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Zhai S, Liu H, Xia X, Li H, Cao X, He Z, Ma W, Liu C, Song J, Liu A, Zhang J, Liu J. Functional analysis of polyphenol oxidase 1 gene in common wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1171839. [PMID: 37583591 PMCID: PMC10424926 DOI: 10.3389/fpls.2023.1171839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/07/2023] [Indexed: 08/17/2023]
Abstract
Polyphenol oxidase (PPO) activity is a major cause of the undesirable brown color of wheat-based products. Ppo1, a major gene for PPO activity, was cloned based on sequence homology in previous studies; however, its function and regulation mechanism remain unclear. In this study, the function and genetic regulation of Ppo1 were analyzed using RNA interference (RNAi) and Targeting Induced Local Lesions IN Genomes (TILLING) technology, and superior mutants were identified. Compared with the control, the level of Ppo1 transcript in RNAi transgenic lines was drastically decreased by 15.5%-60.9% during grain development, and PPO activity was significantly reduced by 12.9%-20.4%, confirming the role of Ppo1 in PPO activity. Thirty-two Ppo1 mutants were identified in the ethyl methanesulfonate (EMS)-mutagenized population, including eight missense mutations, 16 synonymous mutations, and eight intron mutations. The expression of Ppo1 was reduced significantly by 6.7%-37.1% and 10.1%-54.4% in mutants M092141 (G311S) and M091098 (G299R), respectively, in which PPO activity was decreased by 29.7% and 28.8%, respectively, indicating that mutation sites of two mutants have important effects on PPO1 function. Sequence and structure analysis revealed that the two sites were highly conserved among 74 plant species, where the frequency of glycine was 94.6% and 100%, respectively, and adjacent to the entrance of the hydrophobic pocket of the active site. The M092141 and M091098 mutants can be used as important germplasms to develop wheat cultivars with low grain PPO activity. This study provided important insights into the molecular mechanism of Ppo1 and the genetic improvement of wheat PPO activity.
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Affiliation(s)
- Shengnan Zhai
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hang Liu
- Australian-China Joint Centre for Wheat Improvement, Western Australian State Agriculture Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haosheng Li
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xinyou Cao
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wujun Ma
- Australian-China Joint Centre for Wheat Improvement, Western Australian State Agriculture Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Cheng Liu
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jianmin Song
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Aifeng Liu
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jingjuan Zhang
- Australian-China Joint Centre for Wheat Improvement, Western Australian State Agriculture Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Jianjun Liu
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
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Yang W, Zhou L, Wang J, Wang L, Gao S, Wang G. Knockout of a diatom cryptochrome by CRISPR/Cas9 causes an increase in light-harvesting protein levels and accumulation of fucoxanthin. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Chen GQ, Johnson K, Nazarenus TJ, Ponciano G, Morales E, Cahoon EB. Genetic Engineering of Lesquerella with Increased Ricinoleic Acid Content in Seed Oil. PLANTS 2021; 10:plants10061093. [PMID: 34072473 PMCID: PMC8230273 DOI: 10.3390/plants10061093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023]
Abstract
Seeds of castor (Ricinus communis) are enriched in oil with high levels of the industrially valuable fatty acid ricinoleic acid (18:1OH), but production of this plant is limited because of the cooccurrence of the ricin toxin in its seeds. Lesquerella (Physaria fendleri) is being developed as an alternative industrial oilseed because its seeds accumulate lesquerolic acid (20:1OH), an elongated form of 18:1OH in seed oil which lacks toxins. Synthesis of 20:1OH is through elongation of 18:1OH by a lesquerella elongase, PfKCS18. Oleic acid (18:1) is the substrate for 18:1OH synthesis, but it is also used by fatty acid desaturase 2 (FAD2) and FAD3 to sequentially produce linoleic and linolenic acids. To develop lesquerella that produces 18:1OH-rich seed oils such as castor, RNA interference sequences targeting KCS18, FAD2 and FAD3 were introduced to lesquerella to suppress the elongation and desaturation steps. Seeds from transgenic lines had increased 18:1OH to 1.1-26.6% compared with that of 0.4-0.6% in wild-type (WT) seeds. Multiple lines had reduced 18:1OH levels in the T2 generation, including a top line with 18:1OH reduced from 26.7% to 19%. Transgenic lines also accumulated more 18:1 than that of WT, indicating that 18:1 is not efficiently used for 18:1OH synthesis and accumulation. Factors limiting 18:1OH accumulation and new targets for further increasing 18:1OH production are discussed. Our results provide insights into complex mechanisms of oil biosynthesis in lesquerella and show the biotechnological potential to tailor lesquerella seeds to produce castor-like industrial oil functionality.
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Affiliation(s)
- Grace Q. Chen
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan St., Albany, CA 94710, USA; (K.J.); (G.P.); (E.M.)
- Correspondence:
| | - Kumiko Johnson
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan St., Albany, CA 94710, USA; (K.J.); (G.P.); (E.M.)
| | - Tara J. Nazarenus
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (T.J.N.); (E.B.C.)
| | - Grisel Ponciano
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan St., Albany, CA 94710, USA; (K.J.); (G.P.); (E.M.)
| | - Eva Morales
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan St., Albany, CA 94710, USA; (K.J.); (G.P.); (E.M.)
| | - Edgar B. Cahoon
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (T.J.N.); (E.B.C.)
