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Li R, Han Z, Yin Q, Li M, Zhang M, Li Z, Wang P, Jiang L, Ow DW. Target Lines for in Planta Gene Stacking in Japonica Rice. Int J Mol Sci 2022; 23:ijms23169385. [PMID: 36012650 PMCID: PMC9409015 DOI: 10.3390/ijms23169385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 12/02/2022] Open
Abstract
The clustering of transgenes at a chromosome location minimizes the number of segregating loci that needs to be introgressed to field cultivars. Transgenes could be efficiently stacked through site-specific recombination and a recombinase-mediated in planta gene stacking process was described previously in tobacco based on the Mycobacteriophage Bxb1 site-specific integration system. Since this process requires a recombination site in the genome, this work describes the generation of target sites in the Japonica rice genome. Agrobacterium-mediated gene transfer yielded ~4000 random-insertion lines. Seven lines met the criteria of being single copy, not close to a centromere, not inserted within or close to a known gene or repetitive DNA, having precise recombination site sequences on both ends, and able to express the reporter gene. Each target line tested was able to accept the site-specific integration of a new gfp-containing plasmid and in three of those lines, we regenerated fertile plants. These target lines could be used as foundation lines for stacking new traits into Japonica rice.
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Affiliation(s)
- Ruyu Li
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Correspondence: (R.L.); (D.W.O.)
| | - Zhiguo Han
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Qian Yin
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Meiru Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhenzhen Li
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Ping Wang
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Li Jiang
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - David W. Ow
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Correspondence: (R.L.); (D.W.O.)
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Aslam S, Khan SH, Ahmad A, Walawage SL, Dandekar AM. Founder transformants of cotton (Gossypium hirsutum L.) obtained through the introduction of DS-Red, Rec, Rep and CRISPR/Cas9 expressing constructs for developing base lines of recombinase mediated gene stacking. PLoS One 2022; 17:e0263219. [PMID: 35113911 PMCID: PMC8812945 DOI: 10.1371/journal.pone.0263219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/17/2022] [Indexed: 11/25/2022] Open
Abstract
Cotton being the major fiber crop across the world is exposed to numerous biotic and abiotic stresses. Genetic transformation of cotton is vital to meet the world’s food, feed and fiber demands. Genetic manipulation by randomly transferring the genes emanate variable gene expression. Targeted gene insertion by latest genome editing tools results in predictable expression of genes at a specified location. Gene stacking technology emerged as an adaptive strategy to combat biotic and abiotic stresses by integrating 2–3 genes simultaneously and at a specific site to avoid variable gene expression at diverse locations. This study explains the development of cotton’s founder transformants to be used as a base line for multiple gene stacking projects. We introduced Cre and PhiC31 mediated recombination sites to specify the locus of incoming genes. CRISPR-Cas9 gene was integrated for developing CRISPR based founder lines of cotton. Cas9 gene along with gRNA was integrated to target Rep (replication) region of cotton leaf curl virus. Replication region of virus was specifically targeted to diminish further proliferation and preventing the virus to develop new strains. To successfully develop these primary transformants, a model transformation system has been optimized with the red color visualization (DS-Red). Following red color transformation system, three baselines with recombination specified site (Rec), targeted replication region (Rep) and Cas9 founder lines have been developed. These founder transformants are useful for developing recombinase mediated and CRISPR/Cas9 based originator lines of cotton. Moreover, these transformants will set up a base system for all the recombinase mediated gene stacking projects.
