aBIOTECH最新文献

{"title":"Decoding the microbiome for sustainable agriculture","authors":"Kai Sun,&nbsp;Wei Zhang,&nbsp;Xiaolin Wang,&nbsp;Chuan-Chao Dai","doi":"10.1007/s42994-024-00162-8","DOIUrl":"10.1007/s42994-024-00162-8","url":null,"abstract":"<div><p>Root-associated microbiota profoundly affect crop health and productivity. Plants can selectively recruit beneficial microbes from the soil and actively balance microbe-triggered plant-growth promotion and stress tolerance enhancement. The cost associated with this is the root-mediated support of a certain number of specific microbes under nutrient limitation. Thus, it is important to consider the dynamic changes in microbial quantity when it comes to nutrient condition-induced root microbiome reassembly. Quantitative microbiome profiling (QMP) has recently emerged as a means to estimate the specific microbial load variation of a root microbiome (instead of the traditional approach quantifying relative microbial abundances) and data from the QMP approach can be more closely correlated with plant development and/or function. However, due to a lack of detailed-QMP data, how soil nutrient conditions affect quantitative changes in microbial assembly of the root-associated microbiome remains poorly understood. A recent study quantified the dynamics of the soybean root microbiome, under unbalanced fertilization, using QMP and provided data on the use of specific synthetic communities (SynComs) for sustaining crop productivity. In this editorial, we explore potential opportunities for utilizing QMP to decode the microbiome for sustainable agriculture.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 3","pages":"408 - 412"},"PeriodicalIF":4.6,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141003799","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}

{"title":"Publisher Correction: Removal of the C4-domain preserves the drought tolerance enhanced by CsMYB4a and eliminates the negative impact of this transcription factor on plant growth","authors":"Mingzhuo Li,&nbsp;Guoliang Ma,&nbsp;Xiu Li,&nbsp;Lili Guo,&nbsp;Yanzhi Li,&nbsp;Yajun Liu,&nbsp;Wenzhao Wang,&nbsp;Xiaolan Jiang,&nbsp;De-Yu Xie,&nbsp;Liping Gao,&nbsp;Tao Xia","doi":"10.1007/s42994-024-00163-7","DOIUrl":"10.1007/s42994-024-00163-7","url":null,"abstract":"","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 3","pages":"414 - 416"},"PeriodicalIF":4.6,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11399506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142300701","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}

{"title":"Correction: Current overview on the genetic basis of key genes involved in soybean domestication","authors":"Sijia Lu,&nbsp;Chao Fang,&nbsp;Jun Abe,&nbsp;Fanjiang Kong,&nbsp;Baohui Liu","doi":"10.1007/s42994-024-00161-9","DOIUrl":"10.1007/s42994-024-00161-9","url":null,"abstract":"","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 2","pages":"279 - 279"},"PeriodicalIF":4.6,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11224158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141556479","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}

{"title":"Efficient and precise genomic deletion in rice using enhanced prime editing","authors":"Mengyuan Liu,&nbsp;Xiang Zhang,&nbsp;Wen Xu,&nbsp;Guiting Kang,&nbsp;Ya Liu,&nbsp;Xinxiang Liu,&nbsp;Wen Ren,&nbsp;Jiuran Zhao,&nbsp;Jinxiao Yang","doi":"10.1007/s42994-024-00153-9","DOIUrl":"10.1007/s42994-024-00153-9","url":null,"abstract":"<div><p>Efficient and precise genomic deletion shows promise for investigating the function of proteins in plant research and enhancing agricultural traits. In this study, we tested the PRIME-Del (PDel) strategy using a pair of prime editing guide RNAs (pegRNAs) that targeted opposite DNA strands and achieved an average deletion efficiency of 55.8% for 60 bp fragment deletions at six endogenous targets. Moreover, as high as 84.2% precise deletion efficiency was obtained for a 2000 bp deletion at the <i>OsGS1</i> site in transgenic rice plants. To add the bases that were unintentionally deleted between the two nicking sequences, we used the PDel/Syn strategy, which introduced multiple synonymous base mutations in the region that had to be patched in the RT template. The PDel/Syn strategy achieved an average of 58.1% deletion efficiency at six endogenous targets, which was higher than the PDel strategy. The strategies presented in this study contribute to achieving more accurate and flexible deletions in transgenic rice plants.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 2","pages":"214 - 218"},"PeriodicalIF":4.6,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11224055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141556480","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}

