The homeologous Orp1 and Orp2 regions of maize and the orthologous regions in sorghum andrice were compared by generating sequence data for 486 kb of genomic DNA. At least three genicrearrangements differentiate the maize Orp1 and Orp2 segments, including an insertion of a single geneand two deletions that removed one gene each, while no genic rearrangements were detected in the maizeOrp2 region relative to sorghum. Extended comparison of the orthologous Orp regions of sorghum andjaponica rice uncovered numerous genic rearrangements and the presence of a transposon-rich region inrice. Only 11 of 27 genes (40%) are arranged in the same order and orientation between sorghum andrice. Of the 8 genes that are uniquely present in the sorghum region, 4 were found to have single-copyhomologs in both rice and Arabidopsis, but none of these genes are located near each other, indicatingfrequent gene movement. Further comparison of the Orp segments from two rice subspecies, japonica andindica, revealed that the transposon-rich region is both an ancient and current hotspot for retrotransposonaccumulation and genic rearrangement. We also identify unequal gene conversion as a mechanism formaize retrotransposon rearrangement.

It is generally believed that maize (Zea mays L. ssp. mays) arose as a tetraploid; however, the two progenitor genomescannot be unequivocally traced within the genome of modern maize. We have taken a new approach to investigatethe origin of the maize genome. We isolated and sequenced large genomic fragments from the regions surroundingfive duplicated loci from the maize genome and their orthologous loci in sorghum, and then we compared thesesequences with the orthologous regions in the rice genome. Within the studied segments, we identified 11 genes thatwere conserved in location, order, and orientation. We performed phylogenetic and distance analyses and examinedthe patterns of estimated times of divergence for sorghum and maize gene orthologs and also the time of divergencefor maize orthologs. Our results support a tetraploid origin of maize. This analysis also indicates contemporaneousdivergence of the ancestral sorghum genome and the two maize progenitor genomes about 11.9 million years ago(Mya). On the basis of a putative conversion event detected for one of the genes, tetraploidization must haveoccurred before 4.8 Mya, and therefore, preceded the major maize genome expansion by gene amplification andretrotransposition.

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.