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Affiliation(s)
- Sabin Aslam
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
- * E-mail: ,
| | - Sultan Habibullah Khan
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
- Center of Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
| | - Aftab Ahmad
- Center of Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Sriema Lalani Walawage
- Department of Plant Sciences, School of Biological Sciences, University of California, Davis, California, United States of America
| | - Abhaya M. Dandekar
- Department of Plant Sciences, School of Biological Sciences, University of California, Davis, California, United States of America
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Li TT, Zhang JD, Tang JQ, Liu ZC, Li YQ, Chen J, Zou LW. Combined Use of Trichoderma atroviride CCTCCSBW0199 and Brassinolide to Control Botrytis cinerea Infection in Tomato. PLANT DISEASE 2020; 104:1298-1304. [PMID: 32196417 DOI: 10.1094/pdis-07-19-1568-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tomato gray mold caused by Botrytis cinerea is one of the main diseases of tomato and significantly impacts the yield and quality of tomato fruit. The overuse of chemical fungicides has resulted in the development of fungicide-resistant strains. Biological control is becoming an alternative method for the control of plant diseases to replace or decrease the application of traditional synthetic chemical fungicides and genus Trichoderma is widely used as a biological agent for controlling tomato gray mold. Brassinolide (BR) is a plant-growth-promoting steroid. To enhance the efficiency and stability of Trichoderma activity against B. cinerea, an optimal combination of Trichoderma atroviride CCTCCSBW0199 and BR that controls B. cinerea infection in tomato was identified. Strain CCTCCSBW0199 was found to have antagonistic activity against B. cinerea both in vitro and in vivo. In addition, a fermented culture of chlamydospores and metabolites, or metabolites only of strain CCTCCSBW0199 also reduced growth of B. cinerea. BR reduced growth of B. cinerea and had no effect on the sporulation and growth of Trichoderma spp. An application of metabolites of a Trichoderma sp. + BR reduced gray mold on tomato leaves by approximately 70.0%. Furthermore, the activities of induced defense response-related enzyme, such as peroxidase, superoxide dismutase, catalase, and phenylalanine ammonia-lyase were increased in tomato plants treated with a Trichoderma sp. + BR. Our data suggested that applying a mix of metabolites of T. atroviride CCTCCSBW0199 + BR was effective at reducing gray mold of tomato and may lay a theoretical foundation for the development of novel biofungicides.
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Affiliation(s)
- Ting-Ting Li
- School of Agriculture and Biology, Shanghai Jiao Tong University/State Key Laboratory of Microbial Metabolism/Key Laboratory of Urban Agriculture (South), Ministry of Agriculture and Rural Affairs, Shanghai 200240, P.R. China
| | - Jing-di Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University/State Key Laboratory of Microbial Metabolism/Key Laboratory of Urban Agriculture (South), Ministry of Agriculture and Rural Affairs, Shanghai 200240, P.R. China
| | - Jia-Quan Tang
- School of Agriculture and Biology, Shanghai Jiao Tong University/State Key Laboratory of Microbial Metabolism/Key Laboratory of Urban Agriculture (South), Ministry of Agriculture and Rural Affairs, Shanghai 200240, P.R. China
| | - Zhi-Cheng Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University/State Key Laboratory of Microbial Metabolism/Key Laboratory of Urban Agriculture (South), Ministry of Agriculture and Rural Affairs, Shanghai 200240, P.R. China
| | - Ya-Qian Li
- School of Agriculture and Biology, Shanghai Jiao Tong University/State Key Laboratory of Microbial Metabolism/Key Laboratory of Urban Agriculture (South), Ministry of Agriculture and Rural Affairs, Shanghai 200240, P.R. China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University/State Key Laboratory of Microbial Metabolism/Key Laboratory of Urban Agriculture (South), Ministry of Agriculture and Rural Affairs, Shanghai 200240, P.R. China
| | - Li-Wen Zou
- Dalian Wafangdian Agricultural Technology Extension Service Center, Dalian 116300, P.R. China
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Birchler JA, Swyers NC. Engineered minichromosomes in plants. Exp Cell Res 2020; 388:111852. [PMID: 31972219 DOI: 10.1016/j.yexcr.2020.111852] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/14/2020] [Indexed: 11/17/2022]
Abstract
Artificial chromosome platforms are described in plants. Because the function of centromeres is largely epigenetic, attempts to produce artificial chromosomes with plant centromere DNA have failed. The removal of the centromeric sequences from the cell strips off the centromeric histone that is the apparent biochemical marker of centromere activity. Thus, engineered minichromosomes have been produced by telomere mediated chromosomal truncation. The introduction of telomere repeats will cleave the chromosome at the site of insertion and attach the accompanying transgenes in the process. Such truncation events have been documented in maize, Arabidopsis, barley, rice, Brassica and wheat. Truncation of the nonvital supernumerary B chromosome of maize is a favorite target but engineered minichromosomes derived from the normal A chromosomes have also been recovered. Transmission through mitosis of small chromosomes is apparently normal but there is loss during meiosis. Potential solutions to address this issue are discussed. With procedures now well established to produce the foundation for artificial chromosomes in plants, current efforts are directed at building them up to specification using gene stacking methods and editing techniques.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211-7400, USA.
