The GMOseek matrix: a decision support tool for optimizing the detection of genetically modified plants

Abstract

BackgroundSince their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introduced into the host genome. Information available regarding the GMOs’ molecular characterization is dispersed and not appropriately organized. For this reason, GMO testing is very challenging and requires more complex screening strategies and decision making schemes, demanding in return the use of efficient bioinformatics tools relying on reliable information.DescriptionThe GMOseek matrix was built as a comprehensive, online open-access tabulated database which provides a reliable, comprehensive and user-friendly overview of 328 GMO events and 247 different genetic elements (status: 18/07/2013). The GMOseek matrix is aiming to facilitate GMO detection from plant origin at different phases of the analysis. It assists in selecting the targets for a screening analysis, interpreting the screening results, checking the occurrence of a screening element in a group of selected GMOs, identifying gaps in the available pool of GMO detection methods, and designing a decision tree. The GMOseek matrix is an independent database with effective functionalities in a format facilitating transferability to other platforms. Data were collected from all available sources and experimentally tested where detection methods and certified reference materials (CRMs) were available.ConclusionsThe GMOseek matrix is currently a unique and very valuable tool with reliable information on GMOs from plant origin and their present genetic elements that enables further development of appropriate strategies for GMO detection. It is flexible enough to be further updated with new information and integrated in different applications and platforms.

Multiplex PCR system to track authorized and unauthorized genetically modified soybean events in food and feed

“…Randhawa, Chhabra, and Singh (2009) established a multiplex PCR system that targeted selectable markers and reporter genes for GMO screening. Furthermore, Block et al (2013) and Ruttink et al (2010) established decision support tools to identify authorized and unknown GMO screening elements. Waiblinger, Grohmann, Mankertz, Engelbert, and Pietsch (2010) presented a practical approach to screen authorized and unauthorized GM plants, and Randhawa, Morisset, Singh, and Zel (2014) described a cost-effective approach to screen unauthorized GM events in India.…”

GMOseek: a user friendly tool for optimized GMO testing

“…Just a few matrix approach tools are available [8, 11, 12, 22, 23]. These tools are often not amenable for wide use of the GMO testing community because of their lack of flexibility and availability.…”

“…However, it is not feasible to use it with large datasets such as the recent GMOseek matrix [8], given that more than 50 EU-approved GM events, and more than 320 GM events and 240 different genetic elements are listed globally.…”

Challenges for transgene detection in landraces and wild relatives: learning from 15 years of debate over GM maize in Mexico

“…Thus the authors claim, confirming the transgenic Biodivers Conserv (2018) 27:539-566 543 Table 1 Evidence table of sampling In searching for p35-S and T-NOS, Quist and Chapela were applying a screening method based on primers that target common elements of many commercial transgenic constructs. This is still the most widely applied screening matrix worldwide (Bonfini et al 2012;Block et al 2013). The method of nested-PCR was used to confirm non-specific binding and the amplification of unexpected primer binding sites.…”

“…2) and the socio-political nature of the controversy surrounding GMOs (Delborne 2008;Mercer and Wainwright 2008;McAfee 2008;Sarewitz 2004). Translating this interest in the issue to actually controlling transgene flow in Mexico is made particularly challenging by its geographic proximity to the USA and the high level of import that has been encouraged through the North Atlantic Free Trade Agreement (NAFTA) (Bello 2009). Furthermore, prioritising this issue for action is constrained by the availability of the Biodivers Conserv (2018) 27:539-566 541 necessary economic resources and governmental will, and the issue's embeddedness in the broader context of threats facing landrace maize biodiversity, including climate change, low profitability, declining subsidies, and emigration away from rural communities (Wainwright and Mercer 2011;Mercer et al 2012).…”