Loss-of-function mutants are fundamental resources for gene function studies. However, it is difficult to generate viable and heritable knockout mutants for essential genes. Here, we show that targeted editing of the C-terminal sequence of the embryo lethal gene MITOGEN-ACTIVATED PROTEIN KINASES 1 (OsMPK1) results in weak mutants. This C-terminal-edited osmpk1 mutants displayed severe developmental defects and altered disease resistance but generated tens of viable seeds that inherited the mutations. Using the same C-terminal editing approach, we also obtained viable mutants for a wall-associated protein kinase (Os07g0493200) and a leucine-rich repeat receptor-like protein kinase (Os01g0239700), while the null mutations of these genes were lethal. These data suggest that protein kinase activity could be reduced by introducing frameshift mutations adjacent to the C-terminus, which could generate valuable resources for gene function studies and tune protein kinase activity for signaling pathway engineering.
功能缺失突变体是基因功能研究的基本资源。然而,要产生可行且可遗传的重要基因敲除突变体却很困难。在这里,我们发现靶向编辑胚胎致死基因 MITOGEN-ACTIVATED PROTEIN KINASES 1(OsMPK1)的 C 端序列可产生弱突变体。这种C端编辑的osmpk1突变体表现出严重的发育缺陷和抗病性改变,但却能产生数十粒继承了突变基因的可存活种子。利用相同的 C 端编辑方法,我们还获得了一种壁相关蛋白激酶(Os07g0493200)和一种富亮氨酸重复受体样蛋白激酶(Os01g0239700)的可存活突变体,而这些基因的无效突变是致死的。这些数据表明,蛋白激酶的活性可以通过引入C端附近的移帧突变来降低,这可以为基因功能研究提供宝贵的资源,并为信号通路工程调控蛋白激酶的活性。
{"title":"C-terminal frameshift mutations generate viable knockout mutants with developmental defects for three essential protein kinases","authors":"Yun Zhang, Miao-Miao Cui, Run-Nan Ke, Yue-Dan Chen, Kabin Xie","doi":"10.1007/s42994-024-00165-5","DOIUrl":"10.1007/s42994-024-00165-5","url":null,"abstract":"<div><p>Loss-of-function mutants are fundamental resources for gene function studies. However, it is difficult to generate viable and heritable knockout mutants for essential genes. Here, we show that targeted editing of the C-terminal sequence of the embryo lethal gene <i>MITOGEN-ACTIVATED PROTEIN KINASES 1</i> (<i>OsMPK1</i>) results in weak mutants. This C-terminal-edited osmpk1 mutants displayed severe developmental defects and altered disease resistance but generated tens of viable seeds that inherited the mutations. Using the same C-terminal editing approach, we also obtained viable mutants for a wall-associated protein kinase (Os07g0493200) and a leucine-rich repeat receptor-like protein kinase (Os01g0239700), while the null mutations of these genes were lethal. These data suggest that protein kinase activity could be reduced by introducing frameshift mutations adjacent to the C-terminus, which could generate valuable resources for gene function studies and tune protein kinase activity for signaling pathway engineering.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 2","pages":"219 - 224"},"PeriodicalIF":4.6,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00165-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140976732","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}
Basic helix-loop-helix (bHLH) transcription factors are widely distributed in eukaryotes, and in plants, they regulate many biological processes, such as cell differentiation, development, metabolism, and stress responses. Few studies have focused on the roles of bHLH transcription factors in regulating growth, development, and stress responses in maize (Zea mays), even though such information would greatly benefit maize breeding programs. In this study, we cloned the maize transcription factor gene ZmbHLH36 (Gene ID: 100193615, GRMZM2G008691). ZmbHLH36 possesses conserved domains characteristic of the bHLH family. RT-qPCR analysis revealed that ZmbHLH36 was expressed at the highest level in maize roots and exhibited different expression patterns under various abiotic stress conditions. Transgenic Arabidopsis (Arabidopsis thaliana) plants heterologously expressing ZmbHLH36 had significantly longer roots than the corresponding non-transgenic plants under 0.1 and 0.15 mol L−1 NaCl treatment as well as 0.2 mol L−1 mannitol treatment. Phenotypic analysis of soil-grown plants under stress showed that transgenic Arabidopsis plants harboring ZmbHLH36 exhibited significantly enhanced drought tolerance and salt tolerance compared to the corresponding non-transgenic plants. Malondialdehyde contents were lower and peroxidase activity was higher in ZmbHLH36-expressing Arabidopsis plants than in the corresponding non-transgenic plants. ZmbHLH36 localized to the nucleus when expressed in maize protoplasts. This study provides a systematic analysis of the effects of ZmbHLH36 on root growth, development, and stress responses in transgenic Arabidopsis, laying a foundation for further analysis of its roles and molecular mechanisms in maize.