| | - Nathan C Swyers
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211-7400, USA
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Chen W, Kaur G, Hou L, Li R, Ow DW. Replacement of stacked transgenes in planta. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2029-2031. [PMID: 31127663 PMCID: PMC6790365 DOI: 10.1111/pbi.13172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/05/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Weiqiang Chen
- Plant Gene Engineering CenterChinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic ImprovementGuangdong Key Laboratory of Applied BotanySouth China Botanical GardenGuangzhouChina
| | - Gurminder Kaur
- Plant Gene Engineering CenterChinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic ImprovementGuangdong Key Laboratory of Applied BotanySouth China Botanical GardenGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lili Hou
- Plant Gene Engineering CenterChinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic ImprovementGuangdong Key Laboratory of Applied BotanySouth China Botanical GardenGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ruyu Li
- Plant Gene Engineering CenterChinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic ImprovementGuangdong Key Laboratory of Applied BotanySouth China Botanical GardenGuangzhouChina
| | - David W. Ow
- Plant Gene Engineering CenterChinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic ImprovementGuangdong Key Laboratory of Applied BotanySouth China Botanical GardenGuangzhouChina
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Abstract
Previously, we described a method for a recombinase-directed stacking of new DNA to an existing transgenic locus. Here, we describe how we can similarly stack DNA molecules in vitro and that the in vitro derived gene stack can be incorporated into an Agrobacterium transformation vector by in vitro recombination. After transfer to the chromosome by Agroinfection, the transgenic locus harbors a new target site that can be used for the subsequent in vivo stacking of new DNA. Alternatively, the in vitro derived gene stack has the potential to be integrated directly into the plant genome in vivo at a preexisting chromosomal target. Being able to stack DNA in vitro as well as in vivo, and with compatibility between the two systems, brings new flexibility for using the recombinase-mediated approach for transgene stacking.
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Rajaee M, Ow DW. A new location to split Cre recombinase for protein fragment complementation. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1420-1428. [PMID: 28317293 PMCID: PMC5633763 DOI: 10.1111/pbi.12726] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 06/06/2023]
Abstract
We have previously described a recombinase-mediated gene stacking system in which the Cre recombinase is used to remove lox-site flanked DNA no longer needed after each round of Bxb1 integrase-mediated site-specific integration. The Cre recombinase can be conveniently introduced by hybridization with a cre-expressing plant. However, maintaining an efficient cre-expressing line over many generations can be a problem, as high production of this DNA-binding protein might interfere with normal chromosome activities. To counter this selection against high Cre activity, we considered a split-cre approach, in which Cre activity is reconstituted after separate parts of Cre are brought into the same genome by hybridization. To insure that the recombinase-mediated gene stacking system retains its freedom to operate, we tested for new locations to split Cre into complementing fragments. In this study, we describe testing four new locations for splitting the Cre recombinase for protein fragment complementation and show that the two fragments of Cre split between Lys244 and Asn245 can reconstitute activity that is comparable to that of wild-type Cre.
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Affiliation(s)
- Maryam Rajaee
- Plant Gene Engineering CenterSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - David W. Ow
- Plant Gene Engineering CenterSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
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Cardi T, Neal Stewart C. Progress of targeted genome modification approaches in higher plants. PLANT CELL REPORTS 2016; 35:1401-16. [PMID: 27025856 DOI: 10.1007/s00299-016-1975-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/21/2016] [Indexed: 05/07/2023]
Abstract
Transgene integration in plants is based on illegitimate recombination between non-homologous sequences. The low control of integration site and number of (trans/cis)gene copies might have negative consequences on the expression of transferred genes and their insertion within endogenous coding sequences. The first experiments conducted to use precise homologous recombination for gene integration commenced soon after the first demonstration that transgenic plants could be produced. Modern transgene targeting categories used in plant biology are: (a) homologous recombination-dependent gene targeting; (b) recombinase-mediated site-specific gene integration; (c) oligonucleotide-directed mutagenesis; (d) nuclease-mediated site-specific genome modifications. New tools enable precise gene replacement or stacking with exogenous sequences and targeted mutagenesis of endogeneous sequences. The possibility to engineer chimeric designer nucleases, which are able to target virtually any genomic site, and use them for inducing double-strand breaks in host DNA create new opportunities for both applied plant breeding and functional genomics. CRISPR is the most recent technology available for precise genome editing. Its rapid adoption in biological research is based on its inherent simplicity and efficacy. Its utilization, however, depends on available sequence information, especially for genome-wide analysis. We will review the approaches used for genome modification, specifically those for affecting gene integration and modification in higher plants. For each approach, the advantages and limitations will be noted. We also will speculate on how their actual commercial development and implementation in plant breeding will be affected by governmental regulations.