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Qi T, Guo J, Peng H, Liu P, Kang Z, Guo J. Host-Induced Gene Silencing: A Powerful Strategy to Control Diseases of Wheat and Barley. Int J Mol Sci 2019; 20:E206. [PMID: 30626050 PMCID: PMC6337638 DOI: 10.3390/ijms20010206] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 12/31/2018] [Accepted: 01/03/2019] [Indexed: 12/15/2022] Open
Abstract
Wheat and barley are the most highly produced and consumed grains in the world. Various pathogens-viruses, bacteria, fungi, insect pests, and nematode parasites-are major threats to yield and economic losses. Strategies for the management of disease control mainly depend on resistance or tolerance breeding, chemical control, and biological control. The discoveries of RNA silencing mechanisms provide a transgenic approach for disease management. Host-induced gene silencing (HIGS) employing RNA silencing mechanisms and, specifically, silencing the targets of invading pathogens, has been successfully applied in crop disease prevention. Here, we cover recent studies that indicate that HIGS is a valuable tool to protect wheat and barley from diseases in an environmentally friendly way.
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Affiliation(s)
- Tuo Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Huan Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Peng Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
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A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize. Cell 2018; 173:839-850.e18. [DOI: 10.1016/j.cell.2018.03.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 11/13/2017] [Accepted: 03/02/2018] [Indexed: 01/08/2023]
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Zhang J, Yu D, Zhang Y, Liu K, Xu K, Zhang F, Wang J, Tan G, Nie X, Ji Q, Zhao L, Li C. Vacuum and Co-cultivation Agroinfiltration of (Germinated) Seeds Results in Tobacco Rattle Virus (TRV) Mediated Whole-Plant Virus-Induced Gene Silencing (VIGS) in Wheat and Maize. FRONTIERS IN PLANT SCIENCE 2017; 8:393. [PMID: 28382049 PMCID: PMC5360694 DOI: 10.3389/fpls.2017.00393] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/07/2017] [Indexed: 05/06/2023]
Abstract
Tobacco rattle virus (TRV)-mediated virus-induced gene silencing (VIGS) has been frequently used in dicots. Here we show that it can also be used in monocots, by presenting a system involving use of a novel infiltration solution (containing acetosyringone, cysteine, and Tween 20) that enables whole-plant level VIGS of (germinated) seeds in wheat and maize. Using the established system, phytoene desaturase (PDS) genes were successfully silenced, resulting in typical photo-bleaching symptoms in the leaves of treated wheat and maize. In addition, three wheat homoeoalleles of MLO, a key gene repressing defense responses to powdery mildew in wheat, were simultaneously silenced in susceptible wheat with this system, resulting in it becoming resistant to powdery mildew. The system has the advantages generally associated with TRV-mediated VIGS systems (e.g., high-efficiency, mild virus infection symptoms, and effectiveness in different organs). However, it also has the following further advantages: (germinated) seed-stage agroinfiltration; greater rapidity and convenience; whole-plant level gene silencing; adequately stable transformation; and suitability for studying functions of genes involved in seed germination and early plant development stages.
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Affiliation(s)
- Ju Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Deshui Yu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Yi Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Kun Liu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Kedong Xu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Fuli Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Jian Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Guangxuan Tan
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Xianhui Nie
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Qiaohua Ji
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Lu Zhao
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Chengwei Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Technology, Henan Institute of Science and Technology, XinxiangChina
- *Correspondence: Chengwei Li,
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Ben-Amar A, Daldoul S, Reustle GM, Krczal G, Mliki A. Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics. Curr Genomics 2016; 17:460-475. [PMID: 28217003 PMCID: PMC5282599 DOI: 10.2174/1389202917666160520102827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/12/2015] [Accepted: 01/05/2016] [Indexed: 11/22/2022] Open
Abstract
In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism. With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes. Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies. Integration of different omics platforms along with gene annotation and computational analysis may elucidate a complete view in a system biology level. Extensive investigations on reverse genetics methodologies were deployed for assigning biological function to a specific gene or gene product. We provide here an updated overview of these high throughout strategies highlighting recent advances in the knowledge of functional genomics in plants.
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Affiliation(s)
- Anis Ben-Amar
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Samia Daldoul
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
| | - Götz M. Reustle
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Gabriele Krczal
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Ahmed Mliki
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
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Zhai S, Li G, Sun Y, Song J, Li J, Song G, Li Y, Ling H, He Z, Xia X. Genetic analysis of phytoene synthase 1 (Psy1) gene function and regulation in common wheat. BMC PLANT BIOLOGY 2016; 16:228. [PMID: 27769185 PMCID: PMC5073469 DOI: 10.1186/s12870-016-0916-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/06/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Phytoene synthase 1 (PSY1) is the most important regulatory enzyme in carotenoid biosynthesis, whereas its function is hardly known in common wheat. The aims of the present study were to investigate Psy1 function and genetic regulation using reverse genetics approaches. RESULTS Transcript levels of Psy1 in RNAi transgenic lines were decreased by 54-76 % and yellow pigment content (YPC) was reduced by 26-35 % compared with controls, confirming the impact of Psy1 on carotenoid accumulation. A series of candidate genes involved in secondary metabolic pathways and core metabolic processes responded to Psy1 down-regulation. The aspartate rich domain (DXXXD) was important for PSY1 function, and conserved nucleotides adjacent to the domain influenced YPC by regulating gene expression, enzyme activity or alternative splicing. Compensatory responses analysis indicated that three Psy1 homoeologs may be coordinately regulated under normal conditions, but separately regulated under stress. The period 14 days post anthesis (DPA) was found to be a key regulation node during grain development. CONCLUSION The findings define key aspects of flour color regulation in wheat and facilitate the genetic improvement of wheat quality targeting color/nutritional specifications required for specific end products.
