As mentioned previously, all breeding techniques introduce modifications at the DNA level, other than the desired change. However, I hasten to add that, despite the extensive genetic manipulation of crop plants by the many and diverse methods described previously, cases of novel or completely unexpected adverse consequences for commercialized varieties of these crops are extremely rare. Variations due to breeding and the application of modern biotechnology have been studied frequently by scientific experts sponsored by organizations such as the United Nations (UN) Food and Agriculture Organization (FAO), the European Commission, the Royal Society and the US National Academy of Sciences. In each case, the conclusions were that modern biotechnology is no more likely than conventional breeding to produce unintended effects. Indeed, many expert reviews have concluded that the greater precision and more defined nature of the changes introduced into crops via modern biotechnology may actually be safer than changes produced by conventional plant breeding.
Substantial equivalence is the guiding principle for safety assessment. In short, substantial equivalence involves the process of comparing the GM product to a conventional counterpart with a history of safe use. Such a comparison commonly includes agronomic performance, phenotype, expression of transgenes and composition (macro- and micronutrients), and it identifies the similarities and differences between the GM product and the conventional counterpart. Based on the differences identified, further investigations may be carried out to assess the safety of these differences. These assessments include any protein that is produced from the inserted DNA. In fact, several publications have demonstrated that GM crops are often more closely related to the isogenic parental strain used in their development than to other members of the same genus and species. For example, metabolomic studies in potato Solanum tuberosum have shown that conventional plant breeding produces both intended and unintended effects and that insertion of transgenes can occur with little apparent effect on composition, even when the GM variety produces significant quantities of a new metabolite (e.g., the fiber inulin). Indeed, when the introduced gene product (DP2-3 fructans) was removed from the analysis parameters, multivariate statistical analysis showed no significant variation in the metabolic phenotype, including harmful glycoalkaloids, between the GM crop and the progenitor lines, whereas other, conventionally bred cultivars showed clearly separated metabolic phenotypes (Chassy et al., 2008). Similar results have been observed at the proteome level for other plant species. So, bottom line, unexpected changes are less likely to happen using modern biotech techniques than many older breeding systems.
It is also important to keep in mind that the process of product development that selects a single commercial cultivar from hundreds to thousands of initial transformation events eliminates the vast majority of situations that might have resulted in unintended changes. The selected commercial product candidate event undergoes additional detailed phenotypic, agronomic, morphological and compositional analyses to further screen for such effects.
Chassy, B.; Egnin, M.; Gao, Y.; Glenn, K.; Kleter, G.A.; Nestel, P.; Newell-McGloughlin, M.; Phipps, R.H.; Shillito, R. 2008 Nutritional and Safety Assessments of Foods and Feeds Nutritionally Improved through Biotechnology: Case Studies Comprehensive reviews in food science and food safety 7, pp. 50–99.