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Affiliation(s)
- Teodoro Cardi
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Centro di Ricerca per l'Orticoltura, Via Cavalleggeri 25, 84098, Pontecagnano, Italy.
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
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Srivastava V, Thomson J. Gene stacking by recombinases. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:471-82. [PMID: 26332944 DOI: 10.1111/pbi.12459] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/24/2015] [Accepted: 07/28/2015] [Indexed: 05/09/2023]
Abstract
Efficient methods of stacking genes into plant genomes are needed to expedite transfer of multigenic traits to crop varieties of diverse ecosystems. Over two decades of research has identified several DNA recombinases that carryout efficient cis and trans recombination between the recombination sites artificially introduced into the plant chromosome. The specificity and efficiency of recombinases make them extremely attractive for genome engineering. In plant biotechnology, recombinases have mostly been used for removing selectable marker genes and have rarely been extended to more complex applications. The reversibility of recombination, a property of the tyrosine family of recombinases, does not lend itself to gene stacking approaches that involve rounds of transformation for integrating genes into the engineered sites. However, recent developments in the field of recombinases have overcome these challenges and paved the way for gene stacking. Some of the key advancements include the application of unidirectional recombination systems, modification of recombination sites and transgene site modifications to allow repeated site-specific integrations into the selected site. Gene stacking is relevant to agriculturally important crops, many of which are difficult to transform; therefore, development of high-efficiency gene stacking systems will be important for its application on agronomically important crops, and their elite varieties. Recombinases, by virtue of their specificity and efficiency in plant cells, emerge as powerful tools for a variety of applications including gene stacking.
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Affiliation(s)
- Vibha Srivastava
- Department of Crop, Soil & Environmental Science, University of Arkansas, Fayetteville, AR, USA
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10
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Plant minichromosomes. Curr Opin Biotechnol 2016; 37:135-142. [DOI: 10.1016/j.copbio.2015.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/06/2015] [Accepted: 11/23/2015] [Indexed: 11/23/2022]
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11
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Ow DW. The long road to recombinase-mediated plant transformation. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:441-7. [PMID: 26373969 DOI: 10.1111/pbi.12472] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/09/2015] [Accepted: 08/12/2015] [Indexed: 05/10/2023]
Abstract
The use of site-specific recombinases to manipulate eukaryotic genomes began nearly three decades ago. Although seemingly parallel efforts were being made in animal and plant systems, the motivation for its development in plants was unique to, at least at the time, crop bioengineering issues. The impetus behind site-specific deletion in plants was to remove antibiotic resistance genes used during transformation but unnecessary in commercial products. Site-specific integration in plants was more than academic curiosity of position effects on gene expression, but a necessary step towards developing the serial stacking of DNA to the same chromosome locus - to insure that bioengineered crops can be improved over time through transgene additions without inflating the number of segregating loci. This article is not a review of the literature on site-specific recombination, but a first person account of the series of events leading to the development of a gene stacking transformation system in plants.
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Affiliation(s)
- David W Ow
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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12
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Li R, Han Z, Hou L, Kaur G, Yin Q, Ow DW. Method for Biolistic Site-Specific Integration in Plants Catalyzed by Bxb1 Integrase. Methods Mol Biol 2016; 1469:15-30. [PMID: 27557683 DOI: 10.1007/978-1-4939-4931-1_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Crop improvement is a never ending process. With a transgenesis approach, it is not inconceivable to envision a continuous addition of new transgenes to existing cultivars. Previously, we described a recombinase-directed gene stacking method in tobacco (Hou et al., Mol Plant 7:1756-1765, 2014). Being able to stack DNA to a previous location ensures that the number of genetic loci does not increase with each new round of transgene addition. Whereas the previous demonstration was conducted through polyethylene glycol to mediate uptake of DNA into tobacco protoplasts, we now describe protocols for using biolistic transformation to stack DNA in tobacco and rice.
