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Bottero E, Gómez C, Stritzler M, Tajima H, Frare R, Pascuan C, Blumwald E, Ayub N, Soto G. Generation of a multi-herbicide-tolerant alfalfa by using base editing. PLANT CELL REPORTS 2022; 41:493-495. [PMID: 34994854 DOI: 10.1007/s00299-021-02827-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
We present the first report on base editing in alfalfa. Specifically, we showed edited alfalfa with tolerance to both sulfonylurea- and imidazolinone-type herbicides.
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Affiliation(s)
- Emilia Bottero
- Instituto de Agrobiotecnología y Biología Molecular, CONICET-INTA, Buenos Aires, Argentina
- Instituto de Genética "Edwald Alfredo Favret", INTA, De los Reseros S/N, C25 (1712), Castelar, Argentina
| | - Cristina Gómez
- Instituto de Agrobiotecnología y Biología Molecular, CONICET-INTA, Buenos Aires, Argentina
- Instituto de Genética "Edwald Alfredo Favret", INTA, De los Reseros S/N, C25 (1712), Castelar, Argentina
| | - Margarita Stritzler
- Instituto de Agrobiotecnología y Biología Molecular, CONICET-INTA, Buenos Aires, Argentina
- Instituto de Genética "Edwald Alfredo Favret", INTA, De los Reseros S/N, C25 (1712), Castelar, Argentina
| | - Hiromi Tajima
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Romina Frare
- Instituto de Agrobiotecnología y Biología Molecular, CONICET-INTA, Buenos Aires, Argentina
- Instituto de Genética "Edwald Alfredo Favret", INTA, De los Reseros S/N, C25 (1712), Castelar, Argentina
| | - Cecilia Pascuan
- Instituto de Agrobiotecnología y Biología Molecular, CONICET-INTA, Buenos Aires, Argentina
- Instituto de Genética "Edwald Alfredo Favret", INTA, De los Reseros S/N, C25 (1712), Castelar, Argentina
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Nicolás Ayub
- Instituto de Agrobiotecnología y Biología Molecular, CONICET-INTA, Buenos Aires, Argentina
- Instituto de Genética "Edwald Alfredo Favret", INTA, De los Reseros S/N, C25 (1712), Castelar, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular, CONICET-INTA, Buenos Aires, Argentina.
- Instituto de Genética "Edwald Alfredo Favret", INTA, De los Reseros S/N, C25 (1712), Castelar, Argentina.
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Jozefkowicz C, Gómez C, Odorizzi A, Iantcheva A, Ratet P, Ayub N, Soto G. Expanding the Benefits of Tnt1 for the Identification of Dominant Mutations in Polyploid Crops: A Single Allelic Mutation in the MsNAC39 Gene Produces Multifoliated Alfalfa. FRONTIERS IN PLANT SCIENCE 2021; 12:805032. [PMID: 35046986 PMCID: PMC8763170 DOI: 10.3389/fpls.2021.805032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Most major crops are polyploid species and the production of genetically engineered cultivars normally requires the introgression of transgenic or gene-edited traits into elite germplasm. Thus, a main goal of plant research is the search of systems to identify dominant mutations. In this article, we show that the Tnt1 element can be used to identify dominant mutations in allogamous tetraploid cultivated alfalfa. Specifically, we show that a single allelic mutation in the MsNAC39 gene produces multifoliate leaves (mfl) alfalfa plants, a pivot trait of breeding programs of this forage species. Finally, we discuss the potential application of a combination of preliminary screening of beneficial dominant mutants using Tnt1 mutant libraries and genome editing via the CRISPR/Cas9 system to identify target genes and to rapidly improve both autogamous and allogamous polyploid crops.
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Affiliation(s)
- Cintia Jozefkowicz
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
| | - Cristina Gómez
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
| | - Ariel Odorizzi
- Estación Experimental Agropecuaria Manfredi, Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | | | - Pascal Ratet
- Université Paris-Saclay, INRAE, CNRS, Université d’Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Nicolás Ayub
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
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Brambilla S, Soto G, Odorizzi A, Arolfo V, McCormick W, Primo E, Giordano W, Jozefkowicz C, Ayub N. Spontaneous Mutations in the Nitrate Reductase Gene napC Drive the Emergence of Eco-friendly Low-N 2O-Emitting Alfalfa Rhizobia in Regions with Different Climates. MICROBIAL ECOLOGY 2020; 79:1044-1053. [PMID: 31828388 DOI: 10.1007/s00248-019-01473-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
We have recently shown that commercial alfalfa inoculants (e.g., Sinorhizobium meliloti B399), which are closely related to the denitrifier model strain Sinorhizobium meliloti 1021, have conserved nitrate, nitrite, and nitric oxide reductases associated with the production of the greenhouse gas nitrous oxide (N2O) from nitrate but lost the N2O reductase related to the degradation of N2O to gas nitrogen. Here, we screened a library of nitrogen-fixing alfalfa symbionts originating from different ecoregions and containing N2O reductase genes and identified novel rhizobia (Sinorhizobium meliloti INTA1-6) exhibiting exceptionally low N2O emissions. To understand the genetic basis of this novel eco-friendly phenotype, we sequenced and analyzed the genomes of these strains, focusing on their denitrification genes, and found mutations only in the nitrate reductase structural gene napC. The evolutionary analysis supported that, in these natural strains, the denitrification genes were inherited by vertical transfer and that their defective nitrate reductase napC alleles emerged by independent spontaneous mutations. In silico analyses showed that mutations in this gene occurred in ssDNA loop structures with high negative free energy (-ΔG) and that the resulting mutated stem-loop structures exhibited increased stability, suggesting the occurrence of transcription-associated mutation events. In vivo assays supported that at least one of these ssDNA sites is a mutational hot spot under denitrification conditions. Similar benefits from nitrogen fixation were observed when plants were inoculated with the commercial inoculant B399 and strains INTA4-6, suggesting that the low-N2O-emitting rhizobia can be an ecological alternative to the current inoculants without resigning economic profitability.
