Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants
The regulatory classification of genome-edited microorganisms remains a topic of debate, particularly in the agricultural sector. In this study, we analyze the genomic and physiological differences of commercial variants of Bradyrhizobium japonicum E109, a widely used soybean inoculant, to establish...
| Main Authors: | , , , , , , , |
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| Format: | Artículo |
| Language: | Inglés |
| Published: |
Springer
2025
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| Online Access: | http://hdl.handle.net/20.500.12123/22399 https://link.springer.com/article/10.1007/s11240-025-03059-6 https://doi.org/10.1007/s11240-025-03059-6 |
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| author | Cardillo, Maria Eugenia Brambilla, Silvina Maricel Liebrenz, Karen Ivana Frare, Romina Alejandra Maguire, Vanina Giselle Soto, Gabriela Cynthia Ruiz, Oscar Adolfo Ayub, Nicolás Daniel |
| author_browse | Ayub, Nicolás Daniel Brambilla, Silvina Maricel Cardillo, Maria Eugenia Frare, Romina Alejandra Liebrenz, Karen Ivana Maguire, Vanina Giselle Ruiz, Oscar Adolfo Soto, Gabriela Cynthia |
| author_facet | Cardillo, Maria Eugenia Brambilla, Silvina Maricel Liebrenz, Karen Ivana Frare, Romina Alejandra Maguire, Vanina Giselle Soto, Gabriela Cynthia Ruiz, Oscar Adolfo Ayub, Nicolás Daniel |
| author_sort | Cardillo, Maria Eugenia |
| collection | INTA Digital |
| description | The regulatory classification of genome-edited microorganisms remains a topic of debate, particularly in the agricultural sector. In this study, we analyze the genomic and physiological differences of commercial variants of Bradyrhizobium japonicum E109, a widely used soybean inoculant, to establish a reference framework for distinguishing natural genetic variation from intentional genome editing. Specifically, we conducted whole-genome sequencing and phenotypic assessments of E109 variants obtained from commercial inoculants, comparing them to the official strain maintained by INTA. Our results reveal that commercial variants naturally accumulate multiple single-nucleotide substitutions, with an average of 9.7 mutations per variant, comparable to a CRISPR base-editing event targeting at least 6 different loci. Notably, the majority of these mutations occur within coding sequences (91%), and most of them (82%) are non-synonymous, potentially affecting protein function and inoculant fitness. In vitro and in planta assays confirmed that these natural mutations impact key traits, including oxidative stress resistance, root attachment, cell survival, and nitrogen fixation efficiency. These findings provide a scientific basis for regulatory decisions by demonstrating that genomic variability within commercial inoculants is a natural process and support the classification of base-edited inoculants as equivalent to non-genetically modified organisms (non-GMOs). |
| format | Artículo |
| id | INTA22399 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | INTA223992025-05-23T10:47:32Z Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants Cardillo, Maria Eugenia Brambilla, Silvina Maricel Liebrenz, Karen Ivana Frare, Romina Alejandra Maguire, Vanina Giselle Soto, Gabriela Cynthia Ruiz, Oscar Adolfo Ayub, Nicolás Daniel Inoculation Soybeans Gene Editing Genetic Variation Inoculación Rhizobiaceae Soja Edición de Genes Bradyrhizobium japonicum Variación Genética Inoculants Non Genetically Modified Organisms Inoculante Organismo no Modificado Genéticamente The regulatory classification of genome-edited microorganisms remains a topic of debate, particularly in the agricultural sector. In this study, we analyze the genomic and physiological differences of commercial variants of Bradyrhizobium japonicum E109, a widely used soybean inoculant, to establish a reference framework for distinguishing natural genetic variation from intentional genome editing. Specifically, we conducted whole-genome sequencing and phenotypic assessments of E109 variants obtained from commercial inoculants, comparing them to the official strain maintained by INTA. Our results reveal that commercial variants naturally accumulate multiple single-nucleotide substitutions, with an average of 9.7 mutations per variant, comparable to a CRISPR base-editing event targeting at least 6 different loci. Notably, the majority of these mutations occur within coding sequences (91%), and most of them (82%) are non-synonymous, potentially affecting protein function and inoculant fitness. In vitro and in planta assays confirmed that these natural mutations impact key traits, including oxidative stress resistance, root attachment, cell survival, and nitrogen fixation efficiency. These findings provide a scientific basis for regulatory decisions by demonstrating that genomic variability within commercial inoculants is a natural process and support the classification of base-edited inoculants as equivalent to non-genetically modified organisms (non-GMOs). Instituto de Biotecnología Fil: Cardillo, Maria Eugenia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Cardillo, Maria Eugenia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Brambilla, Silvina Maricel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Brambilla, Silvina Maricel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Liebrenz, Karen Ivana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Liebrenz, Karen Ivana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Frare, Romina Alejandra. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Frare, Romina Alejandra. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Maguire, Vanina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina Fil: Soto, Gabriela Cinthia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Soto, Gabriela Cinthia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Ruiz, Oscar Adolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto Tecnológico Chascomús; Argentina Fil: Ayub, Nicolás Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Ayub, Nicolás Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina 2025-05-23T10:37:26Z 2025-05-23T10:37:26Z 2025-04 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/22399 https://link.springer.com/article/10.1007/s11240-025-03059-6 1573-5044 https://doi.org/10.1007/s11240-025-03059-6 eng info:eu-repo/semantics/restrictedAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf Springer Plant Cell, Tissue and Organ Culture (PCTOC) 161 : article number 26. (April 2025) |
| spellingShingle | Inoculation Soybeans Gene Editing Genetic Variation Inoculación Rhizobiaceae Soja Edición de Genes Bradyrhizobium japonicum Variación Genética Inoculants Non Genetically Modified Organisms Inoculante Organismo no Modificado Genéticamente Cardillo, Maria Eugenia Brambilla, Silvina Maricel Liebrenz, Karen Ivana Frare, Romina Alejandra Maguire, Vanina Giselle Soto, Gabriela Cynthia Ruiz, Oscar Adolfo Ayub, Nicolás Daniel Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants |
| title | Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants |
| title_full | Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants |
| title_fullStr | Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants |
| title_full_unstemmed | Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants |
| title_short | Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants |
| title_sort | genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non gmo status of base edited inoculants |
| topic | Inoculation Soybeans Gene Editing Genetic Variation Inoculación Rhizobiaceae Soja Edición de Genes Bradyrhizobium japonicum Variación Genética Inoculants Non Genetically Modified Organisms Inoculante Organismo no Modificado Genéticamente |
| url | http://hdl.handle.net/20.500.12123/22399 https://link.springer.com/article/10.1007/s11240-025-03059-6 https://doi.org/10.1007/s11240-025-03059-6 |
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