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Affiliation(s)
- Ruyu Li
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China
| | - Zhiguo Han
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China
| | - Lili Hou
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gurminder Kaur
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qian Yin
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, China
| | - David W Ow
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China.
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13
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Promises and pitfalls of synthetic chromosomes in plants. Trends Biotechnol 2015; 33:189-94. [DOI: 10.1016/j.tibtech.2014.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/21/2014] [Accepted: 12/30/2014] [Indexed: 12/28/2022]
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15
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Hou L, Yau YY, Wei J, Han Z, Dong Z, Ow DW. An open-source system for in planta gene stacking by Bxb1 and Cre recombinases. MOLECULAR PLANT 2014; 7:1756-65. [PMID: 25281665 DOI: 10.1093/mp/ssu107] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The rapid development of crops with multiple transgenic traits arouses the need for an efficient system for creating stacked cultivars. Most major crops rely on classical breeding to introgress the transgene from a laboratory variety to the numerous cultivars adapted to different growing regions. Even with vegetative propagated crops, genetic crosses are conducted during varietal improvement prior to vegetative cloning. The probability to assort the 'x' number of transgenic loci into a single genome may seem trivial, (¼) (x) for a diploid species, but given the 'y' number of other nontransgenic traits that breeders also need to assemble into the same genome, the (¼) (x+y) probability for a 'breeding stack' could quickly make the line conversion process unmanageable. Adding new transgenes onto existing transgenic varieties without creating a new segregating locus would require site-specific integration of new DNA at the existing transgenic locus. Here, we tested a recombinase-mediated gene-stacking scheme in tobacco. Sequential site-specific integration was mediated by the mycobacteriophage Bxb1 integrase-catalyzed recombination between attP and attB sites. Transgenic DNA no longer needed after integration was excised by Cre recombinase-mediated recombination of lox sites. Site-specific integration occurred in ~10% of the integration events, with half of those events usable as substrates for a next round of gene stacking. Among the site-specific integrants, however, a third experienced gene silencing. Overall, precise structure and reproducible expression of the sequentially added triple traits were obtained at an overall rate of ~3% of the transformed clones--a workable frequency for the development of commercial cultivars. Moreover, since neither the Bxb1-att nor the Cre-lox system is under patent, there is freedom to operate.
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Affiliation(s)
- Lili Hou
- Plant Gene Engineering Center, South China Agricultural Plant Molecular Analysis and Genetic Improvement Key Laboratory, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou 510650, China University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yuan-Yeu Yau
- Plant Gene Engineering Center, South China Agricultural Plant Molecular Analysis and Genetic Improvement Key Laboratory, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou 510650, China Former Affiliation, Plant Gene Expression Center, USDA-ARS & Plant & Microbial Biology, University of California-Berkeley, 800 Buchanan St., Albany, CA 94710, USA
| | - Junjie Wei
- Plant Gene Engineering Center, South China Agricultural Plant Molecular Analysis and Genetic Improvement Key Laboratory, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou 510650, China University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Zhiguo Han
- Plant Gene Engineering Center, South China Agricultural Plant Molecular Analysis and Genetic Improvement Key Laboratory, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou 510650, China
| | - Zhicheng Dong
- Plant Gene Engineering Center, South China Agricultural Plant Molecular Analysis and Genetic Improvement Key Laboratory, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou 510650, China
| | - David W Ow
- Plant Gene Engineering Center, South China Agricultural Plant Molecular Analysis and Genetic Improvement Key Laboratory, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou 510650, China Former Affiliation, Plant Gene Expression Center, USDA-ARS & Plant & Microbial Biology, University of California-Berkeley, 800 Buchanan St., Albany, CA 94710, USA