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Affiliation(s)
- Silvina Brambilla
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF-INTA), Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF-INTA), Buenos Aires, Argentina
| | - Ariel Odorizzi
- Estación Experimental Agropecuaria Manfredi (INTA), Córdoba, Argentina
| | - Valeria Arolfo
- Estación Experimental Agropecuaria Manfredi (INTA), Córdoba, Argentina
| | - Wayne McCormick
- Ottawa Research and Development Centre (AAFC), Ottawa, ON, Canada
| | - Emiliano Primo
- Departamento de Biología Molecular (UNRC), Córdoba, Argentina
| | - Walter Giordano
- Departamento de Biología Molecular (UNRC), Córdoba, Argentina
| | - Cintia Jozefkowicz
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF-INTA), Buenos Aires, Argentina
| | - Nicolás Ayub
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO-CONICET), Buenos Aires, Argentina.
- Instituto de Genética (IGEAF-INTA), Buenos Aires, Argentina.
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Pascuan C, Bottero E, Kapros T, Ayub N, Soto G. pBAR-H3.2, a native-optimized binary vector to bypass transgene silencing in alfalfa. PLANT CELL REPORTS 2020; 39:683-685. [PMID: 32222784 DOI: 10.1007/s00299-020-02521-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE A novel genetic tool to bypass transgene silencing in alfalfa.
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Affiliation(s)
- Cecilia Pascuan
- Instituto de Agrobiotecnología Y Biología Molecular (IABIMO-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF-INTA), De Los Reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina
| | - Emilia Bottero
- Instituto de Agrobiotecnología Y Biología Molecular (IABIMO-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF-INTA), De Los Reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina
| | - Tamas Kapros
- School of Biological and Chemical Sciences, University of Missouri-Kansas City, Kansas City, USA
| | - Nicolás Ayub
- Instituto de Agrobiotecnología Y Biología Molecular (IABIMO-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF-INTA), De Los Reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología Y Biología Molecular (IABIMO-CONICET), Buenos Aires, Argentina.
- Instituto de Genética (IGEAF-INTA), De Los Reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina.
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Brambilla S, Frare R, Stritzler M, Soto G, Berini C, Jozefkowicz C, Ayub N. Synthetic multi-antibiotic resistant plasmids in plant-associated bacteria from agricultural soils. J Glob Antimicrob Resist 2020; 22:113-116. [PMID: 32007617 DOI: 10.1016/j.jgar.2020.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/09/2020] [Accepted: 01/19/2020] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVES Unlike higher organisms such as domestic animals and cultivated plants, which display a robust reproductive isolation and limited dispersal ability, microbes exhibit an extremely promiscuous gene flow and can rapidly disperse across the planet by multiple ways. Thus, microbial plasmids, including synthetic replicons, containing antibiotic resistance genes are a serious risk to public health. In this short communication, we explored the presence of synthetic elements in alfalfa symbionts (Ensifer meliloti strains) from agricultural soils. METHODS A total of 148 E. meliloti isolates from alfalfa plants growing under field conditions were collected from January 2015 to June 2019. Antimicrobial susceptibility testing was performed under laboratory conditions. We identified five kanamycin-resistant E. meliloti strains (named K1-K5). Whole genome sequencing analysis and conjugations were used to identify and study the plasmids of K strains. RESULTS We found that the genomes of K strains contain ampicillin, kanamycin and tetracycline resistance genes, the reporter gene lacZ from Escherichia coli and multiple cloning sites. These sequences were found within <58-kb plasmids related to the self-transmissible IncP plasmid RP4 from human pathogen Pseudomonas aeruginosa. Conjugation experiments confirmed the ability of K strains to transfer antibiotic resistance via conjugation to the Pseudomonas background. CONCLUSION In addition to the traditional analysis of plant growth-promoting factors, the commercial deregulation of putative natural inoculants should also include genomic studies to ensure a reasonable balance between innovation and caution.
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Affiliation(s)
- Silvina Brambilla
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina; Instituto de Genética Ewald A. Favret (INTA), Buenos Aires, Argentina; Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CONICET-INTA, Argentina
| | - Romina Frare
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina; Instituto de Genética Ewald A. Favret (INTA), Buenos Aires, Argentina; Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CONICET-INTA, Argentina
| | - Margarita Stritzler
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina; Instituto de Genética Ewald A. Favret (INTA), Buenos Aires, Argentina; Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CONICET-INTA, Argentina
| | - Gabriela Soto
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina; Instituto de Genética Ewald A. Favret (INTA), Buenos Aires, Argentina; Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CONICET-INTA, Argentina
| | - Carolina Berini
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina; Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CABA, Argentina
| | - Cintia Jozefkowicz
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina; Instituto de Genética Ewald A. Favret (INTA), Buenos Aires, Argentina; Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CONICET-INTA, Argentina
| | - Nicolás Ayub
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina; Instituto de Genética Ewald A. Favret (INTA), Buenos Aires, Argentina; Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CONICET-INTA, Argentina.
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