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Affiliation(s)
- Shengnan Zhai
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Youwei Sun
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Jianmin Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Jihu Li
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Guoqi Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Yulian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Hongqing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
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Wang R, Yang X, Wang N, Liu X, Nelson RS, Li W, Fan Z, Zhou T. An efficient virus-induced gene silencing vector for maize functional genomics research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:102-15. [PMID: 26921244 DOI: 10.1111/tpj.13142] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/01/2016] [Accepted: 02/08/2016] [Indexed: 05/02/2023]
Abstract
Maize is a major crop whose rich genetic diversity provides an advanced resource for genetic research. However, a tool for rapid transient gene function analysis in maize that may be utilized in most maize cultivars has been lacking, resulting in reliance on time-consuming stable transformation and mutation studies to obtain answers. We developed an efficient virus-induced gene silencing (VIGS) vector for maize based on a naturally maize-infecting cucumber mosaic virus (CMV) strain, ZMBJ-CMV. An infectious clone of ZMBJ-CMV was constructed, and a vascular puncture inoculation method utilizing Agrobacterium was optimized to improve its utility for CMV infection of maize. ZMBJ-CMV was then modified to function as a VIGS vector. The ZMBJ-CMV vector induced mild to moderate symptoms in many maize lines, making it useful for gene function studies in critically important maize cultivars, such as the sequenced reference inbred line B73. Using this CMV VIGS system, expression of two endogenous genes, ZmPDS and ZmIspH, was found to be decreased by 75% and 78%, respectively, compared with non-silenced tissue. Inserts with lengths of 100-300 bp produced the most complete transcriptional and visual silencing phenotypes. Moreover, genes related to autophagy, ZmATG3 and ZmATG8a, were also silenced, and it was found that they function in leaf starch degradation. These results indicate that our ZMBJ-CMV VIGS vector provides a tool for rapid and efficient gene function studies in maize.
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Affiliation(s)
- Rong Wang
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xinxin Yang
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Nian Wang
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xuedong Liu
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Richard S Nelson
- Plant Biology Division, The Samuel Roberts Noble Foundation Inc., 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
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Abstract
Maize has a long history of genetic and genomic tool development and is considered one of the most accessible higher plant systems. With a fully sequenced genome, a suite of cytogenetic tools, methods for both forward and reverse genetics, and characterized phenotype markers, maize is amenable to studying questions beyond plant biology. Major discoveries in the areas of transposons, imprinting, and chromosome biology came from work in maize. Moving forward in the post-genomic era, this classic model system will continue to be at the forefront of basic biological study. In this review, we outline the basics of working with maize and describe its rich genetic toolbox.
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11
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Danzer J, Mellott E, Bui AQ, Le BH, Martin P, Hashimoto M, Perez-Lesher J, Chen M, Pelletier JM, Somers DA, Goldberg RB, Harada JJ. Down-Regulating the Expression of 53 Soybean Transcription Factor Genes Uncovers a Role for SPEECHLESS in Initiating Stomatal Cell Lineages during Embryo Development. PLANT PHYSIOLOGY 2015; 168:1025-35. [PMID: 25963149 PMCID: PMC4741349 DOI: 10.1104/pp.15.00432] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/30/2015] [Indexed: 05/18/2023]
Abstract
We used an RNA interference screen to assay the function of 53 transcription factor messenger RNAs (mRNAs) that accumulate specifically within soybean (Glycine max) seed regions, subregions, and tissues during development. We show that basic helix-loop-helix (bHLH) transcription factor genes represented by Glyma04g41710 and its paralogs are required for the formation of stoma in leaves and stomatal precursor complexes in mature embryo cotyledons. Phylogenetic analysis indicates that these bHLH transcription factor genes are orthologous to Arabidopsis (Arabidopsis thaliana) SPEECHLESS (SPCH) that initiate asymmetric cell divisions in the leaf protoderm layer and establish stomatal cell lineages. Soybean SPCH (GmSPCH) mRNAs accumulate primarily in embryo, seedling, and leaf epidermal layers. Expression of Glyma04g41710 under the control of the SPCH promoter rescues the Arabidopsis spch mutant, indicating that Glyma04g41710 is a functional ortholog of SPCH. Developing soybean embryos do not form mature stoma, and stomatal differentiation is arrested at the guard mother cell stage. We analyzed the accumulation of GmSPCH mRNAs during soybean seed development and mRNAs orthologous to MUTE, FAMA, and inducer of C-repeat/dehydration responsive element-binding factor expression1/scream2 that are required for stoma formation in Arabidopsis. The mRNA accumulation patterns provide a potential explanation for guard mother cell dormancy in soybean embryos. Our results suggest that variation in the timing of bHLH transcription factor gene expression can explain the diversity of stomatal forms observed during plant development.
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Affiliation(s)
- John Danzer
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Eric Mellott
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Anhthu Q Bui
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Brandon H Le
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Patrick Martin
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Meryl Hashimoto
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Jeanett Perez-Lesher
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Min Chen
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Julie M Pelletier
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - David A Somers
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Robert B Goldberg
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - John J Harada
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
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12
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Li Q, Eichten SR, Hermanson PJ, Zaunbrecher VM, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess DL, Richmond TA, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Kaeppler SM, Jeddeloh JA, Springer NM. Genetic perturbation of the maize methylome. THE PLANT CELL 2014; 26:4602-16. [PMID: 25527708 PMCID: PMC4311211 DOI: 10.1105/tpc.114.133140] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/17/2014] [Accepted: 12/02/2014] [Indexed: 05/18/2023]
Abstract
DNA methylation can play important roles in the regulation of transposable elements and genes. A collection of mutant alleles for 11 maize (Zea mays) genes predicted to play roles in controlling DNA methylation were isolated through forward- or reverse-genetic approaches. Low-coverage whole-genome bisulfite sequencing and high-coverage sequence-capture bisulfite sequencing were applied to mutant lines to determine context- and locus-specific effects of these mutations on DNA methylation profiles. Plants containing mutant alleles for components of the RNA-directed DNA methylation pathway exhibit loss of CHH methylation at many loci as well as CG and CHG methylation at a small number of loci. Plants containing loss-of-function alleles for chromomethylase (CMT) genes exhibit strong genome-wide reductions in CHG methylation and some locus-specific loss of CHH methylation. In an attempt to identify stocks with stronger reductions in DNA methylation levels than provided by single gene mutations, we performed crosses to create double mutants for the maize CMT3 orthologs, Zmet2 and Zmet5, and for the maize DDM1 orthologs, Chr101 and Chr106. While loss-of-function alleles are viable as single gene mutants, the double mutants were not recovered, suggesting that severe perturbations of the maize methylome may have stronger deleterious phenotypic effects than in Arabidopsis thaliana.
