Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants

Autores
Cardillo, Maria Eugenia; Brambilla, Silvina Maricel; Liebrenz, Karen Ivana; Frare, Romina Alejandra; Maguire, Vanina Giselle; Soto, Gabriela Cynthia; Ruiz, Oscar Adolfo; Ayub, Nicolás Daniel
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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
Fuente
Plant Cell, Tissue and Organ Culture (PCTOC) 161 : article number 26. (April 2025)
Materia
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
Nivel de accesibilidad
acceso restringido
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/22399
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oai_identifier_str oai:localhost:20.500.12123/22399
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculantsCardillo, Maria EugeniaBrambilla, Silvina MaricelLiebrenz, Karen IvanaFrare, Romina AlejandraMaguire, Vanina GiselleSoto, Gabriela CynthiaRuiz, Oscar AdolfoAyub, Nicolás DanielInoculationSoybeansGene EditingGenetic VariationInoculaciónRhizobiaceaeSojaEdición de GenesBradyrhizobium japonicumVariación GenéticaInoculantsNon Genetically Modified OrganismsInoculanteOrganismo no Modificado GenéticamenteThe 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 BiotecnologíaFil: Cardillo, Maria Eugenia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Cardillo, Maria Eugenia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Brambilla, Silvina Maricel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Brambilla, Silvina Maricel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Liebrenz, Karen Ivana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Liebrenz, Karen Ivana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Frare, Romina Alejandra. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Frare, Romina Alejandra. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Maguire, Vanina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Soto, Gabriela Cinthia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Soto, Gabriela Cinthia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Ruiz, Oscar Adolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto Tecnológico Chascomús; ArgentinaFil: Ayub, Nicolás Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Ayub, Nicolás Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaSpringer2025-05-23T10:37:26Z2025-05-23T10:37:26Z2025-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/22399https://link.springer.com/article/10.1007/s11240-025-03059-61573-5044https://doi.org/10.1007/s11240-025-03059-6Plant Cell, Tissue and Organ Culture (PCTOC) 161 : article number 26. (April 2025)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-29T13:47:19Zoai:localhost:20.500.12123/22399instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:47:19.554INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv 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
spellingShingle Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants
Cardillo, Maria Eugenia
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
title_short 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_sort Genomic and physiological plasticity in natural variants of commercial soybean inoculants supports the non-GMO status of base-edited inoculants
dc.creator.none.fl_str_mv 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 Cardillo, Maria Eugenia
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_role author
author2 Brambilla, Silvina Maricel
Liebrenz, Karen Ivana
Frare, Romina Alejandra
Maguire, Vanina Giselle
Soto, Gabriela Cynthia
Ruiz, Oscar Adolfo
Ayub, Nicolás Daniel
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv 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
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
dc.description.none.fl_txt_mv 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
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).
publishDate 2025
dc.date.none.fl_str_mv 2025-05-23T10:37:26Z
2025-05-23T10:37:26Z
2025-04
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv 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
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
identifier_str_mv 1573-5044
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv 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)
eu_rights_str_mv restrictedAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv Plant Cell, Tissue and Organ Culture (PCTOC) 161 : article number 26. (April 2025)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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