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Somleva MN, Xu CA, Ryan KP, Thilmony R, Peoples O, Snell KD, Thomson J. Transgene autoexcision in switchgrass pollen mediated by the Bxb1 recombinase. BMC Biotechnol 2014; 14:79. [PMID: 25148894 PMCID: PMC4148497 DOI: 10.1186/1472-6750-14-79] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/18/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) has a great potential as a platform for the production of biobased plastics, chemicals and energy mainly because of its high biomass yield on marginal land and low agricultural inputs. During the last decade, there has been increased interest in the genetic improvement of this crop through transgenic approaches. Since switchgrass, like most perennial grasses, is exclusively cross pollinating and poorly domesticated, preventing the dispersal of transgenic pollen into the environment is a critical requisite for the commercial deployment of this important biomass crop. In this study, the feasibility of controlling pollen-mediated gene flow in transgenic switchgrass using the large serine site-specific recombinase Bxb1 has been investigated. RESULTS A novel approach utilizing co-transformation of two separate vectors was used to test the functionality of the Bxb1/att recombination system in switchgrass. In addition, two promoters with high pollen-specific activity were identified and thoroughly characterized prior to their introduction into a test vector explicitly designed for both autoexcision and quantitative analyses of recombination events. Our strategy for developmentally programmed precise excision of the recombinase and marker genes in switchgrass pollen resulted in the generation of transgene-excised progeny. The autoexcision efficiencies were in the range of 22-42% depending on the transformation event and assay used. CONCLUSION The results presented here mark an important milestone towards the establishment of a reliable biocontainment system for switchgrass which will facilitate the development of this crop as a biorefinery feedstock through advanced biotechnological approaches.
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Affiliation(s)
| | - Chang Ai Xu
- Metabolix, Inc., 21 Erie St., Cambridge, MA 02139, USA
| | - Kieran P Ryan
- Metabolix, Inc., 21 Erie St., Cambridge, MA 02139, USA
| | | | | | | | - James Thomson
- USDA-ARS-CIU, 800 Buchanan St., Albany, CA 94710, USA
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Sang Y, Millwood RJ, Neal Stewart C. Gene use restriction technologies for transgenic plant bioconfinement. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:649-658. [PMID: 23730743 DOI: 10.1111/pbi.12084] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/03/2013] [Accepted: 04/09/2013] [Indexed: 06/02/2023]
Abstract
The advances of modern plant technologies, especially genetically modified crops, are considered to be a substantial benefit to agriculture and society. However, so-called transgene escape remains and is of environmental and regulatory concern. Genetic use restriction technologies (GURTs) provide a possible solution to prevent transgene dispersal. Although GURTs were originally developed as a way for intellectual property protection (IPP), we believe their maximum benefit could be in the prevention of gene flow, that is, bioconfinement. This review describes the underlying signal transduction and components necessary to implement any GURT system. Furthermore, we review the similarities and differences between IPP- and bioconfinement-oriented GURTs, discuss the GURTs' design for impeding transgene escape and summarize recent advances. Lastly, we go beyond the state of the science to speculate on regulatory and ecological effects of implementing GURTs for bioconfinement.
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Affiliation(s)
- Yi Sang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
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De Paepe A, De Buck S, Nolf J, Van Lerberge E, Depicker A. Site-specific T-DNA integration in Arabidopsis thaliana mediated by the combined action of CRE recombinase and ϕC31 integrase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:172-184. [PMID: 23574114 DOI: 10.1111/tpj.12202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 04/04/2013] [Accepted: 04/08/2013] [Indexed: 06/02/2023]
Abstract
Random T-DNA integration into the plant host genome can be problematic for a variety of reasons, including potentially variable transgene expression as a result of different integration positions and multiple T-DNA copies, the risk of mutating the host genome and the difficulty of stacking well-defined traits. Therefore, recombination systems have been proposed to integrate the T-DNA at a pre-selected site in the host genome. Here, we demonstrate the capacity of the ϕC31 integrase (INT) for efficient targeted T-DNA integration. Moreover, we show that the iterative site-specific integration system (ISSI), which combines the activities of the CRE recombinase and INT, enables the targeting of genes to a pre-selected site with the concomitant removal of the resident selectable marker. To begin, plants expressing both the CRE and INT recombinase and containing the target attP site were constructed. These plants were supertransformed with a T-DNA vector harboring the loxP site, the attB sites, a selectable marker and an expression cassette encoding a reporter protein. Three out of the 35 transformants obtained (9%) showed transgenerational site-specific integration (SSI) of this T-DNA and removal of the resident selectable marker, as demonstrated by PCR, Southern blot and segregation analysis. In conclusion, our results show the applicability of the ISSI system for precise and targeted Agrobacterium-mediated integration, allowing the serial integration of transgenic DNA sequences in plants.