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Affiliation(s)
- Qing Li
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Steven R Eichten
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Peter J Hermanson
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | | | - Jawon Song
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | | | | | - Thelma F Madzima
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - Amy E Sloan
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - Ji Huang
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | | | | | - Karen M McGinnis
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | | | | | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
| | | | - Nathan M Springer
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108
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13
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Dang TVT, Windelinckx S, Henry IM, De Coninck B, Cammue BPA, Swennen R, Remy S. Assessment of RNAi-induced silencing in banana (Musa spp.). BMC Res Notes 2014; 7:655. [PMID: 25230584 PMCID: PMC4177175 DOI: 10.1186/1756-0500-7-655] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 09/11/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In plants, RNA- based gene silencing mediated by small RNAs functions at the transcriptional or post-transcriptional level to negatively regulate target genes, repetitive sequences, viral RNAs and/or transposon elements. Post-transcriptional gene silencing (PTGS) or the RNA interference (RNAi) approach has been achieved in a wide range of plant species for inhibiting the expression of target genes by generating double-stranded RNA (dsRNA). However, to our knowledge, successful RNAi-application to knock-down endogenous genes has not been reported in the important staple food crop banana. RESULTS Using embryogenic cell suspension (ECS) transformed with ß-glucuronidase (GUS) as a model system, we assessed silencing of gusAINT using three intron-spliced hairpin RNA (ihpRNA) constructs containing gusAINT sequences of 299-nt, 26-nt and 19-nt, respectively. Their silencing potential was analysed in 2 different experimental set-ups. In the first, Agrobacterium-mediated co-transformation of banana ECS with a gusAINT containing vector and an ihpRNA construct resulted in a significantly reduced GUS enzyme activity 6-8 days after co-cultivation with either the 299-nt and 19-nt ihpRNA vectors. In the second approach, these ihpRNA constructs were transferred to stable GUS-expressing ECS and their silencing potential was evaluated in the regenerated in vitro plants. In comparison to control plants, transgenic plants transformed with the 299-nt gusAINT targeting sequence showed a 4.5 fold down-regulated gusA mRNA expression level, while GUS enzyme activity was reduced by 9 fold. Histochemical staining of plant tissues confirmed these findings. Northern blotting used to detect the expression of siRNA in the 299-nt ihpRNA vector transgenic in vitro plants revealed a negative relationship between siRNA expression and GUS enzyme activity. In contrast, no reduction in GUS activity or GUS mRNA expression occurred in the regenerated lines transformed with either of the two gusAINT oligo target sequences (26-nt and 19-nt). CONCLUSIONS RNAi-induced silencing was achieved in banana, both at transient and stable level, resulting in significant reduction of gene expression and enzyme activity. The success of silencing was dependent on the targeted region of the target gene. The successful generation of transgenic ECS for second transformation with (an)other construct(s) can be of value for functional genomics research in banana.
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MESH Headings
- Cell Line, Transformed
- Feasibility Studies
- Gene Expression Regulation, Plant
- Gene Knockdown Techniques
- Glucuronidase/genetics
- Glucuronidase/metabolism
- Musa/embryology
- Musa/enzymology
- Musa/genetics
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified/embryology
- Plants, Genetically Modified/enzymology
- Plants, Genetically Modified/genetics
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Time Factors
- Transfection
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Affiliation(s)
- Tuong Vi T Dang
- />Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Saskia Windelinckx
- />Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Isabelle M Henry
- />Department of Plant Biology and Genome Center, U.C.Davis, 451 E. Health Sciences Drive, Davis, CA 95616 USA
| | - Barbara De Coninck
- />Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- />Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - Bruno PA Cammue
- />Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- />Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - Rony Swennen
- />Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- />Bioversity International, Willem de Croylaan 42 bus 2455, 3001 Leuven, Belgium
- />International Institute of Tropical Agriculture, P.O. Box 10, Duluti, Arusha, Tanzania
| | - Serge Remy
- />Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
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14
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Haun W, Coffman A, Clasen BM, Demorest ZL, Lowy A, Ray E, Retterath A, Stoddard T, Juillerat A, Cedrone F, Mathis L, Voytas DF, Zhang F. Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:934-40. [PMID: 24851712 DOI: 10.1111/pbi.12201] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/27/2014] [Accepted: 04/24/2014] [Indexed: 05/03/2023]
Abstract
Soybean oil is high in polyunsaturated fats and is often partially hydrogenated to increase its shelf life and improve oxidative stability. The trans-fatty acids produced through hydrogenation pose a health threat. Soybean lines that are low in polyunsaturated fats were generated by introducing mutations in two fatty acid desaturase 2 genes (FAD2-1A and FAD2-1B), which in the seed convert the monounsaturated fat, oleic acid, to the polyunsaturated fat, linoleic acid. Transcription activator-like effector nucleases (TALENs) were engineered to recognize and cleave conserved DNA sequences in both genes. In four of 19 transgenic soybean lines expressing the TALENs, mutations in FAD2-1A and FAD2-1B were observed in DNA extracted from leaf tissue; three of the four lines transmitted heritable FAD2-1 mutations to the next generation. The fatty acid profile of the seed was dramatically changed in plants homozygous for mutations in both FAD2-1A and FAD2-1B: oleic acid increased from 20% to 80% and linoleic acid decreased from 50% to under 4%. Further, mutant plants were identified that lacked the TALEN transgene and only carried the targeted mutations. The ability to create a valuable trait in a single generation through targeted modification of a gene family demonstrates the power of TALENs for genome engineering and crop improvement.
