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

Abstract

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.

Establishment of an Efficient Sugarcane Transformation System via Herbicide-Resistant CP4-EPSPS Gene Selection

“…In this study, 10–30% of the selected lines lacked the transgenic GFP gene, which points to integration of partial transformation cassettes or other unintended changes to the integration constructs. Such effects are a general feature of GE transformation methods, as reviewed by Chu and Agapito [ 31 ]. As a consequence, the generated transformants need to be assessed for the integrity of the integrated recombinant constructs, as well as the number and the location of transgenic integrations, before they may be employed in practical agricultural use [ 31 ].…”

Recommendations for the Assessment of Potential Environmental Effects of Genome-Editing Applications in Plants in the EU

“…Furthermore, we believe that there is no scientific justification to generally discount the relevance of unintended modifications created with genome editing with regard to risk assessment (see Section 5 for details). The current level of predictability of unintended modifications is not sufficient to preclude their assessment [23,48].…”

“…However, this does not take into consideration the removal of unintended modifications during subsequent breeding steps that are inherently necessary for conventional breeding schemes. Additionally, the effects of the in vitro steps necessary to express genome-editing tools in the target cells and the different tendencies of the existing methods for genome editing to induce unintended modifications [48] are disregarded.…”

Research Progress of Nucleic Acid Detection Technology for Genetically Modified Maize

“…In 2022, Wenkang et al [170] published the latest research results in Science, pointing out that exploring the role of the KRN2/OsKRN2 gene in cereals may provide new opportunities to improve the yield of other global crops, such as maize. In recent years, advances in gene and genome sequencing technologies and the development of gene-editing technology have made precise and targeted editing possible [171,172]. The 2020 Nobel Prize in Chemistry was awarded to the inventors of CRISPR/Cas9 gene editing technology, which is easier, faster, cheaper, more precise, and safer than other technologies.…”