{"title":"Developing a CRISPR/FrCas9 system for core promoter editing in rice","authors":"Hui Wang,&nbsp;Jian Ding,&nbsp;Jingyan Zhu,&nbsp;Xiaoshuang Liu,&nbsp;Rongfang Xu,&nbsp;Ruiying Qin,&nbsp;Dongfang Gu,&nbsp;Min Li,&nbsp;Pengcheng Wei,&nbsp;Juan Li","doi":"10.1007/s42994-024-00157-5","DOIUrl":"10.1007/s42994-024-00157-5","url":null,"abstract":"<div><p>Small mutations in the core promoter region of a gene may result in substantial changes in expression strengths. However, targeting TA-rich sequences of core promoters may pose a challenge for Cas9 variants such as SpCas9 and other G-rich PAM-compatible Cas9s. In this study, we engineered a unique FrCas9 system derived from <i>Faecalibaculum rodentium</i> for plant genome editing. Our findings indicate that this system is efficient in rice when the TATA sequence is used as a PAM. In addition, FrCas9 demonstrated activity against all 16 possible NNTA PAMs, achieving an efficiency of up to 35.3% in calli and generating homozygous or biallelic mutations in 31.3% of the T₀ transgenic plants. A proof-of-concept experiment to examine editing of the rice <i>WX</i> core promoter confirmed that FrCas9-induced mutations could modify gene expression and amylose content. Multiplex mutations and deletions were produced by bidirectional editing, mediated by FrCas9, using a single palindromic TATA sequence as a PAM. Moreover, we developed FrCas9-derived base editors capable of programmable conversion between A·T and G·C pairs in plants. This study highlights a versatile FrCas9 toolset for plant core promoter editing, offering great potential for the fine-tuning of gene expression and creating of new germplasms.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 2","pages":"189 - 195"},"PeriodicalIF":4.6,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00157-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140676941","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}

{"title":"Natural GmACO1 allelic variations confer drought tolerance and influence nodule formation in soybean","authors":"Zhifang Zhang,&nbsp;Junkui Ma,&nbsp;Xia Yang,&nbsp;Shan Liang,&nbsp;Yucheng Liu,&nbsp;Yaqin Yuan,&nbsp;Qianjin Liang,&nbsp;Yanting Shen,&nbsp;Guoan Zhou,&nbsp;Min Zhang,&nbsp;Zhixi Tian,&nbsp;Shulin Liu","doi":"10.1007/s42994-024-00160-w","DOIUrl":"10.1007/s42994-024-00160-w","url":null,"abstract":"<div><p>Soybean [<i>Glycine max</i> (L.) Merr.] is one of the most important, but a drought-sensitive, crops. Identifying the genes controlling drought tolerance is important in soybean breeding. Here, through a genome-wide association study, we identified one significant association locus, located on chromosome 8, which conferred drought tolerance variations in a natural soybean population. Allelic analysis and genetic validation demonstrated that <i>GmACO1</i>, encoding for a 1-aminocyclopropane-1-carboxylate oxidase, was the causal gene in this association locus, and positively regulated drought tolerance in soybean. Meanwhile, we determined that <i>GmACO1</i> expression was reduced after rhizobial infection, and that <i>GmACO1</i> negatively regulated soybean nodule formation. Overall, our findings provide insights into soybean cultivars for future breeding.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 3","pages":"351 - 355"},"PeriodicalIF":4.6,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00160-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140688805","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}

