Dendrograme representation of the relationships between summer squash landraces using the genetic distance of UPGMA, based on SCoT (a), ISSR (b) and combined SCoT & ISSR (c) markers; letters show clusters. In general SCoT markers show higher discriminatory power since they divide the genotypes used in 6 groups the same as the combined analysis SCoT – ISSR. It is interesting to notice LKK58/07 from the island Kalymnos which shows a unique pattern probably due to the isolation. 

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... is a large family consisting of about 130 genera and 900 species. The Cucurbita genus harbours five domesticated species C. argyrosperma Huber, C. ficifolia Bouché, C. maxima , C. moschata and C. pepo, which are considered some of the earliest domesticated species and approximately ten wild species (Robinson and Decker- Walters, 1997; Smith, 2005). Greece hosts three domesticated species, C. pepo , C. maxima and C. moschata . Zucchini types of cultivars ( C. pepo ) are both the most popular types within the genus, and the highest-valued vegetables worldwide., In addition, they are one of the most variable amongst plant species (Paris, 1986) C. pepo fruits are consumed immature. C. pepo and Cucurbita species in general are consumed as food; their fruits they are rich in fat and vitamins and their seeds have high economic value especially the oil - seed industry. In Greece, summer squash is a widespread crop. The majority of production is based on landraces maintained over the years by local farmers, although hybrids are becoming popular. However, landraces of summer squash retain interesting horticultural characteristics, like resistance to diseases and pests. Moreover, landraces are an invaluable source of genes, important for breeding programs. The Greek Gene Bank is actively seeking to collect germplasm and, particularly in this case, Cucurbita spp. landraces, from all around Greece. Subsequently, a molecular characterization of this germplasm is needed, along with tests for biotic and abiotic stress tolerance, in order to render this collection useful to breeders and farmers (Tsivelikas et al., 2009). Lately, genetic diversity of crop plants is continuously being lost due to climate change, introduction of hybrids and improved cultivars. In this context, gene banks hold an extremely important role as reservoirs of biodiversity and source of alleles that can be relatively easily retrieved for genetic enhancement of crop plants. Increased efforts are being made to collect threatened landraces, cultivars that were obsolete, genetic stocks and wild relatives of cultivated species (Ortiz and Engels, 2004). Different marker systems have already been used in the assessment of genetic diversity within C. pepo, like restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphism (AFLP) and inter simple sequence repeats (ISSRs), as reviewed in (Lebeda et al., 2006) and in (Esteras et al., 2011). Yet, these tools are not very well developed in the Cucurbita genus, which reduces the potential gene discovery and the process of breeding (Blanca et al., 2011). The recent development of genomics and DNA sequencing technologies resulted in exponentially increased DNA sequence data, allowing the development of functional markers located in or near candidate genes (Andersen and Lubberstedt, 2003). Start Codon Targeted (SCoT) polymorphism is a novel functional marker system targeting genes (Collard and Mackill, 2009). SCoT primers have been developed based on the short conserved region which flanks the ATG start codon in plant genes. SCoT markers are generally reproducible, and it is suggested that primer length and annealing temperature are not the sole factors determining reproducibility. To our knowledge, this is the first time SCoT analysis has been applied to summer squash genotypes. The present study attempts to make a critical assessment regarding the potential of SCoT and ISSR markers for genotyping C. pepo landraces. In addition, we present the classification of summer squash landraces in different groups. Finally, comparison of the characteristic properties for two types of marker assays, including polymorphic information content (PIC), resolving power (R ) and marker index (MI), is reported. The oligonucleotide sequences of SCoT, ISSR primers, the resultant multiple band patterns and the data on computed Shannon’s index, diversity index and marker index for SCoT and ISSR markers for the thirty six summer squash landraces are summarized in Table 1 respectively. The PCR amplification using SC ο T primer pairs resulted in generation of reproducible amplification products (Fig. 1a). A total of 78 bands were detected among 36 C. pepo