Unintended effects of transgenic rice on grain yield and quality traits determined by quantitative proteomics

Abstract Omics techniques provide effective detection tools for assessing the potential impact of plant composition at the DNA, RNA, and protein levels. Among these, protein is the executor of gene function and the embodiment of biological traits, so that organisms show various genetic characteristics. Proteomics can be used to assess whether genetic engineering will lead to changes in plant traits beyond those introduced by conventional plant breeding. Here, we compare the extent of the proteome occurring in the leaves of three transgenic rice restore lines expressing CRY1C and CRY2A genes developed by genetic engineering and their corresponding recurrent parents developed by conventional breeding. CRY1C and CRY2A genes were inserted into chromosomes 11 and 12, respectively, which significantly improved the resistance of restore lines to Chilo suppressalis. Although differentially expressed proteins could be distinguished between transgenic rice and its recurrent parents, these differences were not sufficient to cause unintended effects on grain yield and quality traits of transgenic rice. In contrast, differences in phenotypic traits are more because of differences in genetic background. Functional cluster analysis showed that the differentially expressed proteins caused by the insertion of exogenous genes did not involve harmful metabolic pathways. The study successfully used 4D label-free quantitative proteomics technology to assess the unexpected changes in new rice varieties, and the results showed that transgenic rice did not cause unintended effects.