Houshyani Benyamin, van der Krol Alexander R, Bino Raoul J, Bouwmeester Harro J
Wageningen University, Plant Sciences Group, Laboratory of Plant Physiology, P,O, Box 658, Wageningen 6700 AR, The Netherlands.
BMC Plant Biol. 2014 Jun 19;14:170. doi: 10.1186/1471-2229-14-170.
Molecular characterization is an essential step of risk/safety assessment of genetically modified (GM) crops. Holistic approaches for molecular characterization using omics platforms can be used to confirm the intended impact of the genetic engineering, but can also reveal the unintended changes at the omics level as a first assessment of potential risks. The potential of omics platforms for risk assessment of GM crops has rarely been used for this purpose because of the lack of a consensus reference and statistical methods to judge the significance or importance of the pleiotropic changes in GM plants. Here we propose a meta data analysis approach to the analysis of GM plants, by measuring the transcriptome distance to untransformed wild-types.
In the statistical analysis of the transcriptome distance between GM and wild-type plants, values are compared with naturally occurring transcriptome distances in non-GM counterparts obtained from a database. Using this approach we show that the pleiotropic effect of genes involved in indirect insect defence traits is substantially equivalent to the variation in gene expression occurring naturally in Arabidopsis.
Transcriptome distance is a useful screening method to obtain insight in the pleiotropic effects of genetic modification.
分子特征分析是转基因作物风险/安全性评估的关键步骤。利用组学平台进行分子特征分析的整体方法，可用于确认基因工程的预期影响，但也能在组学层面揭示非预期变化，作为对潜在风险的初步评估。由于缺乏用于判断转基因植物多效性变化的显著性或重要性的共识参考和统计方法，组学平台在转基因作物风险评估中的潜力很少被用于此目的。在此，我们提出一种对转基因植物进行元数据分析的方法，通过测量与未转化野生型的转录组距离来实现。
在转基因植物与野生型植物转录组距离的统计分析中，将所得值与从数据库中获取的非转基因对应物的自然发生转录组距离进行比较。使用这种方法，我们表明参与间接昆虫防御性状的基因的多效性效应与拟南芥中自然发生的基因表达变化基本相当。
转录组距离是一种有用的筛选方法，可用于深入了解基因修饰的多效性效应。