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Affiliation(s)
- William Haun
- Cellectis plant sciences Inc., New Brighton, MN, USA
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15
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Mascheretti I, Battaglia R, Mainieri D, Altana A, Lauria M, Rossi V. The WD40-repeat proteins NFC101 and NFC102 regulate different aspects of maize development through chromatin modification. THE PLANT CELL 2013; 25:404-20. [PMID: 23424244 PMCID: PMC3608768 DOI: 10.1105/tpc.112.107219] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The maize (Zea mays) nucleosome remodeling factor complex component101 (nfc101) and nfc102 are putative paralogs encoding WD-repeat proteins with homology to plant and mammalian components of various chromatin modifying complexes. In this study, we generated transgenic lines with simultaneous nfc101 and nfc102 downregulation and analyzed phenotypic alterations, along with effects on RNA levels, the binding of NFC101/NFC102, and Rpd3-type histone deacetylases (HDACs), and histone modifications at selected targets. Direct NFC101/NFC102 binding and negative correlation with mRNA levels were observed for indeterminate1 (id1) and the florigen Zea mays CENTRORADIALIS8 (ZCN8), key activators of the floral transition. In addition, the abolition of NFC101/NFC102 association with repetitive sequences of different transposable elements (TEs) resulted in tissue-specific upregulation of nonpolyadenylated RNAs produced by these regions. All direct nfc101/nfc102 targets showed histone modification patterns linked to active chromatin in nfc101/nfc102 downregulation lines. However, different mechanisms may be involved because NFC101/NFC102 proteins mediate HDAC recruitment at id1 and TE repeats but not at ZCN8. These results, along with the pleiotropic effects observed in nfc101/nfc102 downregulation lines, suggest that NFC101 and NFC102 are components of distinct chromatin modifying complexes, which operate in different pathways and influence diverse aspects of maize development.
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16
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Alakonya A, Kumar R, Koenig D, Kimura S, Townsley B, Runo S, Garces HM, Kang J, Yanez A, David-Schwartz R, Machuka J, Sinha N. Interspecific RNA interference of SHOOT MERISTEMLESS-like disrupts Cuscuta pentagona plant parasitism. THE PLANT CELL 2012; 24:3153-66. [PMID: 22822208 PMCID: PMC3426138 DOI: 10.1105/tpc.112.099994] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 06/13/2012] [Accepted: 07/05/2012] [Indexed: 05/17/2023]
Abstract
Infection of crop species by parasitic plants is a major agricultural hindrance resulting in substantial crop losses worldwide. Parasitic plants establish vascular connections with the host plant via structures termed haustoria, which allow acquisition of water and nutrients, often to the detriment of the infected host. Despite the agricultural impact of parasitic plants, the molecular and developmental processes by which host/parasitic interactions are established are not well understood. Here, we examine the development and subsequent establishment of haustorial connections by the parasite dodder (Cuscuta pentagona) on tobacco (Nicotiana tabacum) plants. Formation of haustoria in dodder is accompanied by upregulation of dodder KNOTTED-like homeobox transcription factors, including SHOOT MERISTEMLESS-like (STM). We demonstrate interspecific silencing of a STM gene in dodder driven by a vascular-specific promoter in transgenic host plants and find that this silencing disrupts dodder growth. The reduced efficacy of dodder infection on STM RNA interference transgenics results from defects in haustorial connection, development, and establishment. Identification of transgene-specific small RNAs in the parasite, coupled with reduced parasite fecundity and increased growth of the infected host, demonstrates the efficacy of interspecific small RNA-mediated silencing of parasite genes. This technology has the potential to be an effective method of biological control of plant parasite infection.
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Affiliation(s)
- Amos Alakonya
- Department of Biochemistry and Biotechnology, Kenyatta University, 43844-00100 Nairobi, Kenya
- Section of Plant Biology, University of California, Davis, California 95616
| | - Ravi Kumar
- Section of Plant Biology, University of California, Davis, California 95616
| | - Daniel Koenig
- Section of Plant Biology, University of California, Davis, California 95616
| | - Seisuke Kimura
- Section of Plant Biology, University of California, Davis, California 95616
| | - Brad Townsley
- Section of Plant Biology, University of California, Davis, California 95616
| | - Steven Runo
- Department of Biochemistry and Biotechnology, Kenyatta University, 43844-00100 Nairobi, Kenya
| | - Helena M. Garces
- Section of Plant Biology, University of California, Davis, California 95616
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom M13 9PT
| | - Julie Kang
- Section of Plant Biology, University of California, Davis, California 95616
| | - Andrea Yanez
- Section of Plant Biology, University of California, Davis, California 95616
| | | | - Jesse Machuka
- Department of Biochemistry and Biotechnology, Kenyatta University, 43844-00100 Nairobi, Kenya
| | - Neelima Sinha
- Section of Plant Biology, University of California, Davis, California 95616
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17
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Shigemitsu T, Ozaki S, Saito Y, Kuroda M, Morita S, Satoh S, Masumura T. Production of human growth hormone in transgenic rice seeds: co-introduction of RNA interference cassette for suppressing the gene expression of endogenous storage proteins. PLANT CELL REPORTS 2012; 31:539-49. [PMID: 22108719 DOI: 10.1007/s00299-011-1191-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/05/2011] [Accepted: 11/09/2011] [Indexed: 05/15/2023]
Abstract
Rice seeds are potentially useful hosts for the production of pharmaceutical proteins. However, low yields of recombinant proteins have been observed in many cases because recombinant proteins compete with endogenous storage proteins. Therefore, we attempt to suppress endogenous seed storage proteins by RNA interference (RNAi) to develop rice seeds as a more efficient protein expression system. In this study, human growth hormone (hGH) was expressed in transgenic rice seeds using an endosperm-specific promoter from a 10 kDa rice prolamin gene. In addition, an RNAi cassette for reduction of endogenous storage protein expressions was inserted into the hGH expression construct. Using this system, the expression levels of 13 kDa prolamin and glutelin were effectively suppressed and hGH polypeptides accumulated to 470 μg/g dry weight at the maximum level in transgenic rice seeds. These results suggest that the suppression of endogenous protein gene expression by RNAi could be of great utility for increasing transgene products.