{"title":"Optimized protoplast isolation and transfection with a breakpoint: accelerating Cas9/sgRNA cleavage efficiency validation in monocot and dicot","authors":"Debasmita Panda,&nbsp;Subhasis Karmakar,&nbsp;Manaswini Dash,&nbsp;Swagat Kumar Tripathy,&nbsp;Priya Das,&nbsp;Sagar Banerjee,&nbsp;Yiping Qi,&nbsp;Sanghamitra Samantaray,&nbsp;Pradipta Kumar Mohapatra,&nbsp;Mirza J. Baig,&nbsp;Kutubuddin A. Molla","doi":"10.1007/s42994-024-00139-7","DOIUrl":"10.1007/s42994-024-00139-7","url":null,"abstract":"<div><p>The CRISPR-Cas genome editing tools are revolutionizing agriculture and basic biology with their simplicity and precision ability to modify target genomic loci. Software-predicted guide RNAs (gRNAs) often fail to induce efficient cleavage at target loci. Many target loci are inaccessible due to complex chromatin structure. Currently, there is no suitable tool available to predict the architecture of genomic target sites and their accessibility. Hence, significant time and resources are spent on performing editing experiments with inefficient guides. Although in vitro-cleavage assay could provide a rough assessment of gRNA efficiency, it largely excludes the interference of native genomic context. Transient in-vivo testing gives a proper assessment of the cleavage ability of editing reagents in a native genomic context. Here, we developed a modified protocol that offers highly efficient protoplast isolation from rice, <i>Arabidopsis,</i> and chickpea, using a sucrose gradient, transfection using PEG (polyethylene glycol), and validation of single guide RNAs (sgRNAs) cleavage efficiency of CRISPR-Cas9. We have optimized various parameters for PEG-mediated protoplast transfection and achieved high transfection efficiency using our protocol in both monocots and dicots. We introduced plasmid vectors containing Cas9 and sgRNAs targeting genes in rice, <i>Arabidopsis,</i> and chickpea protoplasts. Using dual sgRNAs, our CRISPR-deletion strategy offers straightforward detection of genome editing success by simple agarose gel electrophoresis. Sanger sequencing of PCR products confirmed the editing efficiency of specific sgRNAs. Notably, we demonstrated that isolated protoplasts can be stored for up to 24/48 h with little loss of viability, allowing a pause between isolation and transfection. This high-efficiency protocol for protoplast isolation and transfection enables rapid (less than 7 days) validation of sgRNA cleavage efficiency before proceeding with stable transformation. The isolation and transfection method can also be utilized for rapid validation of editing strategies, evaluating diverse editing reagents, regenerating plants from transfected protoplasts, gene expression studies, protein localization and functional analysis, and other applications.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 2","pages":"151 - 168"},"PeriodicalIF":4.6,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00139-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140702659","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}

{"title":"Zig, Zag, and ’Zyme: leveraging structural biology to engineer disease resistance","authors":"Alexander J. McClelland,&nbsp;Wenbo Ma","doi":"10.1007/s42994-024-00152-w","DOIUrl":"10.1007/s42994-024-00152-w","url":null,"abstract":"<div><p>Dynamic host–pathogen interactions determine whether disease will occur. Pathogen effector proteins are central players in such disease development. On one hand, they improve susceptibility by manipulating host targets; on the other hand, they can trigger immunity after recognition by host immune receptors. A major research direction in the study of molecular plant pathology is to understand effector-host interactions, which has informed the development and breeding of crops with enhanced disease resistance. Recent breakthroughs on experiment- and artificial intelligence-based structure analyses significantly accelerate the development of this research area. Importantly, the detailed molecular insight of effector–host interactions enables precise engineering to mitigate disease. Here, we highlight a recent study by Xiao et al., who describe the structure of an effector-receptor complex that consists of a fungal effector, with polygalacturonase (PG) activity, and a plant-derived polygalacturonase-inhibiting protein (PGIP). PGs weaken the plant cell wall and produce immune-suppressive oligogalacturonides (OGs) as a virulence mechanism; however, PGIPs directly bind to PGs and alter their enzymatic activity. When in a complex with PGIPs, PGs produce OG polymers with longer chains that can trigger immunity. Xiao et al. demonstrate that a PGIP creates a new active site tunnel, together with a PG, which favors the production of long-chain OGs. In this way, the PGIP essentially acts as both a PG receptor and enzymatic manipulator, converting virulence to defense activation. Taking a step forward, the authors used the PG-PGIP complex structure as a guide to generate PGIP variants with enhanced long-chain OG production, likely enabling further improved disease resistance. This study discovered a novel mechanism by which a plant receptor plays a dual role to activate immunity. It also demonstrates how fundamental knowledge, obtained through structural analyses, can be employed to guide the design of proteins with desired functions in agriculture.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 3","pages":"403 - 407"},"PeriodicalIF":4.6,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00152-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140716615","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}

