Data from cytological and genetic mapping studies suggest that maize arose asa tetraploid. Two previous studies investigating the most likely mode of maizeorigin arrived at different conclusions. Gaut and Doebley [7] proposed a segmentalallotetraploid origin of the maize genome and estimated that the two maizeprogenitors diverged at 20.5 million years ago (mya). In a similar study, using largerdata set, Brendel and colleagues (quoted in [8]) suggested a single genome duplicationat 16 mya. One of the key components of such analyses is to examine sequencedivergence among strictly orthologous genes. In order to identify such genes, Laiand colleagues [10] sequenced five duplicated chromosomal regions from the maizegenome and the orthologous counterparts from the sorghum genome. They alsoidentified the orthologous regions in rice. Using positional information of geneticcomponents, they identified 11 orthologous genes across the two duplicated regionsof maize, and the sorghum and rice regions. Swigonova et al. [12] analyzed the 11orthologues, and showed that all five maize chromosomal regions duplicated at thesame time, supporting a tetraploid origin of maize, and that the two maize progenitorsdiverged from each other at about the same time as each of them diverged fromsorghum, about 11.9 mya. Copyright  2004 John Wiley & Sons, Ltd.