{"title":"Heterologous expression of the maize transcription factor ZmbHLH36 enhances abiotic stress tolerance in Arabidopsis","authors":"Zhenggang Dai, Keyong Zhao, Dengyu Zheng, Siyu Guo, Huawen Zou, Zhongyi Wu, Chun Zhang","doi":"10.1007/s42994-024-00159-3","DOIUrl":"10.1007/s42994-024-00159-3","url":null,"abstract":"<div><p>Basic helix-loop-helix (bHLH) transcription factors are widely distributed in eukaryotes, and in plants, they regulate many biological processes, such as cell differentiation, development, metabolism, and stress responses. Few studies have focused on the roles of bHLH transcription factors in regulating growth, development, and stress responses in maize (<i>Zea mays</i>), even though such information would greatly benefit maize breeding programs. In this study, we cloned the maize transcription factor gene <i>ZmbHLH36</i> (Gene ID: 100193615, GRMZM2G008691). ZmbHLH36 possesses conserved domains characteristic of the bHLH family. RT-qPCR analysis revealed that <i>ZmbHLH36</i> was expressed at the highest level in maize roots and exhibited different expression patterns under various abiotic stress conditions. Transgenic <i>Arabidopsis</i> (<i>Arabidopsis thaliana</i>) plants heterologously expressing <i>ZmbHLH36</i> had significantly longer roots than the corresponding non-transgenic plants under 0.1 and 0.15 mol L<sup>−1</sup> NaCl treatment as well as 0.2 mol L<sup>−1</sup> mannitol treatment. Phenotypic analysis of soil-grown plants under stress showed that transgenic <i>Arabidopsis</i> plants harboring <i>ZmbHLH36</i> exhibited significantly enhanced drought tolerance and salt tolerance compared to the corresponding non-transgenic plants. Malondialdehyde contents were lower and peroxidase activity was higher in <i>ZmbHLH36</i>-expressing <i>Arabidopsis</i> plants than in the corresponding non-transgenic plants. ZmbHLH36 localized to the nucleus when expressed in maize protoplasts. This study provides a systematic analysis of the effects of ZmbHLH36 on root growth, development, and stress responses in transgenic <i>Arabidopsis</i>, laying a foundation for further analysis of its roles and molecular mechanisms in maize.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 3","pages":"339 - 350"},"PeriodicalIF":4.6,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00159-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140982769","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}
Pub Date : 2024-05-13DOI: 10.1007/s42994-024-00164-6
Man Zhang, Yu Ming, Hong-Bin Wang, Hong-Lei Jin
Plants absorb light energy for photosynthesis via photosystem complexes in their chloroplasts. However, excess light can damage the photosystems and decrease photosynthetic output, thereby inhibiting plant growth and development. Plants have developed a series of light acclimation strategies that allow them to withstand high light. In the first line of defense against excess light, leaves and chloroplasts move away from the light and the plant accumulates compounds that filter and reflect the light. In the second line of defense, known as photoprotection, plants dissipate excess light energy through non-photochemical quenching, cyclic electron transport, photorespiration, and scavenging of excess reactive oxygen species. In the third line of defense, which occurs after photodamage, plants initiate a cycle of photosystem (mainly photosystem II) repair. In addition to being the site of photosynthesis, chloroplasts sense stress, especially light stress, and transduce the stress signal to the nucleus, where it modulates the expression of genes involved in the stress response. In this review, we discuss current progress in our understanding of the strategies and mechanisms employed by plants to withstand high light at the whole-plant, cellular, physiological, and molecular levels across the three lines of defense.
