Short communication Discrimination of ‘San Marzano’ accessions: A comparison of minisatellite, CAPS and SSR markers in relation to morphological traits Martina Caramante, Rosa Rao, Luigi Maria Monti, Giandomenico Corrado * Dipartimento di Scienze del Suolo, della Pianta, dell’’Ambiente e delle Produzioni Animali, Universita ` degli Studi di Napoli ‘Federico II’, 80055 Portici, Napoli, Italy 1. Introduction The tomato variety ‘San Marzano’ (SM) is a symbol of the Italian food-industry and represents, arguably, its most significant horticultural product. However, during the past few decades, the use of this variety has suffered a decline due to its genetic deficiencies and the subsequent diffusion of more productive tomato cultivars with similar fruit shapes (Monti et al., 2004). Modern hybrids possess morphological and quantitative traits that undoubtedly make them more suitable for fresh market or food- processing purposes, but they are genetically different from the original variety. Hence, they should be considered as such and labelled as ‘San Marzano-type’. The approval of the EU Protected Denomination of Origin (PDO) certification for ‘San Marzano’ is a valid action to protect and value the ‘San Marzano’ trade name, but additional measures should be undertaken for its long-term preservation. In many instances, it is essential to have adequate tools to discriminate the original variety from genetic material of different origins. A previous study indicated that DNA fingerprinting based on the (GATA) 4 minisatellite can identify San Marzano plants (Rao et al., 2006), and proved that there are two main problems for ‘San Marzano’ accessions in the PDO area. The first issue is the presence of similar plants that possess many but not all the ‘San Marzano’ phenotypic attributes. The second is the variable occurrence in several accessions of contaminant genotypes among true ‘San Marzano’ plants. To solve these problems, it would be useful to be able to distinguish ‘San Marzano’ with a fast, cost-effective and accurate means of genetic identification. Different molecular markers are available for detecting genetic variation. In tomato, high levels of polymorphism have been reported with the use of a (GATA) 4 oligonucleotide probe, which proved to be useful for distinguishing cultivars and accessions that are otherwise difficult to differentiate (Kaemmer et al., 1995; Rao et al., 2006). Cleaved amplified polymorphic sequence (CAPS) polymorphisms are differences in restriction fragment lengths caused by single nucleotide polymorphisms (SNPs) that modify restriction sites in PCR amplicons (Yang et al., 2004). CAPSs are therefore the less technically demanding approach for SNP analysis. Simple sequence repeats (SSRs) have the advantage of being highly informative (Bredemeijer et al., 1998; Cooke et al., 2003), and unlike SNPs, knowledge of the amplified sequences or further enzymatic manipulations are not needed (Schlotterer, 2004). However, SSRs require high resolution fluorescent-based capillary systems to fully exploit the information they can provide. Typically, different DNA marker systems have been evaluated for the detection of inter-varietal differences but the morphological similarity of the plant material analysed is rarely indicated. For these reasons, the aim of this work was to compare the efficacy of minisatellite, CAPS and SSR molecular markers for the distinction Scientia Horticulturae 120 (2009) 560–564 ARTICLE INFO Article history: Received 1 September 2008 Received in revised form 24 November 2008 Accepted 9 December 2008 Keywords: Tomato GATA SNP Microsatellite Genetic distance Morphological analysis ABSTRACT ‘San Marzano’ (SM) is one of the most widely known tomato (Solanum lycopersicum L.) cultivars, and is a classic example of a local variety with a premium value. Unfortunately, the original cultivated form is underrepresented in the Protected Denomination of Origin (PDO) area because of the incidence of contaminant and phenotypically similar genotypes. Our aim was to examine the ability of three DNA marker systems (minisatellite, cleaved amplified polymorphic sequence (CAPS) and simple sequence repeat (SSR)) to reveal the genetic diversity of tomato accessions that were, based on a morphological analysis, very similar. The data indicate that both minisatellites and SSRs can be used to genetically distinguish the analysed materials. Furthermore, these two marker systems depict relationships consistent with the hierarchal pattern obtained by the morphological data. As locally cultivated tomato accessions are often characterised by some degree of genetic variability, our results will be valuable in facilitating the purification, management and breeding of tomato germplasms. The differences between the marker systems employed are also discussed in relation to their usefulness in the agro-food chain. ß 2008 Elsevier B.V. All rights reserved. * Corresponding author. Tel.: +39 081 2539209; fax: +39 081 7753579. E-mail address: giandomenico.corrado@unina.it (G. Corrado). Contents lists available at ScienceDirect Scientia Horticulturae journal homepage: www.elsevier.com/locate/scihorti 0304-4238/$ – see front matter ß 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.scienta.2008.12.004