GLOBAL PROFILING TECHNOLOGIES ASSESS UNINTENDED EFFECTS IN TRANSGENIC PLANTS
Jaimie Schnell, Phil Macdonald, and Brian Miki
In the creation of a transgenic plant, one or more transgenes are inserted into the plant genome. While this is typically done to introduce some novel trait, there is also the possibility for other unintended effects. It is important to understand the types of unintended effects that can occur in transgenic plant systems and to employ a unified terminology for their description, as has recently been reviewed by Miki et al.1.
There are two main types of unintended effects that can occur in transgenic plants. First, position effects are locus-specific unintended effects that result from the interruption or alteration of processes occurring at the site of transgene insertion. Second, phenotypic traits are directly related to the presence of the transgene and constitute the pleiotropic effects. While one or more of these may be the intended trait, others may result from unexpected interactions of the transgene with plant processes and are unintended pleiotropic effects. These unintended effects in transgenic plants represent potential safety concerns. It is important to understand the nature of these effects and their potential for occurring in order to identify any potential risks that could affect the safe use of transgenic plants.
Global profiling technologies assess unintended effects
Risk assessment of transgenic crops is guided by the concepts of familiarity and substantial equivalence2. Generally, a transgenic plant is compared to a suitable non-transgenic counterpart that has a history of safe use, and if they are substantially equivalent, the transgenic plant can be considered safe as well. Identified differences between the plants would be a starting point for more focused risk assessment. Typically, a transgenic plant is assessed for a number of specific parameters that may include specific phenotypic traits and any changes in agronomic performance, levels of important nutrients, and endogenous levels of harmful allergens and toxins or the production of new ones.
Global profiling technologies provide an additional tool for assessing the safety of transgenic plants. These technologies contribute a comprehensive, global view of the levels of transcripts, proteins, and metabolites. They can be an important addition to the analysis of transgenic plants because they are non-targeted and therefore are not limited to those unintended effects that can be predicted3. Several studies have applied these technologies to different transgenic plant systems, demonstrating the effectiveness of such an approach and providing information about the potential for unintended effects to occur in transgenic plant systems.
What global profiling studies reveal
Global profiling studies have significantly contributed to our understanding of the potential for unintended effects in transgenic plant systems. The focus of several of these studies has been on selectable markers, since they are used in most transgenic plant systems. Unintended effects and plant selectable markers have recently been reviewed by Miki et al.1, and will be further examined here to demonstrate some of what we have learned from global profiling studies.
First, these studies reveal that it is possible to create transgenic plants that are substantially equivalent to their non-transgenic counterparts apart from the intended novel trait. This is illustrated by the insertion of the commonly used selectable marker gene nptII into the model plant Arabidopsis thaliana. The presence of the nptII gene is correlated with only small changes in the transcriptome, and these changes are considered a natural variation inherent to plant systems since they do not reproducibly occur across multiple plant lines4. The transgenic plants also respond similarly to their counterparts to various abiotic stresses, further demonstrating their equivalence. This study illustrates that the transformation process itself does not alter the gene expression patterns of the plant and that selectable marker genes can be inserted into the genome without altering the transcriptome.
In contrast, the insertion of the selectable marker gene bar into the genome of Arabidopsis results in the consistent differential regulation of a small number of genes, and these plants also exhibit a unique response to the application of the herbicide glufosinate5. This study illustrates that unintended effects can occur in transgenic plant systems that are specific to the transgene. Furthermore, it demonstrates that global profiling technologies are an effective means of identifying unintended effects, and thereby informing any further safety assessment if required.
Importantly, these technologies also show similar results for the traits found in two classic transgenic plants, demonstrating their effectiveness for the analysis of commercial crops. Microarray analysis of glyphosate-resistant soybean has identified changes in the transcriptome in a small number of genes, but greater changes are seen between different soybean cultivars, suggesting that the transgene has a minimal effect on the transcriptome6. Maize plantlets expressing the Cry1Ab protein from Bacillus thuringiensis, which renders the plants resistant to the European corn borer, do not show consistent differences in gene expression that could be attributable to the Cry1Ab gene7, while analysis of the proteome and metabolome of maize seed reveal small differences8,9.
