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Next Generation DNA Sequencing Based Strategies; Towards a New Era for the Traceability of Endangered Species and Genetically Modified Organisms

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Next Generation DNA Sequencing Based Strategies; Towards a New Era for the Traceability of Endangered Species and Genetically Modified Organisms Next generation DNA sequencing based strategies; towards a new era for the traceability of endangered species and genetically modified organisms Alfred Joseph Arulandhu Next generation DNA sequencing based strategies; towards a new era for the traceability of endangered species and genetically modified organisms Alfred Joseph Arulandhu Thesis committee Promotor Prof. Dr Saskia M. van Ruth Special professor Food Authenticity and Integrity Wageningen University & Research Co-promotor Dr Esther J. Kok Head Unit Novel Foods, programme leader Product Composition RIKILT Wageningen University & Research Other members Prof. Dr Marcel H. Zwietering, Wageningen University & Research Prof. Dr Ate D. Kloosterman, Netherlands Forensic Institute, Den Haag/University of Amsterdam Dr Frédéric Debode, CRA-W, Gembloux, Belgium Dr Bert Pöpping, FOCOS GbR, Alzenau, Germany This research was conducted under the auspices of the Graduate School VLAG (Advanced studies in Food Technology, Agrobiotechnology, Nutrition and Health Sciences) Next generation DNA sequencing based strategies; towards a new era for the traceability of endangered species and genetically modified organisms Alfred Joseph Arulandhu Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus, Prof. Dr A.P.J. Mol, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Wednesday 19th December 2018 at 1:30 p.m. in the Aula. Alfred Joseph Arulandhu Next generation DNA sequencing based strategies; towards a new era for the traceability of endangered species and genetically modified organisms, 179 pages. PhD thesis, Wageningen University, Wageningen, the Netherlands (2018) With references, with summary in English ISBN: 978-94-6343-368-6 DOI: https://doi.org/10.18174/463307 In memory of my mother Anthony Rajathi Table of Contents Chapter 1 General introduction 9 Chapter 2 Review: Advances in DNA metabarcoding for food and wildlife forensic 19 species identification Chapter 3 Development and validation of a multi-locus DNA metabarcoding 39 method to identify endangered species in complex samples Chapter 4 The application of multi-locus DNA metabarcoding in traditional 67 medicines Chapter 5 Review: DNA enrichment approaches to identify unauthorised 81 genetically modified organisms (GMOs) Chapter 6 NGS-based amplicon sequencing approach; towards a new era in GMO 105 screening and detection Chapter 7 ALF: a strategy for identification of unauthorised GMOs in complex 123 mixtures by a GW-NGS method and dedicated bioinformatics analysis Chapter 8 General discussion 141 References 155 Summary 171 About the author 174 Acknowledgements 178 Chapter 1 General Introduction 9 1.1 Introduction Food products are for the larger part composed of multiple ingredients that may be heavily processed. As a result, it is generally difficult, or even impossible, to determine the ingredient composition by visual inspection. At the same time, consumers demand detailed information on the composition of their food products before purchasing [1,2]. In the European Union (EU) food products and their ingredients are subjected to law. The basic law in this respect is the General Food Law that states that the labelling of food should not mislead consumers (European Commission (EC) regulation, 178/2002). More detailed legislation on labelling states that: ‘labelling should allow consumers to make informed choices and to make safe use of food, while at the same time ensure the free movement of legally produced and marketed foods’ (EC regulation, 1169/2011). Food authenticity studies have proven mislabelling for a wide range of food products, such as, meat, milk, honey, rice, edible oils, and spices [3-7]. Mislabelling might be caused by ignorance or lack of information regarding regulations, however, in many cases fraudulent intentions have shown to be the cause of mislabelling [3]. Fraud with foods and food ingredients raises concerns about food quality and safety, potentially poses health risks and, in addition, it may raise ethical issues when food products contain illegal ingredients. An example of food fraud with illegal ingredients is the use of endangered species as an ingredient. Some endangered species may be considered to have medicinal properties, and the addition of such species, or parts thereof, increases the value of a product [8]. Multiple studies have shown that endangered species are used in a variety of products, including food products [8-10]. Globally an increasing number of species are overexploited, which poses the threat of extinction