Alterations in genetically modified crops assessed by omics studies: Systematic review and meta-analysis

Benevenuto, Rafael Fonseca; Venter, Hermoine J.; Zanatta, Caroline Bedin; Nodari, Rubens Onofre; Agapito-Tenfen, Sarah Zanon

doi:10.1016/j.tifs.2022.01.002

Cited by 11 publications

(6 citation statements)

References 67 publications

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“…For example, a previous study showed that the unintended compositional alterations as well as unintended change of physical characteristic in transgenic rice compared with non-transgenic rice might be related to the genetic transformation . Meta-analysis revealed that the most frequently unintended effects on metabolic pathways were related to metabolism of carbohydrates, energy, lipids, and amino acids as well as genetic information processing and environmental information processing . In this study, MALDI-MSI analysis successfully revealed the significant differences in expressions and distributions of several classes of lipids ( e.g.…”

Section: Discussionmentioning

confidence: 58%

Spatial Lipidomics of EPSPS and PAT Transgenic and Non-Transgenic Soybean Seeds Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

Ren

Qin

Chen

et al. 2023

J. Agric. Food Chem.

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Herbicide-resistant soybeans are among the most widely planted transgenic crops. The in situ evaluation of spatial lipidomics in transgenic and non-transgenic soybeans is important for directly assessing the unintended effects of exogenous gene introduction. In this study, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI)-based nontargeted analytical strategies were used for the first time for in situ detection and imaging of endogenous lipid distributions in transgenic (EPSPS and PAT genes) herbicide-resistant soybean (Glycine max Merrill) (S4003.14) and non-transgenic soybean (JACK) seeds. Statistical analysis revealed significant differences in lipids between S4003.14 and JACK seeds. The variable importance of projection analysis further revealed that 18 identified lipids, including six phosphatidylcholines (PCs), four phosphatidylethanolamines (PEs), five triacylglycerols (TAGs), and three cytidine diphosphate-diacylglycerols (CDP-DAGs), had the strongest differential expression between S4003.14 and JACK seeds. Among those, the upregulated expressions of PC(P-36:1),

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Section: Discussionmentioning

confidence: 58%

Spatial Lipidomics of EPSPS and PAT Transgenic and Non-Transgenic Soybean Seeds Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

Ren

Qin

Chen

et al. 2023

J. Agric. Food Chem.

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“…Most importantly, there is a need for a framework for the definition of biological relevance of the generated data. We have observed the same pattern when we investigated alterations in the proteomic and metabolomic profile analyses of GM plants [ 39 ]. Nevertheless, the lack of harmonized methods seems to be due to the rapid progress of omics technologies rather than inconsistent reporting.…”

Section: Discussionmentioning

confidence: 71%

Unintended Genomic Outcomes in Current and Next Generation GM Techniques: A Systematic Review

Chu

Agapito-Tenfen

2022

Plants

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Classical genetic engineering and new genome editing techniques, especially the CRISPR/Cas technology, increase the possibilities for modifying the genetic material in organisms. These technologies have the potential to provide novel agricultural traits, including modified microorganisms and environmental applications. However, legitimate safety concerns arise from the unintended genetic modifications (GM) that have been reported as side-effects of such techniques. Here, we systematically review the scientific literature for studies that have investigated unintended genomic alterations in plants modified by the following GM techniques: Agrobacterium tumefaciens-mediated gene transfer, biolistic bombardment, and CRISPR-Cas9 delivered via Agrobacterium-mediated gene transfer (DNA-based), biolistic bombardment (DNA-based) and as ribonucleoprotein complexes (RNPs). The results of our literature review show that the impact of such techniques in host genomes varies from small nucleotide polymorphisms to large genomic variation, such as segmental duplication, chromosome truncation, trisomy, chromothripsis, breakage fusion bridge, including large rearrangements of DNA vector-backbone sequences. We have also reviewed the type of analytical method applied to investigate the genomic alterations and found that only five articles used whole genome sequencing in their analysis methods. In addition, larger structural variations detected in some studies would not be possible without long-read sequencing strategies, which shows a potential underestimation of such effects in the literature. As new technologies are constantly evolving, a more thorough examination of prospective analytical methods should be conducted in the future. This will provide regulators working in the field of genetically modified and gene-edited organisms with valuable information on the ability to detect and identify genomic interventions.

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“…Biases are defined as systematic errors in scientific studies that cause distortions in the results, compromising the internal validity of these studies. It is not possible to state with certainty whether a study is biased or not, but we can evaluate the risk of bias of the studies through a careful evaluation of its methodological quality [ 46 ]. There are several tools available to assess risk of bias (Robins, Cochrane, and Quadas-2, among others), and they are of great value in health studies and with related questions.…”

Section: Discussionmentioning

confidence: 99%

“…[ 39 , 40 , 41 , 42 ]. For this approach, systematic and defined methods are used a priori in the identification and selection of studies, data extraction, and analysis of results [ 43 , 44 , 45 , 46 ]. Thus, this SR involves the identification and comparison of data from the last seven years on the use of CRISPR/Cas technology in the editing of genes for tolerance to abiotic stresses.…”

Section: Introductionmentioning

confidence: 99%

Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review

Nascimento

Rocha

Soares

et al. 2023

Plants

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Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats—CRISPR/Cas—is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.

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Alterations in genetically modified crops assessed by omics studies: Systematic review and meta-analysis

Cited by 11 publications

References 67 publications

Spatial Lipidomics of EPSPS and PAT Transgenic and Non-Transgenic Soybean Seeds Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

Spatial Lipidomics of EPSPS and PAT Transgenic and Non-Transgenic Soybean Seeds Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

Unintended Genomic Outcomes in Current and Next Generation GM Techniques: A Systematic Review

Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review

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