Despite extensive availability of tomato molecular markers, many markers were developed based on polymorphism in wide crosses and are not informative when used within closely related germplasm. For example, whereas a saturated linkage map of tomato is available from a wide cross, S. lycopersicum x S. pen-nelli (Fulton et al. 2002b), populations derived from crosses of closely related species and crosses within S. lycopersicum require substantial additional effort to construct molecular linkage maps and to associate a marker with a phenotype. For this reason the development of markers continues to be important in tomato despite the availability of high-density linkage maps and the emerging genome sequence (Mueller et al. 2005b). In this section methods to exploit the available genetic and genomic resources of tomato to improve mapping and marker development for populations derived from closely related parents are presented. How these available resources were used to develop a polymerase chain reaction (PCR) based linkage map of an F2 population derived from a cross between S. pimpinellifolium LA1589 and S. lycopersicum cv Rio Grande is then highlighted.
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