Comparative mapping is the side-by-side comparison of gene order and other genomic features in related individuals. It is a very useful tool in the analysis of genomes. Comparative mapping can aid in the (i) identification of gene function, and (ii) choice of additional markers for linkage mapping, marker-assisted selection, and positional cloning; it also provides insights into genome evolution. Our knowledge of the location and function of a morphological gene in tomato, for example, may provide insights into the function of a putative gene in the homologous region in pepper (Capsicum spp.). Knowledge of comparative maps can be of great assistance in positional cloning experiments, where additional genetic and physical markers from a dense map of a related species can be selected for application in the species of interest, provided an area of conserved synteny is under investigation. Questions about genome evolution have become increasingly interesting since the realization that the genomes of many crops have been shuffled (through inversions and translocations) over evolutionary time, but often retain large syntenic blocks when compared to related genera.
The ultimate comparative map between two genomes is a complete DNA sequence. Other types of maps are available, and plant geneticists and breeders work with the maps available for the given species of interest. In the Solanaceae, tomato genomics was initially the main force and is currently the driving force behind much of the progress in the study of genomics for the entire family (see Sect. 1.18).
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