Ophir et al. BMC Genomics 2010, 11:269 http://www.biomedcentral.com/1471-2164/11/269 Table 1: Sequence validation of putative SFPs SFP per UniGene 1 2 3 >3 Total No. of genes 118 62 21 12 213 FP 21 17 9 8 55 TP 97 60 20 13 190 PPV* 0.82 0.78 0.69 0.62 *0.79 0.68 0.19 0.07 0.06 1 that SFPs can be used across different genetic back- grounds in melon. Discussion In the present study, we tested the feasibility of identify- ing genetic polymorphism in melon crops by hybridizing gDNA to custom-designed microarrays based on a partial transcriptome. SFP technology has been previously applied for a variety of genetic applications, such as link- age analysis and association studies, mostly in model organisms such as Arabidopsis and yeast [5,32], with lim- ited use in some other agricultural organisms [29,33,34]. One of the main reasons for the limited use of this tech- nology is that the technological platform (Affymetrix arrays) is not available for many biological systems. In this study, we used custom-designed arrays with 45-55 mer probes (limitation of the Agilent CGH protocols) covering a substantial area of the partial transcriptome to discover genetic variation in melon. As a result, we increased the number of markers available for melon by Table 2: Transition-to-transversion ratios in SFPs Transversions 14 2 CG<->GC AT<->TA AC<->CA TG<->GT 21 7 18 2 17 5 Summary of bioinformatics analysis of 245 SFPs sequenced from the two different DNA pools of PI and 'Dulce'. The sequence data were compared to the database data. TP-True positive. FP-False positive. PPV-Positive predictive value. *Total PPV was recalculated by taking into account the actual representation of the different SFPs per UniGene group in the population. PPV = TP/[TP+FP] for each number of SFPs per gene category. The calculations were performed to adjust the validated SFP results with the proportions discovered by bioinformatics analysis. Bioinformatics analysis revealed transitions/transversions by comparing sequence data of SFPs to the melon EST database http:// www.icugi.org. 0.55 0.29 0.10 0.06 1 Page 4 of 10 Proportion of genes by SFP on array Proportion of genes by SFP number in sequence validation an order of magnitude using the cost-effective SFP tech- nology. The melon cultivars showed substantial within-popula- tion genetic variation (Additional file 2), as can be expected in agricultural crops. This needs to be consid- ered when defining the variation between different culti- vars. Based on our results, the use of pools of different parents is essential to overcoming this issue. With some exception [5,32], studies have reported dis- crepancies between calculated and observed false discov- ery rates (FDRs) for SFPs. Sequence validation (Table 1) showed that the FDRs in our array (melon, 21%) were similar to those found in rice (19%) [29] and unsequenced Arabidopsis strains (15-20%) [33], better than those found in tomato (25-30%) [34], and not as good as those found in some of the Arabidopsis studies [5,7]. One reason for this discrepancy is that genetic variation in loci near a target may influence its affinity to probes [35]. In our study, we eliminated all putative SFPs that did not harbor changes inside the SFP, because we could not evaluate the connection between these differences and hybridization Transitions AG<->GA 53 24 TC<->CT 61 17 PI414723 'Dulce'