Scarano, Daria (2014) DNA AND TRANSCRIPTOMIC MARKERS AS TOOLS TO AUTHENTICATE PRIMARY PRODUCTS IN FOOD CHAIN. [Tesi di dottorato]

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Abstract

Tomato (Solanum lycopersicum) has an important economic role in the world thanks to the different applications on the market. It is the eleventh among commodities produced worldwide with a yield average of 37 tons/ha and about 160 million tons of tomatoes were produced in the world in 2011. China is the largest producer followed by India and United States while Italy, with 6 million of tons, is the seventh producer country (FAOSTAT 2011; http://faostat.fao.org). The tomato genome sequencing project started in 2004 by a consortium of 10 countries and the release of the complete tomato genome sequence was in 2012 (Tomato Genome Consortium). Among different tomato varieties, ‘San Marzano’ is a premium variety covered by an EU Protected Designation of Origin (PDO) label, cultivated in different areas of Campania region. Unfortunately, media constantly refer of unscrupulous producers that adulterate, alter or replace the premium products in tomato food chain with the goal to maximize illegally profits. There are rules aimed to protect against fraudulent substitution of quality product in food chain but this is not enough without tools able to verify the material incoming and outcoming. Food traceability, that is the possibility to identify an agricultural product at every step of production, processing and commercialisation, from farm to table, is central for the identification of improper labelling of processed food and feed. The present work evaluates the potential use of two types of markers, DNA and transcriptomic markers, in order to authenticate and trace ‘San Marzano’ tomato food chain. A set of 13 SSR (He et al., 2003; Smulders et al., 1997) markers was used to characterize a population of 145 tomato genotypes. Selected SSRs revealed an high polymorphism able to discriminate 72% of the genotype under analysis. Furthermore, SSR allelic profiles allowed verifying that industrial varieties are grouped separately from the local varieties from Campania Region and suggest that several sub- grouping are present, such as ‘San Marzano’ types subgroup. The same set of SSR was employed to study specifically the subgroup composed by 40 ‘San Marzano’ types, which contains 'San Marzano 2' and 'Kiros' (varieties included in the procedure guideline for tomato 'San Marzano' PDO production). The analysis revealed that all ‘San Marzano’ types were homozygotes and confirmed the power of selected SSR markers to discriminate 'San Marzano 2' and 'Kiros' from other 'San Marzano' types, which can also be sold as 'San Marzano' but without the PDO label. Six out of the 13 SSR loci were then selected for analysis of 33 peeled tomatoes labeled as ‘San Marzano’ PDO in order to verify the correspondence between what is declared on the label and the contents. SSR allelic profiles were compared with those produced for 'San Marzano' PDO types showing no match. The analyzed peeled tomatoes do not contain tomato berries from 'San Marzano' PDO varieties. On the other hand, the transcriptomic approach provides the identification of gene expression profiles characteristic of genotype-environment association. In particular, the transcriptome from berries of 'Kiros' plants collected from two different production areas (Acerra and Brusciano) was analyzed and the same analysis was conducted on ‘Docet' genotype. Among up-regulated highlighted genes in both comparisons most are involved in UV and oxidative stress response and signalling transduction. The occurrence of genes whose products are involved in DNA damage repair should have a biological meaning of plant self-protection from UV-radiation and can reflect in fruits compounds bouquet. Gene expression analysis suggested a clear distinction between locations for the analyzed genotypes. Furthermore, the combined study of two different tomato varieties in the same two fields has allowed a better understanding of which genes, among those differentially expressed, are strongly influenced by the environment and which are more related to the genotype, although, of course, influenced by the location. In conclusion, the present work has shown that the use of DNA markers and transcriptomic markers can help in authentication of genetic and geographical origin of raw materials used in the tomato agro-food chain and can be a tool to contrast food fraud. Traceability, supported by appropriate molecular tools, can really represent the bridge between consumers and producers making food production transparent and safety.

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