Metabolomics should be deployed in identification and characterization of gene-edited crops

Authors: FRASER, PAUL - University Of London; AHARONI, ASAPH - Weizmann Institite Of Science; HALL, ROBERT - Wageningen University; HUANG, SANWEN - Chinese Academy Of Agricultural Sciences; Giovannoni, James; SONNEWALD, UWE - Max Planck Institute Of Molecular Plant Physiology; FERNIE, ALISDAIR - Max Planck Institute Of Molecular Plant Physiology

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2019
Publication Date: 1/10/2020
Citation: Fraser, P., Aharoni, A., Hall, R., Huang, S., Giovannoni, J.J., Sonnewald, U., Fernie, A. 2020. Metabolomics should be deployed in identification and characterization of gene-edited crops. Plant Journal. https://doi.org/10.1111/tpj.14679.
DOI: https://doi.org/10.1111/tpj.14679

Interpretive Summary: The advent and increasing usage of gene editing technologies raises the question of how the resulting products will be charcterized and regulated. We argue for metabolomics as an efficient means to both discriminate gene-edited from non-edited control plants and as an important tool to assess both intended and unanticipated metabolic outcomes, which could suggest the need for further characterization. Finally, we provide a perspective which we anticipate will aid in establishing a road-map for metabolomics-based identification and safety-assessment of gene-edited plants. Whether achieved via gene editing, induced or natural mutation or from available genetic diversity , the critical question remains: if a biochemical step or component of a physiological process is altered, what is the final outcome in chemical composition of the product and how will the scientific community detect, quantify and communicate these changes? Comprehensive metabolic characterization is the optimal means of describing such biochemical changes.

Technical Abstract: Gene editing techniques are currently revolutionizing biology allowing far greater precision than previous mutagenic and transgenic approaches. They are becoming applicable to a wide range of plant species and biological processes. Gene editing can rapidly improve a range of crop traits including disease resistance, abiotic stress tolerance, yield, nutritional quality and additional consumer traits. Unlike transgenic approaches, however, it is not facile to forensically detect gene-editing events at the molecular level, as no foreign DNA exists in the elite line. These limitations in molecular detection approaches are likely to focus more attention on the products generated from the technology, than the process per se. Rapid advances in sequencing and genome assembly increasingly facilitate genome sequencing as a means of characterizing new varieties generated by gene editing techniques. Nevertheless, subtle edits such as single base changes or small deletions may be difficult to distinguish from normal variation within a genotype. Given these emerging scenarios, downstream ‘omics’ technologies reflective of edited affects, such as metabolomics, need to be utilized in a more prominent manner to fully assess compositional changes in novel foodstuffs. To achieve this goal, metabolomics or “non-targeted metabolite analysis” needs to make significant advances to deliver greater representation across the metabolome. With the emergence of new edited crop varieties we advocate; (i) concerted efforts in the advancement of ‘omics’ technologies such as metabolomics and (ii) redress the use of the technology in the regulatory assessment for metabolically-engineered biotech crops.