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'Nebbiolo' is a well-known grapevine variety used to produce prestigious monovarietal Italian red wines. Genetic traceability is an important tool used to protect the authenticity of high-quality wines. SNP-based assays are an effective method to reach this aim in wines, but several issues have been reported for the authentication of commercial wines. In this study, the impact of the most common commercial additives and processing aids used in winemaking was analysed in 'Nebbiolo' wine using SNP-based traceability. Gelatine and bentonite had the strongest impact on the turbidity, colour and phenolic composition of wines and on residual grapevine DNA. The DNA reduction associated with the use of bentonite and gelatine (> 99% compared to the untreated control) caused issues in the SNP-based assay, especially when the DNA concentration was below 0.5 pg/mL of wine. This study contributed to explaining the causes of the reduced varietal identification efficiency in commercial wines.

Pasta, the Italian product par excellence, is made of pure durum wheat. The use of Triticum durum derived semolina is in fact mandatory for Italian pasta, in which Triticum aestivum species is considered a contamination that must not exceed the 3% maximum level. Over the last 50 years, various electrophoretic, chemical, and immuno-chemical methods have been proposed aimed to track the possible presence of common wheat in semolina and pasta. More recently, a new generation of methods, based on DNA (DeoxyriboNucleic Acid ) analysis, has been developed to this aim. Species traceability can be now enforced by a new technology, namely digital Polymerase Chain Reaction (dPCR) which quantify the number of target sequence present in a sample, using limiting dilutions, PCR, and Poisson statistics. In our work we have developed a duplex chip digital PCR (cdPCR) assay able to quantify common wheat presence along pasta production chain, from raw materials to final products. The assay was verified on reference samples at known level of common wheat contamination and applied to commercial pastas sampled in the Italian market.

The European flat oyster (Ostrea edulis) is a highly appreciated mollusk with an important aquaculture production throughout the 20th century, in addition to playing an important role on coastal ecosystems. Overexploitation of natural beds, habitat degradation, introduction of non‐native species, and epidemic outbreaks have severely affected this important resource, particularly, the protozoan parasite Bonamia ostreae, which is the main concern affecting its production and conservation. In order to identify genomic regions and markers potentially associated with bonamiosis resistance, six oyster beds distributed throughout the European Atlantic coast were sampled. Three of them have been exposed to this parasite since the early 1980s and showed some degree of innate resistance (long‐term affected group, LTA), while the other three were free of B. ostreae at least until sampling date (naïve group, NV). A total of 14,065 SNPs were analyzed, including 37 markers from candidate genes and 14,028 from a medium‐density SNP array. Gene diversity was similar between LTA and NV groups suggesting no genetic erosion due to long‐term exposure to the parasite, and three population clusters were detected using the whole dataset. Tests for divergent selection between NV and LTA groups detected the presence of a very consistent set of 22 markers, located within a putative single genomic region, which suggests the presence of a major quantitative trait locus associated with B. ostreae resistance. Moreover, 324 outlier loci associated with factors other than bonamiosis were identified allowing fully discrimination of all the oyster beds. A practical tool which included the 84 highest discriminative markers for tracing O. edulis populations was developed and tested with empirical data. Results reported herein could assist the production of stocks with improved resistance to bonamiosis and facilitate the management of oyster beds for recovery production and ecosystem services provided by this species. This work was funded by the OYSTERECOVER project (FP7‐SME‐2008‐2‐243583) from the European Community's Seventh Framework Programme, the European Regional Development's funds (FEDER), and Xunta de Galicia local government (GRC2014/010, R2014/046). The development and provision of the medium‐density SNP array for oysters was supported by Biotechnology and Biological Sciences Research Council (BBSRC), and National Environment Research Council (NERC) grants (BB/M026140/1, NE/P010695/1), in addition to BBSRC Institute Strategic Program Grants (BBS/E/D/20002172 and BBS/E/D/30002275) SI

A colorimetric assay, exploiting the combination of loop-mediated isothermal amplification (LAMP) with DNA barcoding, was developed to address the authentication of some cephalopod species, a relevant group in the context of seafood traceability, due to the intensive processing from the fishing sites to the shelf. The discriminating strategy relies on accurate design of species-specific LAMP primers within the conventional 5’ end of the mitochondrial COI DNA barcode region and allows for the identification of Loligo vulgaris among two closely related and less valuable species. The assay, coupled to rapid genomic DNA extraction, is suitable for large-scale screenings and on-site applications due to its easy procedures, with fast (30 min) and visual readout.