{"title":"Strategies for adaptation to high light in plants","authors":"Man Zhang, Yu Ming, Hong-Bin Wang, Hong-Lei Jin","doi":"10.1007/s42994-024-00164-6","DOIUrl":"10.1007/s42994-024-00164-6","url":null,"abstract":"<div><p>Plants absorb light energy for photosynthesis via photosystem complexes in their chloroplasts. However, excess light can damage the photosystems and decrease photosynthetic output, thereby inhibiting plant growth and development. Plants have developed a series of light acclimation strategies that allow them to withstand high light. In the first line of defense against excess light, leaves and chloroplasts move away from the light and the plant accumulates compounds that filter and reflect the light. In the second line of defense, known as photoprotection, plants dissipate excess light energy through non-photochemical quenching, cyclic electron transport, photorespiration, and scavenging of excess reactive oxygen species. In the third line of defense, which occurs after photodamage, plants initiate a cycle of photosystem (mainly photosystem II) repair. In addition to being the site of photosynthesis, chloroplasts sense stress, especially light stress, and transduce the stress signal to the nucleus, where it modulates the expression of genes involved in the stress response. In this review, we discuss current progress in our understanding of the strategies and mechanisms employed by plants to withstand high light at the whole-plant, cellular, physiological, and molecular levels across the three lines of defense.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 3","pages":"381 - 393"},"PeriodicalIF":4.6,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00164-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140984916","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}
Pub Date : 2024-05-08DOI: 10.1007/s42994-024-00147-7
Yilin Shen, Tao Ye, Zihan Li, Torotwa Herman Kimutai, Hao Song, Xiaoou Dong, Jianmin Wan
Genome editing holds great promise for the molecular breeding of plants, yet its application is hindered by the shortage of simple and effective means of delivering genome editing reagents into plants. Conventional plant transformation-based methods for delivery of genome editing reagents into plants often involve prolonged tissue culture, a labor-intensive and technically challenging process for many elite crop cultivars. In this review, we describe various virus-based methods that have been employed to deliver genome editing reagents, including components of the CRISPR/Cas machinery and donor DNA for precision editing in plants. We update the progress in these methods with recent successful examples of genome editing achieved through virus-based delivery in different plant species, highlight the advantages and limitations of these delivery approaches, and discuss the remaining challenges.
基因组编辑为植物的分子育种带来了巨大希望,但由于缺乏简单有效的方法将基因组编辑试剂输送到植物体内,基因组编辑的应用受到了阻碍。将基因组编辑试剂输送到植物体内的传统植物转化方法往往涉及长时间的组织培养,对于许多优良作物栽培品种来说,这是一个劳动密集型且具有技术挑战性的过程。在本综述中,我们介绍了各种基于病毒的基因组编辑试剂输送方法,包括用于植物精准编辑的 CRISPR/Cas 机器和供体 DNA 的组件。我们介绍了这些方法的最新进展,以及最近在不同植物物种中通过病毒递送实现基因组编辑的成功实例,强调了这些递送方法的优势和局限性,并讨论了仍然存在的挑战。
{"title":"Exploiting viral vectors to deliver genome editing reagents in plants","authors":"Yilin Shen, Tao Ye, Zihan Li, Torotwa Herman Kimutai, Hao Song, Xiaoou Dong, Jianmin Wan","doi":"10.1007/s42994-024-00147-7","DOIUrl":"10.1007/s42994-024-00147-7","url":null,"abstract":"<div><p>Genome editing holds great promise for the molecular breeding of plants, yet its application is hindered by the shortage of simple and effective means of delivering genome editing reagents into plants. Conventional plant transformation-based methods for delivery of genome editing reagents into plants often involve prolonged tissue culture, a labor-intensive and technically challenging process for many elite crop cultivars. In this review, we describe various virus-based methods that have been employed to deliver genome editing reagents, including components of the CRISPR/Cas machinery and donor DNA for precision editing in plants. We update the progress in these methods with recent successful examples of genome editing achieved through virus-based delivery in different plant species, highlight the advantages and limitations of these delivery approaches, and discuss the remaining challenges.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 2","pages":"247 - 261"},"PeriodicalIF":4.6,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00147-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141001110","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}
Pub Date : 2024-05-07DOI: 10.1007/s42994-024-00162-8
Kai Sun, Wei Zhang, Xiaolin Wang, Chuan-Chao Dai
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.