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Affiliation(s)
- Takanari Shigemitsu
- Laboratory of Genetic Engineering, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Kyoto 606-8522, Japan
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18
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Pan Q, van der Laan LJW, Janssen HLA, Peppelenbosch MP. A dynamic perspective of RNAi library development. Trends Biotechnol 2012; 30:206-15. [PMID: 22305928 DOI: 10.1016/j.tibtech.2012.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 01/09/2012] [Accepted: 01/09/2012] [Indexed: 01/22/2023]
Abstract
Shortly after the dissertation of the mechanism of RNA interference (RNAi), various RNAi libraries for invertebrates, plants or mammals that enable loss-of-function genetic screens on a genome-wide scale have been developed. Joint academic and industrial effort has led to the commercial launch of many of these libraries and this field is expected to continuously evolve at incredible speed. This article comparatively reviews the principles and applications of different RNAi libraries: from earlier synthetic to recent lentiviral RNAi libraries. The unique properties and limitations of each library will be important references for instigators to choose a particular library for their specific application.
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Affiliation(s)
- Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
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19
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Sestili F, Janni M, Doherty A, Botticella E, D'Ovidio R, Masci S, Jones HD, Lafiandra D. Increasing the amylose content of durum wheat through silencing of the SBEIIa genes. BMC PLANT BIOLOGY 2010; 10:144. [PMID: 20626919 PMCID: PMC3095290 DOI: 10.1186/1471-2229-10-144] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 07/14/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND High amylose starch has attracted particular interest because of its correlation with the amount of Resistant Starch (RS) in food. RS plays a role similar to fibre with beneficial effects for human health, providing protection from several diseases such as colon cancer, diabetes, obesity, osteoporosis and cardiovascular diseases. Amylose content can be modified by a targeted manipulation of the starch biosynthetic pathway. In particular, the inactivation of the enzymes involved in amylopectin synthesis can lead to the increase of amylose content. In this work, genes encoding starch branching enzymes of class II (SBEIIa) were silenced using the RNA interference (RNAi) technique in two cultivars of durum wheat, using two different methods of transformation (biolistic and Agrobacterium). Expression of RNAi transcripts was targeted to the seed endosperm using a tissue-specific promoter. RESULTS Amylose content was markedly increased in the durum wheat transgenic lines exhibiting SBEIIa gene silencing. Moreover the starch granules in these lines were deformed, possessing an irregular and deflated shape and being smaller than those present in the untransformed controls. Two novel granule bound proteins, identified by SDS-PAGE in SBEIIa RNAi lines, were investigated by mass spectrometry and shown to have strong homologies to the waxy proteins. RVA analysis showed new pasting properties associated with high amylose lines in comparison with untransformed controls. Finally, pleiotropic effects on other starch genes were found by semi-quantitative and Real-Time reverse transcription-polymerase chain reaction (RT-PCR). CONCLUSION We have found that the silencing of SBEIIa genes in durum wheat causes obvious alterations in granule morphology and starch composition, leading to high amylose wheat. Results obtained with two different methods of transformation and in two durum wheat cultivars were comparable.
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Affiliation(s)
- Francesco Sestili
- University of Tuscia, Department of Agrobiology & Agrochemistry, Viterbo, Italy
| | - Michela Janni
- University of Tuscia, Department of Agrobiology & Agrochemistry, Viterbo, Italy
| | - Angela Doherty
- Rothamsted Research, Department of Plant Science, Harpenden, UK
| | | | - Renato D'Ovidio
- University of Tuscia, Department of Agrobiology & Agrochemistry, Viterbo, Italy
| | - Stefania Masci
- University of Tuscia, Department of Agrobiology & Agrochemistry, Viterbo, Italy
| | - Huw D Jones
- Rothamsted Research, Department of Plant Science, Harpenden, UK
| | - Domenico Lafiandra
- University of Tuscia, Department of Agrobiology & Agrochemistry, Viterbo, Italy
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20
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Petsch KA, Ma C, Scanlon MJ, Jorgensen RA. Targeted forward mutagenesis by transitive RNAi. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:873-882. [PMID: 20003132 DOI: 10.1111/j.1365-313x.2009.04104.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A novel technique is described that targets specific populations of transcripts for homology-based gene silencing using transitive RNAi. This approach is designed to target a subset of the transcriptome in order to identify genes involved in a particular localized process, such as photosynthesis. As a proof-of-concept approach, mesophyll cells from Arabidopsis thaliana were laser-microdissected from whole leaves to generate a focused cDNA library that was bi-directionally cloned into a transitive RNAi vector that had been designed to induce silencing of homologous, endogenous genes. Approximately 15% of the transformant plants identified from both sense and antisense libraries exhibited visible phenotypes indicative of photosynthetic defects. Amplification from the genome and sequencing of cDNA inserts identified candidate genes underlying the phenotypes. For 10 of 11 such mutants, re-transformation with an RNAi construct corresponding to the candidate gene recapitulated the original mutant phenotype, and reduction of corresponding endogene transcripts was confirmed. In addition, one of the re-transformed transgenes also silenced transcripts of closely related family members, thereby demonstrating the utility of this approach for mutagenesis of redundant gene functions. Preliminary results using tissue-specific transitive RNAi forward mutagenesis of the Arabidopsis vegetative shoot apical meristem demonstrate the broad applicability of this forward mutagenesis technique for a variety of plant cell types.