Global profiling studies have also emphasized the need to establish the natural range of variation of genetic products in a given plant species. While rigorous experimental design employing controlled growth conditions and multiple plant lines can minimize natural variability, allowing a more precise identification of unintended effects, it may also be important to assess plants grown under more natural conditions. In such cases, differences between the transgenic plant and its non-transgenic counterpart are only considered to be significant if they fall outside the range of natural variability. One means of assessing the natural variability in a given plant species is to compare different cultivars. This approach has demonstrated that differences in global profiles are often greater between different cultivars than they are between transgenic plants and their non-transgenic counterparts, leading to a conclusion of substantial equivalence6,10. Alternatively, variation in a single cultivar grown at different sites and during different years is another means of assessing natural variability and again this has been successfully employed to demonstrate substantial equivalence11.
Global profiling technologies may become a useful tool for the risk assessment of transgenic crops and have also contributed significantly to our understanding of unintended effects in transgenic plant systems. They have been employed to assess the substantial equivalence of two transgenic plant systems currently grown commercially, as well as a number of other model systems.
Future perspectives
Studies employing global profiling technologies to assess unintended effects in transgenic plants have to date focused primarily on simple monogenic traits. In contrast, the next generation of transgenic crops is predicted to involve manipulation of more complex traits, focusing on enhancing yield as well as maintaining yield in suboptimal growing conditions. Examples include drought-tolerant corn12 and drought-tolerant canola13.
These second generation traits will involve manipulating complex networks that are typically under multipoint regulation. Therefore, alterations to these networks are expected to have a greater potential for producing unintended effects. Significantly, global profiling technologies have been developed to a level where they can be employed to understand potential unintended effects resulting from these traits before they become commercialized, unlike many first generation crops that were commercialized before the advent of these technologies.
Second generation crops will likely be created by manipulating key points of regulation in target pathways, and many of these key points will be transcription factors. Manipulation of the level of expression of transcription factors is a common approach for altering plant characteristics12. Transcription factors therefore represent a good model for predicting the potential for unintended effects in transgenic plants with complex traits.
In plants, transcription factors typically exist as members of large families that have undergone complex histories of evolution, allowing them to function in a wide range of plant processes from development to stress response. Gene redundancies have repeatedly occurred throughout evolution as a result of genome duplications, and these can be found at various stages of resolution as a result of subfunctionalization and neofunctionalization processes. In some cases, transcription factors can retain ancestral function, and this functional redundancy may not be revealed until normal gene expression is altered. The MADS-box family, for example, is a large transcription factor family in plants that has undergone a complex history of gene evolution14. In Arabidopsis, the MADS-box gene AGAMOUS (AG) functions in the development of the stamen, carpel, ovule, and floral meristem, while two paralogs of AG, SHATTERPROOF 1 (SHP1) and SHP2, primarily function in fruit development. However, SHP1 and SHP2 also function redundantly with AG in carpel and ovule development and in ectopic expression, since they are not normally expressed in stamens15. Interestingly, in Antirrhinum, the functional homolog of AG, PLENA, is actually paralogous to AG and orthologous to SHP1 and SHP2, suggesting the evolution of the AG clade followed different patterns of subfunctionalization in the two species16.
The AGAMOUS subfamily of MADS-box transcription factors provides an excellent example of the complex history of evolution both within and between species that has shaped the function of transcription factors. It illustrates the potential for unpredictable functional redundancies and residual activities that may only be revealed by ectopic expression, leading to unintended pleiotropic effects. It also suggests that transgenic plants with complex traits may be more likely to exhibit such unintended effects. Global profiling technologies will be fundamental in the assessment of these unintended effects at the molecular level, thus providing a useful tool for identifying any potential resulting new risks.
Concluding remarks
Despite the relatively recent development of many global profiling technologies and their application to transgenic plant systems, they have already proven an effective means of analyzing unintended effects resulting from genetic engineering. A number of studies have demonstrated that plant transformation can occur without significantly altering plant processes. Other studies have identified the occurrence of unintended effects in transgenic plants, providing very useful data for safety assessment. To date, identified differences have been relatively minor but it is imperative that these studies be extended to more complex traits.
Second generation transgenic crops are beginning to enter the regulatory system and this knowledge will be useful in developing the appropriate methods for a complete safety assessment of these plants. Manipulating complex traits is more likely to produce unintended effects in plant systems, making non-targeted assessment of unintended effects a crucial part of their analysis, whether at the genotypic or phenotypic level. Global profiling technologies will be a useful tool in guiding the risk assessment process for increasingly complex plants with novel traits.
References
- Miki B, Abdeen A, Manabe Y, MacDonald P. (2009) Selectable marker genes and unintended changes to the plant transcriptome. Plant Biotechnol J 7, 1-8