The pepper EST data enabled the generation of a genetic map using COS markers. These markers were developed using various existing plant EST databases, including those for pepper, tomato, tobacco and Arabidopsis. Comparative analysis of the EST databases allowed the identifi cation of conserved orthologous EST sets, which were developed into the molecular markers used to generate the genetic map. By linking the COS markers in the genetic map, it became possible to compare the genomic structures between different species. Using this method, Wu et al. (2009) compared the pepper genome to that of the tomato. A total of 299 orthologous markers were used in the comparison, which included all of the 12 linkage groups (Chapter 3, Fig. 6-2). The analysis identifi ed 19 inversions and six chromosomal translocations between pepper and tomato. Both genomes shared 35 conserved syntenic segments, indicating a highly conserved gene order and content, except for the inversions and translocations.