{"title":"Expanding the targeting scope of CRISPR/Cas9-mediated genome editing by Cas9 variants in Brassica","authors":"Wenjing Li,&nbsp;Xuan Li,&nbsp;Chunyang Wang,&nbsp;Guanzhong Huo,&nbsp;Xinru Zhang,&nbsp;Jintai Yu,&nbsp;Xiaoxiao Yu,&nbsp;Jing Li,&nbsp;Chao Zhang,&nbsp;Jianjun Zhao,&nbsp;Yan Li,&nbsp;Jun Li","doi":"10.1007/s42994-024-00155-7","DOIUrl":"10.1007/s42994-024-00155-7","url":null,"abstract":"<div><p>CRISPR/Cas9, presently the most widely used genome editing technology, has provided great potential for functional studies and plant breeding. However, the strict requirement for a protospacer adjacent motif (PAM) has hindered the application of the CRISPR/Cas9 system because the number of targetable genomic sites is limited. Recently, the engineered variants Cas9-NG, SpG, and SpRY, which recognize non-canonical PAMs, have been successfully tested in plants (mainly in rice, a monocot). In this study, we evaluated the targeted mutagenesis capabilities of these Cas9 variants in two important <i>Brassica</i> vegetables, Chinese cabbage (<i>Brassica rapa</i> spp. <i>pekinensis</i>) and cabbage (<i>Brassica oleracea</i> var. <i>capitata</i>). Both Cas9-NG and SpG induced efficient mutagenesis at NGN PAMs, while SpG outperformed Cas9-NG at NGC and NGT PAMs. SpRY achieved efficient editing at almost all PAMs (NRN &gt; NYN), albeit with some self-targeting activity at transfer (T)-DNA sequences. And SpRY-induced mutants were detected in cabbage plants in a PAM-less fashion. Moreover, an adenine base editor was developed using SpRY and TadA8e deaminase that induced A-to-G conversions within target sites using non-canonical PAMs. Together, the toolboxes developed here induced successful genome editing in Chinese cabbage and cabbage. Our work further expands the targeting scope of genome editing and paves the way for future basic research and genetic improvement in <i>Brassica</i>.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 2","pages":"202 - 208"},"PeriodicalIF":4.6,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00155-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140737111","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}

{"title":"Consumer transparency in the production chain for plant varieties produced using new genomic techniques","authors":"J. M. Lukasiewicz,&nbsp;C. C. M. van de Wiel,&nbsp;L. A. P. Lotz,&nbsp;M. J. M. Smulders","doi":"10.1007/s42994-024-00142-y","DOIUrl":"10.1007/s42994-024-00142-y","url":null,"abstract":"<div><p>Plants edited with new genomic techniques (NGTs) currently fall under the Genetically Modified Organisms Directive (2001/18/EC) in the European Union. In the proposal of the European Commission, NGT plants are partially exempted from the regulations of this directive. The proposal makes a distinction between two categories of NGT plants: NGT-1 and NGT-2. NGT-1 category plants are considered equal to plants obtained through conventional breeding methods. These plants will not be labelled for the consumer, although they will be labelled as seeds. NGT-2 category plants may be labelled with additional information as a positive incentive. Labelling of seeds of varieties made with gene editing, but not the products, would mean that most steps in the production chain are transparent, but not the last step towards consumers. The “right to know” and increasing knowledge of gene-edited food is a common theme in food labelling towards consumers. Here, we describe current labelling regimes and registers and how these may be applied to provide transparency on gene-edited products to consumers. Furthermore, we also look into consumer studies, which indicate a greater acceptance of gene-edited food among consumers, especially when additional benefits such as sustainability are mentioned.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 2","pages":"239 - 246"},"PeriodicalIF":4.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11224161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555971","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}