The development of a colorimetric mono-varietal discriminating assay, aimed at improving traceability and quality control checks of durum wheat products, is described. A single nucleotide polymorphism (SNP) was identified as a reliable marker for wheat varietal discrimination, and a rapid test for easy and clear identification of specific wheat varieties was developed. Notably, an approach based on the loop-mediated isothermal amplification reaction (LAMP) as an SNP discrimination tool, in combination with naked-eye visualization of the results, was designed and optimized. Our assay was proven to be effective in the detection of adulterated food products, including both substitution and mixing with different crop varieties.

The genetic varietal authentication of wine was investigated according to DNA isolation procedures reported for enological matrices and also by testing 11 commercial extraction kits and various protocol modifications. Samples were collected at different stages of the winemaking process of renowned Italian wines Brunello di Montalcino, Lambruschi Modenesi, and Trento DOC. Results demonstrated not only that grape DNA loss is produced by the fermentation process but also that clarification and stabilization operations contribute to the reduction of double-stranded DNA content on wine. Despite the presence of inhibitors, downstream PCR genotyping yielded reliable nuclear and chloroplast SSR markers for must samples, whereas no amplification or inconsistent results were obtained at later stages of the vinification. In addition, a TaqMan genotyping assay based on cultivar-specific single-nucleotide polymorphisms (SNPs) was designed, which allowed assessment of grapevine DNA mixtures. Once the wine matrix limitations are overcome, this sensitive tool may be implemented for the relative quantification of cultivars used for blend wines or frauds.

'Nebbiolo' (Vitis vinifera L.) is renowned for its use in producing monovarietal high-quality red wines, such Barolo and Barbaresco. The fight against fraud to safeguard high-quality productions requires an effective varietal identification system applicable in musts and wines. 'Nebbiolo'-specific single-nucleotide polymorphisms (SNPs) were identified starting from available databases and 260 genotypes analysed by Vitis18kSNP array. Two SNPs were sufficient to identify 'Nebbiolo' from 1157 genotypes. The SNP TaqMan® genotyping assays developed in this work successfully identified 'Nebbiolo' in all musts and wines collected at different experimental wine-making steps. The high sensitivity of the assays allowed identification of must mixtures at 1% and wine mixtures at 10-20% with non-'Nebbiolo' genotypes. In commercial wines, the amplification efficiency was limited by the low amount of grapevine DNA and the presence of PCR inhibitors. The TaqMan® genotyping assay is a rapid, highly sensitive and specific methodology with remarkable potential for varietal identification in wines.

DNA barcoding is a molecular technology that allows the identification of any biological species by amplifying, sequencing and querying the information from genic and/or intergenic standardized target regions belonging to the extranuclear genomes. Although these sequences represent a small fraction of the total DNA of a cell, both chloroplast and mitochondrial barcodes chosen for identifying plant and animal species, respectively, have shown sufficient nucleotide diversity to assess the taxonomic identity of the vast majority of organisms used in agriculture. Consequently, cpDNA and mtDNA barcoding protocols are being used more and more in the food industry and food supply chains for food labeling, not only to support food safety but also to uncover food piracy in freshly commercialized and technologically processed products. Since the extranuclear genomes are present in many copies within each cell, this technology is being more easily exploited to recover information even in degraded samples or transformed materials deriving from crop varieties and livestock species. The strong standardization that characterizes protocols used worldwide for DNA barcoding makes this technology particularly suitable for routine analyses required by agencies to safeguard food safety and quality. Here we conduct a critical review of the potentials of DNA barcoding for food labeling along with the main findings in the area of food piracy, with particular reference to agrifood and livestock foodstuffs.