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21
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Abstract
RNAi refers to several different types of gene silencing mediated by small, dsRNA molecules. Over the course of 20 years, the scientific understanding of RNAi has developed from the initial observation of unexpected expression patterns to a sophisticated understanding of a multi-faceted, evolutionarily conserved network of mechanisms that regulate gene expression in many organisms. It has also been developed as a genetic tool that can be exploited in a wide range of species. Because transgene-induced RNAi has been effective at silencing one or more genes in a wide range of plants, this technology also bears potential as a powerful functional genomics tool across the plant kingdom. Transgene-induced RNAi has indeed been shown to be an effective mechanism for silencing many genes in many organisms, but the results from multiple projects which attempted to exploit RNAi on a genome-wide scale suggest that there is a great deal of variation in the silencing efficacy between transgenic events, silencing targets and silencing-induced phenotype. The results from these projects indicate several important variables that should be considered in experimental design prior to the initiation of functional genomics efforts based on RNAi silencing. In recent years, alternative strategies have been developed for targeted gene silencing, and a combination of approaches may also enhance the use of targeted gene silencing for functional genomics.
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Affiliation(s)
- Karen M McGinnis
- Department of Biological Sciences, Florida State University, Tallahassee, 32306-4295, USA.
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22
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Fused sister kinetochores initiate the reductional division in meiosis I. Nat Cell Biol 2009; 11:1103-8. [PMID: 19684578 DOI: 10.1038/ncb1923] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 06/01/2009] [Indexed: 12/12/2022]
Abstract
During meiosis I the genome is reduced to the haploid content by a coordinated reductional division event. Homologous chromosomes align, recombine and segregate while the sister chromatids co-orient and move to the same pole. Several data suggest that sister kinetochores co-orient early in metaphase I and that sister chromatid cohesion (which requires Rec8 and Shugoshin) supports monopolar orientation. Nevertheless, it is unclear how the sister kinetochores function as single unit during this period. A gene (monopolin) with a co-orienting role was identified in Saccharomyces cerevisiae; however, it does not have the same function in fission yeast and no similar genes have been found in other species. Here we pursue this issue using knockdown mutants of the core kinetochore protein MIS12 (minichromosome instability 12). MIS12 binds to base of the NDC80 complex, which in turn binds directly to microtubules. In maize plants with systemically reduced levels of MIS12, a visible MIS12-NDC80 bridge between sister kinetochores at meiosis I is broken. Kinetochores separate and orient randomly in metaphase I, causing chromosomes to stall in anaphase due to normal cohesion, marked by Shugoshin, between the chromatids. The data establish that sister kinetochores in meiosis I are fused by a shared microtubule-binding face and that this direct linkage is required for reductional division.
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Nicholson SJ, Srivastava V. Transgene constructs lacking transcription termination signal induce efficient silencing of endogenous targets in Arabidopsis. Mol Genet Genomics 2009; 282:319-28. [DOI: 10.1007/s00438-009-0467-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Accepted: 06/10/2009] [Indexed: 10/20/2022]
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McGinnis K. Use of transgene-induced RNAi to regulate endogenous gene expression. Methods Mol Biol 2009; 526:91-99. [PMID: 19378000 DOI: 10.1007/978-1-59745-494-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
RNAi can be an effective means to regulate endogenous gene expression in maize and as such represents an important reverse genetics tool. This approach involves designing a transgenic construct that creates a double stranded RNA (dsRNA) upon transcription, and introducing the transgene into maize plants. Transgenic lines bearing such a construct can be generated and characterized that are deficient in the gene of interest. Some variability has been observed in the efficiency of this technique, and there are several important aspects to consider. Herein, a basic protocol for using transgene-induced RNAi in maize is described, and some important considerations that can influence the success of this approach are discussed.
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Affiliation(s)
- Karen McGinnis
- Plant Sciences, University of Arizona, 303 Forbes Hall, Tucson, AZ 85721, USA.
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Abstract
Regions of DNA that bind to the nuclear matrix, or nucleoskeleton, are known as Matrix Attachment Regions (MARs). MARs are thought to play an important role in higher-order structure and chromatin organization within the nucleus. MARs are also thought to act as boundaries of chromosomal domains that act to separate regions of gene-rich, decondensed euchromatin from highly repetitive, condensed heterochromatin. Herein I will present evidence that MARs do indeed act as domain boundaries and can prevent the spread of silencing into active genes. Many fundamental questions remain unanswered about how MARs function in the nucleus. New findings in epigenetics indicate that MARs may also play an important role in the organization of genes and the eventual transport of their mRNAs through the nuclear pore.
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Travella S, Keller B. Down-regulation of gene expression by RNA-induced gene silencing. Methods Mol Biol 2008; 478:185-99. [PMID: 19009447 DOI: 10.1007/978-1-59745-379-0_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Down-regulation of endogenous genes via post-transcriptional gene silencing (PTGS) is a key to the characterization of gene function in plants. Many RNA-based silencing mechanisms such as post-transcriptional gene silencing, co-suppression, quelling, and RNA interference (RNAi) have been discovered among species of different kingdoms (plants, fungi, and animals). One of the most interesting discover ies was RNAi, a sequence-specific gene-silencing mechanism initiated by the introduction of double-stranded RNA (dsRNA), homologous in sequence to the silenced gene, which triggers degradation of mRNA. Infection of plants with modified viruses can also induce RNA silencing and is referred to as virus-induced gene silencing (VIGS). In contrast to insertional mutagenesis, these emerging new reverse genetic approaches represent a powerful tool for exploring gene function and for manipulating gene expression experimentally in cereal species such as barley and wheat. We examined how RNAi and VIGS have been used to assess gene function in barley and wheat, including molecular mechanisms involved in the process and available methodological elements, such as vectors, inoculation procedures, and analysis of silenced phenotypes.
