Proteomics Insight into the Biological Safety of Transgenic Modification of Rice As Compared with Conventional Genetic Breeding and Spontaneous Genotypic Variation

The potential of unintended effects caused by transgenic events is a key issue in the commercialization of genetically modified (GM) crops. To investigate whether transgenic events cause unintended effects, we used comparative proteomics approaches to evaluate proteome differences in seeds from 2 sets of GM <i>indica</i> rice, herbicide-resistant Bar68-1 carrying <i>bar</i> and insect-resistant 2036-1a carrying <i>cry1Ac</i>/<i>sck</i>, and their respective controls D68 and MH86, as well as <i>indica</i> variety MH63, a parental line for breeding MH86, and <i>japonica</i> variety ZH10. This experimental design allowed for comparing proteome difference caused by transgenes, conventional genetic breeding, and natural genetic variation. Proteomics analysis revealed the maximum numbers of differentially expressed proteins between <i>indica</i> and <i>japonica</i> cultivars, second among <i>indica</i> varieties with relative small difference between MH86 and MH63, and the minimum between GM rice and respective control, thus indicating GM events do not substantially alter proteome profiles as compared with conventional genetic breeding and natural genetic variation. Mass spectrometry analysis revealed 234 proteins differentially expressed in the 6 materials, and these proteins were involved in different cellular and metabolic processes with a prominent skew toward metabolism (31.2%), protein synthesis and destination (25.2%), and defense response (22.4%). In these seed proteomes, proteins implicated in the 3 prominent biological processes showed significantly different composite expression patterns and were major factors differentiating <i>japonica</i> and <i>indica</i> cultivars, as well as <i>indica</i> varieties. Thus, metabolism, protein synthesis and destination, and defense response in seeds are important in differentiating rice cultivars and varieties