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Affiliation(s)
- Annelies De Paepe
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Sylvie De Buck
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jonah Nolf
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Els Van Lerberge
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Ann Depicker
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
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19
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Yau YY, Stewart CN. Less is more: strategies to remove marker genes from transgenic plants. BMC Biotechnol 2013; 13:36. [PMID: 23617583 PMCID: PMC3689633 DOI: 10.1186/1472-6750-13-36] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Selectable marker genes (SMGs) and selection agents are useful tools in the production of transgenic plants by selecting transformed cells from a matrix consisting of mostly untransformed cells. Most SMGs express protein products that confer antibiotic- or herbicide resistance traits, and typically reside in the end product of genetically-modified (GM) plants. The presence of these genes in GM plants, and subsequently in food, feed and the environment, are of concern and subject to special government regulation in many countries. The presence of SMGs in GM plants might also, in some cases, result in a metabolic burden for the host plants. Their use also prevents the re-use of the same SMG when a second transformation scheme is needed to be performed on the transgenic host. In recent years, several strategies have been developed to remove SMGs from GM products while retaining the transgenes of interest. This review describes the existing strategies for SMG removal, including the implementation of site specific recombination systems, TALENs and ZFNs. This review discusses the advantages and disadvantages of existing SMG-removal strategies and explores possible future research directions for SMG removal including emerging technologies for increased precision for genome modification.
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Affiliation(s)
- Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
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20
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Recombinase-mediated cassette exchange (RMCE) — A rapidly-expanding toolbox for targeted genomic modifications. Gene 2013. [DOI: 10.1016/j.gene.2012.11.016] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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21
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Kapusi E, Kempe K, Rubtsova M, Kumlehn J, Gils M. phiC31 integrase-mediated site-specific recombination in barley. PLoS One 2012; 7:e45353. [PMID: 23024817 PMCID: PMC3443236 DOI: 10.1371/journal.pone.0045353] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 08/17/2012] [Indexed: 12/28/2022] Open
Abstract
The Streptomyces phage phiC31 integrase was tested for its feasibility in excising transgenes from the barley genome through site-specific recombination. We produced transgenic barley plants expressing an active phiC31 integrase and crossed them with transgenic barley plants carrying a target locus for recombination. The target sequence involves a reporter gene encoding green fluorescent protein (GFP), which is flanked by the attB and attP recognition sites for the phiC31 integrase. This sequence disruptively separates a gusA coding sequence from an upstream rice actin promoter. We succeeded in producing site-specific recombination events in the hybrid progeny of 11 independent barley plants carrying the above target sequence after crossing with plants carrying a phiC31 expression cassette. Some of the hybrids displayed fully executed recombination. Excision of the GFP gene fostered activation of the gusA gene, as visualized in tissue of hybrid plants by histochemical staining. The recombinant loci were detected in progeny of selfed F(1), even in individuals lacking the phiC31 transgene, which provides evidence of stability and generative transmission of the recombination events. In several plants that displayed incomplete recombination, extrachromosomal excision circles were identified. Besides the technical advance achieved in this study, the generated phiC31 integrase-expressing barley plants provide foundational stock material for use in future approaches to barley genetic improvement, such as the production of marker-free transgenic plants or switching transgene activity.
