The genetic identification of crop plant varieties has the potential to bring about relevant improvements in the agricultural-food chain, not only to better guarantee the consumers, but also to give an added value to local and high quality products with special regards to Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) labeled ones. Cultivated populations are actually characterized and recorded in varietal registers mainly or exclusively based on morphological descriptors, fomenting numerous cases of misidentification, accidental or fraudulent exchanges and synonymous products. Moreover tracing crop plant products within a food chain is quite difficult especially for processed and/or transformed derivatives, making it difficult to trust in label information. Molecular markers are assuming an increasing importance on assessing genetic identity of species and varieties. Below the species as taxonomic operational unit, the simple sequence repeat (SSR) markers are known to be standardizable, transferable and suitable molecular tools to ensure the traceability and the authenticity of crop plants and food derivatives. In fact, on one hand, microsatellite genotyping at mapped loci is a discriminant The genetic identification of crop plant varieties has the potential to bring about relevant improvements in the agricultural-food chain, not only to better guarantee the consumers, but also to give an added value to local and high quality products with special regards to Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) labeled ones. Cultivated populations are actually characterized and recorded in varietal registers mainly or exclusively based on morphological descriptors, fomenting numerous cases of misidentification, accidental or fraudulent exchanges and synonymous products. Moreover tracing crop plant products within a food chain is quite difficult especially for processed and/or transformed derivatives, making it difficult to trust in label information. Molecular markers are assuming an increasing importance on assessing genetic identity of species and varieties. Below the species as taxonomic operational unit, the simple sequence repeat (SSR) markers are known to be standardizable, transferable and suitable molecular tools to ensure the traceability and the authenticity of crop plants and food derivatives. In fact, on one hand, microsatellite genotyping at mapped loci is a discriminant and efficient method able to improve the management of varietal registers and to genetically characterize varieties. On the other, microsatellite genotyping at mapped loci allows identifying in a uniquely way, and hence to trace and to authenticate, a given food product throughout the food chain in order to support the statement reported on the label. A total of 90 original articles concerning the varietal characterization and identification by means of SSR analysis of the five most economically relevant crops in Italy (i.e. Olea europaea L., Solanum lycopersicum L., Vitis vinifera L., Triticum spp. and Malus x domestica Borkh.) have been selected and reviewed. Since the genetic traceability of processed products may result more complex, wine and olive oil have been considered too. Specifically, this chapter deals with three main aspects: i) the criteria adopted for the selection of the most appropriate number, type and distribution of SSR marker loci to be employed for varietal genotyping; ii) the use of genetic statistics and parameters for the evaluation of the discriminant ability and applicability of SSR marker loci; iii) how to make different experimental works on the same species standardized, reliable and comparable. What emerges from the studies here reviewed is a lack of wider consensus among the authors regarding the strategy to design and to adopt for genotyping plant varieties with SSR markers. This finding highlights the urgent need to establish a common procedure, especially for characterizing and preserving landraces, and for supporting its rediscovery and valorization locally.
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