Moreover, traditional enrichment-based approaches for isolating microsatellite loci require a priori choices about what types of microsatellite loci to target (both repeat size, and repeat motif sequence) which will ultimately lead to limited success in obtaining sufficient numbers of different types of useful microsatellite loci [ 26].
One approach to improving the reliability of microsatellite markers is to target single-copy regions in the genome.
Subtypes were identified by using a multilocus fragment-size analysis approach to target 3 microsatellite markers (ML1, ML2, and gp60 [synonymous with gp15]) as previously described (25 ).
Subsequently, identification of nonredundant microsatellites was targeted to underrepresented scaffolds.
In a subsequent pilot study, we showed that it was possible to obtain polymorphic microsatellites targeted towards candidate genes related to immunity and growth by selecting loci that appear variable in silico[ 30].
To date only one GWA-based study of variation in eggplant has been performed [ 16] but the present study used a larger number of accessions (191 vs 141 ) and a more densely populated genetic map (384 SNPs (single nucleotide polymorphisms) vs 105 microsatellites) and targeted traits related to anthocyanin accumulation and fruit color.
Several methods have been developed to differentiate genotypes currently dominated by microsatellite markers targeting single-copy loci.
Most of the microsatellites targeted were simple rather than compound with a total of 203 microsatellites (81.6%) targeting a single motif and 45 microsatellites (18.4%) targeting more than one motif.
Samples (three out of 54), lacking microsatellite alterations (patients 18, 25 and 36), showed, in fact, AI at two other microsatellites targeting 3p (D3S1293 and D3S3700), thus confirming the presence of tumour cells.
Interestingly, EWS-FLI1 gene modulation via microsatellites targeting might be more general than suggested by the present analysis as a number of EWS-FLI1 up-regulated genes that present long GGAA microsatellite sequences within 1 Mb of their transcription start sites are not detected here.