of certain species, i.e. elephants, rhino etc., but also many plant species. Around 35,000 species, belonging to various plant and animal taxa, are classified as endangered by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) www.cites.org. Worldwide, the legal trade in endangered species is regulated by a permit system linked to the CITES convention (1973). In the EU, enforcement of the CITES convention is based on EC regulation, 338/97 on the Protection of species of wild fauna and flora which are threatened by trade. This regulation defines necessary procedures and documents required for import, export and re-export (permits) for the species listed under CITES law. Besides the regulated legal trade in endangered species, a significant portion of the trade in endangered plant and animals is illegal (www.traffic.org), this involves billions of dollars per year [11,12]. Although international trade agreements are being implemented, illegal trading and the use of endangered species parts are still common practice, as can be seen from reports from, amongst others, European and other customs authorities [8]. In other food fraud categories, food ingredients may also relate to food safety regulations, such is the case for genetically modified organisms (GMOs). The use of GMOs in food products has been the subject of public debates, since the first GMO entered the world market in 1996 [13]. In the last two decades, the development and production of a wide range of different GM plants have been observed [14]. GM plants and their derived products have been commercialised for the use in food/feed in many countries [15]. The regulations for the use of genetically modified (GM) crops in food and feed products vary between countries. The consequence of different regulations may be asynchronous approval. For example, 195 GM varieties are allowed in the USA, while in the European Union (EU) 55 GM varieties (without stacks) are authorised for use in food or feed products in 2017 (http://www.isaaa.org/gmapprovaldatabase/). Within the EU the introduction of new GMOs in food and feed supply chains is regulated by, primarily, two regulations, EC regulation, 1829/2003 and EC, 1830/2003. EC regulation, 1829/2003 on genetically modified food and feed states that approved GMOs need to be assessed for their food/feed and environmental safety prior to market introduction, and that unauthorised GMOs (UGMOs) are not allowed on the European market. It is furthermore stipulated 10 that labelling of GMOs is mandatory in the EU for products that contain more than 0.9% of authorised GMO per ingredient. EC regulation, 1830/2003 is focused on the traceability and labelling requirement for GMOs entering EU market. In recent years, the number of incidents related to the presence of unauthorised GMOs (UGMOs) and UGMO-derived products (food and feed) have globally increased and this has also affected the EU markets [15]. 1.2 Current analytical methods to address authenticity In order to assess the authenticity of food/feed products entering the EU market, both traditional and modern analytical methods are used. Frequently applied analytical techniques to determine general authenticity aspects of food products are thin layer chromatography, gas chromatography, capillary electrophoresis, high-performance liquid chromatography and mass spectrometry-based techniques [16,17]. In the last three decades, molecular techniques have become more widely applied in routine set- ups to determine the composition of food products [18,19]. Currently, for the identification of endangered species polymerase chain reaction (PCR) with DNA barcode markers is performed and followed by Sanger sequencing, which is the most commonly applied molecular biological procedure to identify a single product [20,21]. For GMOs, crop-specific and GMO-specific (element, construct and event) TaqMan PCRs are usually performed to determine the presence of a GMO in a sample [22]. Unexplained targets in GMO screening may indicate the presence of UGMO. Generally for identifying the unknown region of a UGMO a genome walking approach, where known GM targets are used to ‘read’ into the unknown region, is applied in combination with Sanger sequencing [23]. In recent years the field of molecular biology is increasingly using Next Generation Sequencing (NGS) technologies to address issues in the identification of species, strains, varieties etc [24,25]. NGS allows for massive parallel sequencing of targeted DNA, potentially enabling an overview of the genetic composition of a product in a single analysis. The application of NGS-based approaches for the detection and identification of endangered species as well as of GMOs and UGMOs is currently, however, still limited. Nonetheless, the potential of such NGS approaches based on an initial selective amplification step is large for
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