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Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants

BACKGROUND: The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this st...

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Autores principales: Anderson, Justin E., Michno, Jean-Michel, Kono, Thomas J. Y., Stec, Adrian O., Campbell, Benjamin W., Curtin, Shaun J., Stupar, Robert M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866027/
https://www.ncbi.nlm.nih.gov/pubmed/27176220
http://dx.doi.org/10.1186/s12896-016-0271-z
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author Anderson, Justin E.
Michno, Jean-Michel
Kono, Thomas J. Y.
Stec, Adrian O.
Campbell, Benjamin W.
Curtin, Shaun J.
Stupar, Robert M.
author_facet Anderson, Justin E.
Michno, Jean-Michel
Kono, Thomas J. Y.
Stec, Adrian O.
Campbell, Benjamin W.
Curtin, Shaun J.
Stupar, Robert M.
author_sort Anderson, Justin E.
collection PubMed
description BACKGROUND: The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. RESULTS: On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. CONCLUSIONS: Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12896-016-0271-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-48660272016-05-14 Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants Anderson, Justin E. Michno, Jean-Michel Kono, Thomas J. Y. Stec, Adrian O. Campbell, Benjamin W. Curtin, Shaun J. Stupar, Robert M. BMC Biotechnol Research Article BACKGROUND: The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. RESULTS: On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. CONCLUSIONS: Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12896-016-0271-z) contains supplementary material, which is available to authorized users. BioMed Central 2016-05-12 /pmc/articles/PMC4866027/ /pubmed/27176220 http://dx.doi.org/10.1186/s12896-016-0271-z Text en © Anderson et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Anderson, Justin E.
Michno, Jean-Michel
Kono, Thomas J. Y.
Stec, Adrian O.
Campbell, Benjamin W.
Curtin, Shaun J.
Stupar, Robert M.
Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants
title Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants
title_full Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants
title_fullStr Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants
title_full_unstemmed Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants
title_short Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants
title_sort genomic variation and dna repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866027/
https://www.ncbi.nlm.nih.gov/pubmed/27176220
http://dx.doi.org/10.1186/s12896-016-0271-z
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