Comparative Genomics and Collinearity/Synteny in Maps
Detailed molecular maps, available in all major crops, also allow comparative genetic analyses in several groups of plants, involving families like Poaceae, Solanaceae, Fabaceae and Brassicaceae. This will be briefly illustrated using the examples of the grass family, and those from Solanaceae. It has been shown that all genomes of grass species can now be described in terms of their relationships to a single reference, i.e. rice genome. Less than 30 linkage blocks are needed to represent genomes of all grass species including the following: wheat, rye, barley, oats, maize, sorghum, sugarcane, rice, wild rice (Zizaniapalustris),foxtail millet, pearl millet, finger millet (Eleusine coracana) and tef (Eragrostis tef).

Two important examples of genes that have already been studied through comparative genome analysis include gibberillin-insensitive dwarfing genes which have been found to be orthologous between wheat and maize and the QTLs controlling shattering, which have been found to be orthologous among foxtail millet, maize, sorghum, rice and pearl millet.

Another important feature which has been brought to light through comparative genome analysis is the presence of large number of duplicate segments, suggesting that several species that are believed to be diploid may have an ancient polyploid origin (e.g. maize and Arabidopsis).For instance, large scale duplicate RFLPs were earlier detected in maize and more recently, 60% of the Arabidopsisgenome has been shown to carry duplications suggesting tetraploid origin in both these cases.