Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridizationof two closely related progenitors. To investigate the fate of its genes after tetraploidization, we analyzed thesequence of five duplicated regions from different chromosomal locations. We also compared corresponding regionsfrom sorghum and rice, two important crops that have largely collinear maps with maize. The split of sorghum andmaize progenitors was recently estimated to be 11.9 Mya, whereas rice diverged from the common ancestor of maizeand sorghum ∼50 Mya. A data set of roughly 4 Mb yielded 206 predicted genes from the three species, excludingany transposon-related genes, but including eight gene remnants. On average, 14% of the genes within the alignedregions are noncollinear between any two species. However, scoring each maize region separately, the set ofnoncollinear genes between all four regions jumps to 68%. This is largely because at least 50% of the duplicatedgenes from the two progenitors of maize have been lost over a very short period of time, possibly as short as 5million years. Using the nearly completed rice sequence, we found noncollinear genes in other chromosomalpositions, frequently in more than one. This demonstrates that many genes in these species have moved to newchromosomal locations in the last 50 million years or less, most as single gene events that did not dramatically altergene structure.

The cereal endosperm is a major organ of the seed and an important component of the world’s food supply. Tounderstand the development and physiology of the endosperm of cereal seeds, we focused on the identification ofgenes expressed at various times during maize endosperm development. We constructed several cDNA libraries toidentify full-length clones and subjected them to a twofold enrichment. A total of 23,348 high-qualitysequence-reads from 5-and 3-ends of cDNAs were generated and assembled into a unigene set representing 5326genes with paired sequence-reads. Additional sequencing yielded a total of 3160 (59%) completely sequenced,full-length cDNAs. From 5326 unigenes, 4139 (78%) can be aligned with 5367 predicted rice genes and by takingonly the "best hit" be mapped to 3108 positions on the rice genome. The 22% unigenes not present in rice indicatea rapid change of gene content between rice and maize in only 50 million years. Differences in rice and maize genenumbers also suggest that maize has lost a large number of duplicated genes following tetraploidization. The largernumber of gene copies in rice suggests that as many as 30% of its genes arose from gene amplification, which wouldextrapolate to a significant proportion of the estimated 44,027 candidate genes of its entire genome. Functionalclassification of the maize endosperm unigene set indicated that more than a fourth of the novel functionallyassignable genes found in this study are involved in carbohydrate metabolism, consistent with its role as a storageorgan.

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.