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Affiliation(s)
- Eszter Kapusi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Gatersleben, Germany
| | - Katja Kempe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Gatersleben, Germany
| | - Myroslava Rubtsova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Gatersleben, Germany
| | - Mario Gils
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Gatersleben, Germany
- * E-mail:
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22
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Thomson JG, Chan R, Smith J, Thilmony R, Yau YY, Wang Y, Ow DW. The Bxb1 recombination system demonstrates heritable transmission of site-specific excision in Arabidopsis. BMC Biotechnol 2012; 12:9. [PMID: 22436504 PMCID: PMC3341217 DOI: 10.1186/1472-6750-12-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/21/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mycobacteriophage large serine recombinase Bxb1 catalyzes site-specific recombination between its corresponding attP and attB recognition sites. Previously, we and others have shown that Bxb1 has catalytic activity in various eukaryotic species including Nicotiana tabacum, Schizosaccharomyces pombe, insects and mammalian cells. RESULTS In this work, the Bxb1 recombinase gene was transformed and constitutively expressed in Arabidopsis thaliana plants harboring a chromosomally integrated attP and attB-flanked target sequence. The Bxb1 recombinase successfully excised the target sequence in a conservative manner and the resulting recombination event was heritably transmitted to subsequent generations in the absence of the recombinase transgene. In addition, we also show that Bxb1 recombinase expressing plants can be manually crossed with att-flanked target transgenic plants to generate excised progeny. CONCLUSION The Bxb1 large serine recombinase performs site-specific recombination in Arabidopsis thaliana germinal tissue, producing stable lines free of unwanted DNA. The precise site-specific deletion produced by Bxb1 in planta demonstrates that this enzyme can be a useful tool for the genetic engineering of plants without selectable marker transgenes or other undesirable exogenous sequences.
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Affiliation(s)
- James G Thomson
- Crop Improvement and Utilization Research Unit, Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA.
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Ow DW. Recombinase-mediated gene stacking as a transformation operating system. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:512-9. [PMID: 21676171 DOI: 10.1111/j.1744-7909.2011.01061.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The current method for combining transgenes into a genome is through the assortment of independent loci, a classical operating system compatible with transgenic traits created by different developers, at different times and/or through different transformation techniques. However, as the number of transgenic loci increases over time, increasingly larger populations are needed to find the rare individual with the desired assortment of transgenic loci along with the non-transgenic elite traits. Introducing a transgene directly into a field cultivar would bypass the need to introgress the engineered trait. However, this necessitates separate transformations into numerous field cultivars, along with the characterization and regulatory approval of each independent transformation event. Reducing the number of segregating transgenic loci could be achieved if multiple traits are introduced at the same time, a preferred option if each of the many traits is new or requires re-engineering. If re-engineering of previously introduced traits is not needed, then appending a new trait to an existing locus would be a rational strategy. The insertion of new DNA at a known locus can be accomplished by site-specific integration, through a host-dependent homology-based process, or a heterologous site-specific recombination system. Here, we discuss gene stacking through the use of site-specific recombinases.
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Affiliation(s)
- David W Ow
- South China Botanical Garden, Guangzhou 510650, China.
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24
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Wang Y, Yau YY, Perkins-Balding D, Thomson JG. Recombinase technology: applications and possibilities. PLANT CELL REPORTS 2011; 30:267-85. [PMID: 20972794 PMCID: PMC3036822 DOI: 10.1007/s00299-010-0938-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/06/2010] [Accepted: 10/08/2010] [Indexed: 05/02/2023]
Abstract
The use of recombinases for genomic engineering is no longer a new technology. In fact, this technology has entered its third decade since the initial discovery that recombinases function in heterologous systems (Sauer in Mol Cell Biol 7(6):2087-2096, 1987). The random insertion of a transgene into a plant genome by traditional methods generates unpredictable expression patterns. This feature of transgenesis makes screening for functional lines with predictable expression labor intensive and time consuming. Furthermore, an antibiotic resistance gene is often left in the final product and the potential escape of such resistance markers into the environment and their potential consumption raises consumer concern. The use of site-specific recombination technology in plant genome manipulation has been demonstrated to effectively resolve complex transgene insertions to single copy, remove unwanted DNA, and precisely insert DNA into known genomic target sites. Recombinases have also been demonstrated capable of site-specific recombination within non-nuclear targets, such as the plastid genome of tobacco. Here, we review multiple uses of site-specific recombination and their application toward plant genomic engineering. We also provide alternative strategies for the combined use of multiple site-specific recombinase systems for genome engineering to precisely insert transgenes into a pre-determined locus, and removal of unwanted selectable marker genes.
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Affiliation(s)
- Yueju Wang
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
| | - Yuan-Yeu Yau
- Department of Plant and Microbial Biology, Plant Gene Expression Center, USDA-ARS, University of California-Berkeley, 800 Buchanan St., Albany, CA 94710 USA
| | | | - James G. Thomson
- Crop Improvement and Utilization Unit, USDA-ARS WRRC, 800 Buchanan St., Albany, CA 94710 USA
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