{"title":"Decoding the microbiome for sustainable agriculture","authors":"Kai Sun, Wei Zhang, Xiaolin Wang, 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, Guoliang Ma, Xiu Li, Lili Guo, Yanzhi Li, Yajun Liu, Wenzhao Wang, Xiaolan Jiang, De-Yu Xie, Liping Gao, 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}
Pub Date : 2024-04-30DOI: 10.1007/s42994-024-00161-9
Sijia Lu, Chao Fang, Jun Abe, Fanjiang Kong, Baohui Liu
{"title":"Correction: Current overview on the genetic basis of key genes involved in soybean domestication","authors":"Sijia Lu, Chao Fang, Jun Abe, Fanjiang Kong, 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}
Pub Date : 2024-04-29DOI: 10.1007/s42994-024-00153-9
Mengyuan Liu, Xiang Zhang, Wen Xu, Guiting Kang, Ya Liu, Xinxiang Liu, Wen Ren, Jiuran Zhao, Jinxiao Yang
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 OsGS1 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.
高效、精确的基因组缺失为植物研究中的蛋白质功能调查和提高农业性状带来了希望。在这项研究中,我们测试了 PRIME-Del (PDel) 策略,该策略使用一对以相反 DNA 链为目标的质粒编辑向导 RNA(pegRNA),在 6 个内源靶点的 60 bp 片段缺失中实现了 55.8% 的平均缺失效率。此外,在转基因水稻植株中,对 OsGS1 位点 2000 bp 片段的精确删除效率高达 84.2%。为了添加两个核酸序列之间被无意删除的碱基,我们采用了 PDel/Syn 策略,在 RT 模板中需要修补的区域引入多个同义碱基突变。PDel/Syn策略在六个内源性靶点平均实现了58.1%的删除效率,高于PDel策略。本研究提出的策略有助于在转基因水稻植物中实现更准确、更灵活的删除:在线版本包含补充材料,可查阅 10.1007/s42994-024-00153-9。
{"title":"Efficient and precise genomic deletion in rice using enhanced prime editing","authors":"Mengyuan Liu, Xiang Zhang, Wen Xu, Guiting Kang, Ya Liu, Xinxiang Liu, Wen Ren, Jiuran Zhao, 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}
Pub Date : 2024-04-22DOI: 10.1007/s42994-024-00157-5
Hui Wang, Jian Ding, Jingyan Zhu, Xiaoshuang Liu, Rongfang Xu, Ruiying Qin, Dongfang Gu, Min Li, Pengcheng Wei, Juan Li
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 Faecalibaculum rodentium 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 WX 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.
{"title":"Developing a CRISPR/FrCas9 system for core promoter editing in rice","authors":"Hui Wang, Jian Ding, Jingyan Zhu, Xiaoshuang Liu, Rongfang Xu, Ruiying Qin, Dongfang Gu, Min Li, Pengcheng Wei, 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 T<sub>0</sub> 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}
Pub Date : 2024-04-18DOI: 10.1007/s42994-024-00160-w
Zhifang Zhang, Junkui Ma, Xia Yang, Shan Liang, Yucheng Liu, Yaqin Yuan, Qianjin Liang, Yanting Shen, Guoan Zhou, Min Zhang, Zhixi Tian, Shulin Liu
Soybean [Glycine max (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 GmACO1, 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 GmACO1 expression was reduced after rhizobial infection, and that GmACO1 negatively regulated soybean nodule formation. Overall, our findings provide insights into soybean cultivars for future breeding.
{"title":"Natural GmACO1 allelic variations confer drought tolerance and influence nodule formation in soybean","authors":"Zhifang Zhang, Junkui Ma, Xia Yang, Shan Liang, Yucheng Liu, Yaqin Yuan, Qianjin Liang, Yanting Shen, Guoan Zhou, Min Zhang, Zhixi Tian, 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}