The development of a reference genetic map covering the entire genome with PCR-based markers demonstrates how public resources can be used to facilitate genetic investigations of tomato populations. Frary et al. (2005) reported on the first sequence-dependent PCR-based map for tomato for a population derived from a cross between S. lycopersicum and S. pennellii. Using many of the techniques reviewed above, a set of 87 PCR-based markers were mapped between two much more closely related red-fruited species, S. lycopersicum cv. Rio Grande and S. pimpinellifolium LA1589 (Gonzalo and van der Knaap, unpublished) (Fig. 2). Since markers that are polymorphic in sub sets of species or within the cultivated germplasm pool have a higher chance of being polymorphic in other lines (Francis and Wang, unpublished), some of the previously developed PCR-based markers were directly applicable to this population. Fifteen markers were derived from the tomato intron sequence mining project (Van Deynze et al. 2006; Table 5), seven were derived from the in silico SNP project (Yang et al. 2004), 31 were SSRs available at SGN, whereas the remainder were converted from RFLP and BAC-ends or entire BACs using the sequence information available at SGN followed by sequencing of alleles. The map spans a total genetic distance of 974 cM with only a few gaps remaining (Fig. 2). All SSR markers and 21 indel markers were mapped on the Beckman CEQ8800 whereas nine SNP markers were mapped on the Luminex. The remaining markers were mapped as CAPS and dCAPS on agarose gels.
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