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Affiliation(s)
- Silvia Travella
- Institute of Plant Biology, University of Zürich, Zürich, Switzerland
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Epigenetic Phenomena and Epigenomics in Maize. Epigenomics 2008. [DOI: 10.1007/978-1-4020-9187-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Xu X, Zhu D, Zhao Q, Ao G, Ma C, Yu J. RNA silencing mediated by direct repeats in maize: a potential tool for functional genomics. Mol Biotechnol 2008; 41:213-23. [PMID: 19031013 DOI: 10.1007/s12033-008-9124-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
It has been shown in tobacco and Arabidopsis that transgenes with multiple direct repeats induce RNA silencing at high frequency. In this study, we tried to establish a direct repeat-induced RNA silencing system in maize and evaluate whether it can be developed as a high throughput tool for functional genomics. Our results showed that the construct phC4, which carries four direct repeats of a chloramphenicol acetyl-transferase (CAT) gene, was able to induce silencing of itself with high efficiency in maize. Using a transient expression system, we further demonstrated that construct phC3G with a beta-glucuronidase (GUS) gene located downstream of three direct repeats of CAT gene silenced not only itself in maize calli but also an "endogenous" GUS gene, which was stably expressed in maize calli. Most importantly, when constructs with the maize iojap (ij) gene inserted in either sense or antisense orientation into the downstream of four direct repeats of CAT gene were transformed into maize plants, co-suppression of endogenous and transgenic ij genes was detected in majority of transgenic maize plants. Our co-suppression results suggest that with improvements, this new approach has the potential to become an efficient research tool for high throughput functional genomics.
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Affiliation(s)
- Xiuping Xu
- State Key Laboratory for Agro-biotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100094, People's Republic of China
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Dafny-Yelin M, Chung SM, Frankman EL, Tzfira T. pSAT RNA interference vectors: a modular series for multiple gene down-regulation in plants. PLANT PHYSIOLOGY 2007; 145:1272-81. [PMID: 17766396 PMCID: PMC2151715 DOI: 10.1104/pp.107.106062] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
RNA interference (RNAi) is a powerful tool for functional gene analysis, which has been successfully used to down-regulate the levels of specific target genes, enabling loss-of-function studies in living cells. Hairpin (hp) RNA expression cassettes are typically constructed on binary plasmids and delivered into plant cells by Agrobacterium-mediated genetic transformation. Realizing the importance of RNAi for basic plant research, various vectors have been developed for RNAi-mediated gene silencing, allowing the silencing of single target genes in plant cells. To further expand the collection of available tools for functional genomics in plant species, we constructed a set of modular vectors suitable for hpRNA expression under various constitutive promoters. Our system allows simple cloning of the target gene sequences into two distinct multicloning sites and its modular design provides a straightforward route for replacement of the expression cassette's regulatory elements. More importantly, our system was designed to facilitate the assembly of several hpRNA expression cassettes on a single plasmid, thereby enabling the simultaneous suppression of several target genes from a single vector. We tested the functionality of our new vector system by silencing overexpressed marker genes (green fluorescent protein, DsRed2, and nptII) in transgenic plants. Various combinations of hpRNA expression cassettes were assembled in binary plasmids; all showed strong down-regulation of the reporter genes in transgenic plants. Furthermore, assembly of all three hpRNA expression cassettes, combined with a fourth cassette for the expression of a selectable marker, resulted in down-regulation of all three different marker genes in transgenic plants. This vector system provides an important addition to the plant molecular biologist's toolbox, which will significantly facilitate the use of RNAi technology for analyses of multiple gene function in plant cells.
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Affiliation(s)
- Mery Dafny-Yelin
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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RNA interference for wheat functional gene analysis. Transgenic Res 2007; 16:689-701. [PMID: 17952622 DOI: 10.1007/s11248-007-9150-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Accepted: 10/04/2007] [Indexed: 10/22/2022]
Abstract
RNA interference (RNAi) refers to a common mechanism of RNA-based post-transcriptional gene silencing in eukaryotic cells. In model plant species such as Arabidopsis and rice, RNAi has been routinely used to characterize gene function and to engineer novel phenotypes. In polyploid species, this approach is in its early stages, but has great potential since multiple homoeologous copies can be simultaneously silenced with a single RNAi construct. In this article, we discuss the utilization of RNAi in wheat functional gene analysis and its effect on transcript regulation of homoeologous genes. We also review recent examples of RNAi modification of important agronomic and quality traits in wheat and discuss future directions for this technology.
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Efficient and stable transgene suppression via RNAi in field-grown poplars. Transgenic Res 2007; 17:679-94. [PMID: 17929189 DOI: 10.1007/s11248-007-9148-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 09/22/2007] [Indexed: 12/23/2022]
Abstract
The efficiency and stability of RNA interference (RNAi) in perennial species, particularly in natural environments, is poorly understood. We studied 56 independent poplar RNAi transgenic events in the field over 2 years. A resident BAR transgene was targeted with two different types of RNAi constructs: a 475-bp IR of the promoter sequence and a 275-bp IR of the coding sequence, each with and without the presence of flanking matrix attachment regions (MARs). RNAi directed at the coding sequence was a strong inducer of gene silencing; 80% of the transgenic events showed more than 90% suppression. In contrast, RNAi targeting the promoter resulted in only 6% of transgenic events showing more than 90% suppression. The degree of suppression varied widely but was highly stable in each event over 2 years in the field, and had no association with insert copy number or the presence of MARs. RNAi remained stable during a winter to summer seasonal cycle, a time when expression of the targeted transgene driven by an rbcS promoter varied widely. When strong gene suppression was induced by an IR directed at the promoter sequence, it was accompanied by methylation of the homologous promoter region. DNA methylation was also observed in the coding region of highly suppressed events containing an IR directed at the coding sequence; however, the methylation degree and pattern varied widely among those suppressed events. Our results suggest that RNAi can be highly effective for functional genomics and biotechnology of perennial plants.
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