Ab initio and in silico Discovery of SSR Indel and SNP Markers Without a priori Knowledge of Map Position

The identification of tomato SSRs and SNPs was greatly improved once sufficient sequence database resources became available. In particular, large collections of expressed sequence tags (ESTs) hosted in various databases greatly facilitated molecular marker development (Table 5). In the first attempt at in silico marker discovery for tomato, the search for SSRs by computational screening of genomic sequences from EMBL and GenBank databases resulted in the identification and confirmation of 36 polymorphic SSR markers between tomato cultivars and species (Smulders etal. 1997). Subsequently using different search parameters, putative SSRs were detected in the ESTs and genomic sequences (He et al. 2002; Frary et al. 2005). Tomato EST databases contained over 600 unique sequences with SSR motifs, of which a set of 109 were confirmed and mapped in a reference population de rived from a S. lycopersicum x S. pennellii cross (Frary et al. 2005). These confirmed SSRs were used to detect size polymorphisms within and between species (He et al. 2002; Frary et al. 2005; Yang et al. 2005b) (Fig. 2). The same EST databases were also mined for SNPs. Since tomato EST collections are derived from more than one cultivar, this approach has been practical (Yang et al. 2004; Labate and Baldo 2005). Putative SNPs were verified via restriction enzyme digests or resequencing and mapped in different tomato populations and cultivars (Yang et al. 2004) (Fig. 2). ESTs from other varieties and putative SNP information are available at other websites (Tsugane et al. 2005), in addition to bacterial artificial chromosome (BAC) and BAC-end sequences which can be mined for additional putative SNPs.

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