Development of a multiplex DNA-based traceability tool for crop plant materials

Abstract

The authenticity of food is of increasing importance for producers, retailers and consumers. All groups benefit from the correct labelling of the contents of food products. Producers and retailers want to guarantee the origin of their products and check for adulteration with cheaper or inferior ingredients. Consumers are also more demanding about the origin of their food for various socioeconomic reasons. In contrast to this increasing demand, correct labelling has become much more complex because of global transportation networks of raw materials and processed food products. Within the European integrated research project ‘Tracing the origin of food’ (TRACE), a DNA-based multiplex detection tool was developed—the padlock probe ligation and microarray detection (PPLMD) tool. In this paper, this method is extended to a 15-plex traceability tool with a focus on products of commercial importance such as the emmer wheat Farro della Garfagnana (FdG) and Basmati rice. The specificity of 14 plant-related padlock probes was determined and initially validated in mixtures comprising seven or nine plant species/varieties. One nucleotide difference in target sequence was sufficient for the distinction between the presence or absence of a specific target. At least 5% FdG or Basmati rice was detected in mixtures with cheaper bread wheat or non-fragrant rice, respectively. The results suggested that even lower levels of (un-)intentional adulteration could be detected. PPLMD has been shown to be a useful tool for the detection of fraudulent/intentional admixtures in premium foods and is ready for the monitoring of correct labelling of premium foods worldwide.

Review of methods for the detection and quantification of adulteration of rice: Basmati as a case study

“…The availability of thousands of DNA markers and cheaper sequencing methods offer unprecedented applications of DNA based methods to unravel the authentication crisis in food industry in general and rice market in particular (Arvanitoyannis 2008;Blair et al 2002;Lockley and Bardsley 2008;Dhanya and Sasikumar 2010;Saini et al 2004;Voorhuijzen et al 2012) (Table 2). Wide array of DNA-based markers are available for cultivar identification which includes random amplified polymorphic DNA (RAPD) Choudhury et al (2001), restriction fragment length polymorphism (RFLP) (Zhang et al 1992), amplified fragment length polymorphisms (AFLP) (Mackill et al 1996), fluorescent labelled inter simple sequence repeat (F-ISSR) Nagaraju et al (2002), insertion and deletions (indels) (Steele et al 2008), single nucleotide polymorphism (SNP) (Shirasawa et al 2006) and microsatellites (Bligh 2000;Archak et al 2007;Vemireddy et al 2007) (Table 2).…”

“…Recently, a DNA-based multiplex detection tool, the padlock probe ligation and microarray detection (PPLMD) tool was developed which is extended to a 15-plex traceability tool with a focus on products of wheat and Basmati rice (Voorhuijzen et al 2012). One nucleotide difference in target sequence was sufficient for the distinction between the presence or absence of a specific target.…”

Identification of biomarkers in hydrosoluble extracts from spelt and wheat cultivated in different production systems

“…The farming systems mostly differed in plant protection and fertilization strategies: conventional farming (CON) according to the Slovenian Agriculture Act and Good Agricultural Practice; integrated farming (INT) according to the Slovenian Standards for Integrated Farming; organic farming (ORG) according to the European Commission Regulation on Organic Farming; and biodynamic farming (BD) according to the Demeter International Production Standards and the European Commission Regulation on Organic Farming. 20 In the control treatment (C), no fertilization or plant protection means were used. Ploughing, seedbed preparation, sowing and harvesting were common agricultural operations in all systems.…”

“…9 A variety of genetic methods have been developed for detection of adulteration in cereal products: polymerase chain reaction (PCR), [10][11][12][13] quantitative PCR 14 and tubulin-based polymorphism (TBP) profiling for detection of soft wheat in durum wheat pasta; 15 PCR focusing on variable regions between genes to differentiate wheat from non-wheat cereals or non-gluten cereals from gluten-containing cereals; [16][17][18] the two polymorphisms on the γ-gliadine gene of the D genome to distinguish between spelt and bread wheat 19 ; and polymorphism of the Q locus to detect durum wheat addition to emmer wheat. 20 The main limit of genetic methods based on DNA is that the possible adulterant has to be known in advance. 21 PCR assays (restriction fragment length polymorphism-lab-on-a-chip-capillary electrophoresis; RFLP-LOC-CE) using γ-gliadine gene polymorphism are suitable for differentiation of pure spelt cultivars but not for spelt cultivars carrying wheat typical sequences.…”

Review, typology and evaluation of traceability technologies: case of the French forest supply chain

“…(2) DNA and synthetic DNA analysis (Voorhuijzen et al 2012;Madesis et al 2014;Mi et al 2015): DNA and synthetic DNA analysis that allows certifying the origin and the authentication of the product, use similar analysis technologies. The difference is that the DNA is initially created within the product while the synthetic DNA is independently developed in the laboratory and then added in or on the product.…”