Editing of Mixed Lines (TREDMIL) produced transformed individuals representing 101 of 104 (97%) mixed elite genotypes in soybean; and 22 of 40 (55%) and 9 of 36 (25%) mixed maize female and male elite inbred genotypes, respectively. Characterization of edited genotypes for the regenerated individuals identified over 800 distinct edits at the Determinate1 (Dt1) locus in samples from 101 soybean genotypes and 95 distinct Brown midrib3 (Bm3) edits in samples from 17 maize genotypes. These results illustrate how TREDMIL can help accelerate the development and deployment of customized crop varieties for future precision breeding.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 2","pages":"169 - 183"},"PeriodicalIF":4.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11224177/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome editing in plants using the TnpB transposase system 利用 TnpB 转座酶系统进行植物基因组编辑

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-06-08 DOI: 10.1007/s42994-024-00172-6

Qi Li, Yongqiang Wang, Zhuoting Hou, Hang Zong, Xuping Wang, Yong E. Zhang, Haoyi Wang, Haitao Chen, Wen Wang, Kang Duan

{"title":"Genome editing in plants using the TnpB transposase system","authors":"Qi Li, Yongqiang Wang, Zhuoting Hou, Hang Zong, Xuping Wang, Yong E. Zhang, Haoyi Wang, Haitao Chen, Wen Wang, Kang Duan","doi":"10.1007/s42994-024-00172-6","DOIUrl":"10.1007/s42994-024-00172-6","url":null,"abstract":"<div>The widely used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas) system is thought to have evolved from IS200/IS605 transposons. TnpB proteins, encoded by one type of IS200/IS605 transposon, are considered to be the evolutionary ancestors of Cas12 nucleases, which have been engineered to function as RNA-guided DNA endonucleases for genome editing in bacteria and human cells. TnpB nucleases, which are smaller than Cas nucleases, have been engineered for use in genome editing in animal systems, but the feasibility of this approach in plants remained unknown. Here, we obtained stably transformed genome-edited mutants in rice (Oryza sativa) by adapting three recently identified TnpB genome editing vectors, encoding distinct TnpB nucleases (ISAam1, ISDra2, and ISYmu1), for use in plants, demonstrating that the hypercompact TnpB proteins can effectively edit plant genomes. ISDra2 and ISYmu1 precisely edited their target sequences, with no off-target mutations detected, showing that TnpB transposon nucleases are suitable for development into a new genome editing tool for plants. Future modifications improving the genome-editing efficiency of the TnpB system will facilitate plant functional studies and breeding programs.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 2","pages":"225 - 230"},"PeriodicalIF":4.6,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00172-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141369077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0