landraces, using seven SCoT markers, of which 49 were polymorphic (Table 1). The number of polymorphic bands ranged from 14 (SCoT70) to 3 (SCoT61 and SCoT34) with an average of 7 per primer. The overall size of amplified products ranged from 250 to 3,800 bp. Percent polymorphism ranged from 30 to as high as 100 with average polymorphism of 62.82 % across all landraces. PIC values ranged from 0.103 (SCoT61) to 0.309 (SCoT33), with an average value of 0.207 per primer. The diversity of the Genebank collection was represented with Nei’s gene diversity (GD), as well as Shannon’s information index (I). Data for GD and I for all the thirty six landraces was analyzed using seven SCoT markers and their corresponding mean values were found as 0.251 and 0.393 respectively (Table 1). The resolving power R P provided a modest indication of the ability of SCoT primers to distinguish among landraces. Thus, the R P of each primer was estimated in order to determine the most informative ones for the discrimination between summer squash landraces. The R P of the seven primers ranged from 0.612 for primer SCoT61 to 10.054 for primer SCoT13 (Table 1), with a mean value of 4.595. Three of the SCoT primers (SCoT13, SCoT70 and SCoT14) possessed high R P values (10.054, 8.78 and 4.556, respectively) and are the most efficient for surveying genetic diversity in the thirty six landraces of the Genebank collection. The highest MI was observed with the SCoT primer 70 (3.094) and the lowest in the SCoT primer 61 (0.315). The set of six ISSR primers used showed multiband patterns (Fig. 1b) for each landrace analysed (Table 1). This primer set amplified a total of forty two reliable and reproducible bands from the DNA of thirty six summer squash landraces tested. The total number of bands scored ranged from six to nine and the number of polymorphic fragments from three to seven per primer. Primers UBC811, UBC823, UBC827 and UBC834 resulted in the lowest number of fragments (three) and primer UBC860 and UBC881 generated the highest number of fragments (seven). The average number of fragments per primer was 7.1. Band size ranged from 600 bp (UBC811 and UBC834) to 4.0 kb (UBC860). Among the analysed landraces, 60.5% of the ISSR fragments were polymorphic. For the ISSR markers, GD and I were estimated to be 0.294 and 0.451 respectively (Table 1). The information obtained on the genetic profile of each landrace, using the six ISSR primers, was used to assess the marker performance through the evaluation of three parameters: PIC, MI and R P . To determine PIC values for each ISSR primer, we analyzed the mean of PIC values for all loci regarding each ISSR primer. We obtained a high PIC value for the ISSR primer UBC834 (0.302) and a low PIC value for the ISSR primer UBC881 (0.189), (Table 1). The average value of PIC per primer was 0.237. Moreover, R P and MI were used in order to determine the general usefulness of the system markers used, for each ISSR primer (Table 1). The average R P was 3.350 per ISSR primer (Table 1). The highest R P value was observed with the ISSR primer UBC881 (5.662) and the lowest with the ISSR primer UBC827 (1.504). The highest MI was observed with the ISSR primer UBC860 (1.330) and lowest with the ISSR primer UBC823 (0.672). Both molecular marker systems (SCoT and ISSR) were able to discriminate between 36 summer squash landraces. The level of polymorphism generated by SCoT markers (62.82%) was relatively similar to that of ISSR (60.5%) markers. Genetic relationships as determined by cluster analysis for SCoT, ISSR and pooled allelic data (SCoT + ISSR), are shown in Fig. 2 respectively. Dendrogrammes obtained by SCoT (Fig. 2a) and ISSR (Fig. 2b) markers were relatively similar and most of the landraces were placed in their respective groups. The values of the Mantel test showed positive correlation between the two marker types. The correlation coefficient was 0.25 between SCoT and ISSR, 0.78 between SCoT and pooled markers data (SCoT + ISSR) and 0.53 between ISSR and polled data. The dendrogramme from SCoT data was most consistent with the general dendrogramme from pooled (SCoT + ISSR) data. Cluster analysis using SCoT and ISSR data grouped the 36 squash genotypes into six and five distinct clusters, respectively (Fig. 2a and 2b). Genotypes belonging to cluster F in both SCoT and ISSR dendrogrammes were relatively similar. In the general dendrogramme (Fig. 2c), genotypes grouped in six distinct clusters (A-F). The detected polymorphic bands originating from the SCoT markers were used to calculate firstly: the Similarity Coefficient Matrix and then to construct a similarity dendrogramme using the UPGMA cluster algorithm. In this similarity dendrogram, the thirty six ...