Omic analyses on genetically modified soybean

Mutation breeding and molecular breeding which utilizes genetic engineering, has enabled the development of plants with desired characteristics in a shorter time as an supportive to conventional plant breeding. Genetically modified plants that have been developed by genetic engineering approaches brought along debates on biosafety, ethics, environmental assessment and risk management. Therefore, evaluation of intended and potentially unintended changes contribute to the GM risk assessments. The commonly-held concept of 'substantial equivalence' has been used for many years for the safety assessments of GM products. In this context, profile-based genomic and proteomic approaches are often preferred due to their power and accuracy in safety assessment. In this thesis, within the scope of substantial equivalence, it was aimed to conduct comparative genomic, proteomic and gene expression studies in transgenic (GM), non-transgenic, mutant, Ataem-07 soybean plants and Agrobacterium-mediated transgenic hairy roots of Ataem-07. Alterations in genome, gene expression and proteome level were detected by comparative analyzes of transgenic and mutant plants with their counterparts. Genomic comparison through Bagy2 and Nikita retrotransposon mediated IRAP analysis revealed polymorphism between roots of transgenic, mutant, Ataem-07 soybean plants and transgenic hairy roots. According to Bagy2, polymorphism rates were determined as 0-69% for hairy root, 20-42% for transgenic; 0-25% for mutant compared to Ataem-07 among experimental groups from the highest to the lowest. Likewise, these values were determined as 0-71%, 18-42% and 0-36%, respectively for Nikita. The highest polymorphism rates for Bagy2 and Nikita retrotransposes were detected as 56-69% and 62-71% in transgenic hairy samples, respectively. These results suggested that transgenesis exerts a greater effect on Bagy2 and Nikita-related genome changes than mutation breeding in comparison to Ataem-07. In transgenic, mutant, non-transgenic and Ataem-07 soybean cultivars, expression profiles of development related genes were determined and proteomic analyzes were performed. Development-related dt1, e1, elf3, luxb, luxc and siz1a genes were selected for gene expression analyses due to distinct differences in height and flowering time of experimental groups (in fifth trifoliolate stage, transgenic, 43 cm and no flowering; non-transgenic, 61 cm and with flowering; mutant, 18 cm and no flowering, Ataem-07, 22 cm and no flowering). It was determined that the expression of sız1a and elf3 genes in Ataem-07 plants compared to mutants and dt1, e1, luxb and luxc genes in non-transgenic plants compared to transgenic plants were significantly decreased. For these 6 development related genes, transgenesis caused more differences in gene expression profiles. The results of 2-D electrophoresis analysis in the experimental groups revealed that the protein spots varied between 533 and 674. It was determined that 25,7% of the total protein spots in mutant plants were not found in Ataem-07, and 11% of the total protein spots in transgenic plants were not found in non-transgenic plants. In addition, this study showed that many protein spots detected in mutant and transgenic plant groups have differences in expression levels compared to conventional counterpart soybean plants. Scatter plot analyzes revealed that the distribution of 2, 3, 4 and 5 times up- and down-regulated proteins showed a wider distribution in mutant plants than in transgenic plants. It has been determined that up-regulated proteins in mutant plants have various biological roles in processes such as development, stress response, photorespiration and ribosomal subunit assembly, mRNA processing, carbohydrate metabolism, homeostasis, chromosomal stability and transcription regulation. On the other hand, it has been determined that the up-regulated proteins in transgenic plants have biological roles related to ribosomal subunit assembly, electron transport, amino acid and nucleic acid metabolism, carbohydrate metabolism, signaling pathways and cell wall biogenesis. The proteomic analysis results showed that the number of both unexpressed and altered proteins were higher in mutants than transgenics. This suggested that the random changes in the genome induced by gamma radiation were more expressed in the proteome than the effect of transgene insertion. Since it was determined that the proteins presenting increased expression were related to basic biological processes in both groups, it was concluded that the effects of the mutation on the proteome did not cause significant differences in terms of the examined protein compared to transgenesis. In conclusion, the findings of this study within the scope of retrotransposon mobility in terms of Bagy2 and Nikita, expression analyzes of dt1, e1, elf3, luxb, luxc, sız1a development genes and 674 proteins showed that transgenesis affected changes more than mutagenesis in the genome and transcript level, and mutagenesis affected the changes more than transgenesis in the proteome which is the last stage of gene expression. Discussions on the potential of unintended changes induced by different breeding methods in plants and their associated risks are biased focusing on GM organisms. However, we suggest that it would be beneficial to characterize each of the plants with new features individually, and all of the different approaches from mutations to new generation breeding methods used for plant breeding in terms of these effects should be evaluated within the scope of risk assessment. Characterization of the variations that may occur due to plant breeding methods by omic technologies will provide deeper insight into the composition of plants and foods, which will aid to inform producers, consumers, regulators and other stakeholders for biosafety and risk assessment.