Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses

The maize genome contains extensive chromosomal duplications that probably were produced by an ancient tetraploid event. Comparative cereal maps have identified at least 10 duplicated, or homologous, chromosomal regions within maize. However, the methods used to document chromosomal homologies from comparative maps are not statistical, and their criteria are often unclear. This paper describes the development of a simulation method to test for the statistical significance of marker colinearity between chromosomes, and the application of the method to a molecular map of maize. The method documents colinearity among 24 pairs of maize chromosomes, suggesting homology in maize is more complex than represented by comparative cereal maps. The results also reveal that 60%-82% of the genome has been retained in colinear regions and that as much as a third of the genome could be present in multiple copies. Altogether, the complex pattern of colinearity among maize chromosomes suggests that current comparative cereal maps do not adequately represent the evolution and organization of the maize genome.