One plant genome, Arabidopsis, has been sequenced, and a second one, rice, is nearing completion. These plant species represent the major taxonomic division of the plant kingdom and include the first major crop. Rice is also a member of the cereals that include crops like wheat and maize, which are much larger in genome size, 35-times and 5-times, respectively, and, therefore, more difficult to sequence. However, since maize is a major crop in agriculture and a significant factor to the economy of the United States, sequencing its genome will provide a critical infrastructure to advance food supply, quality, and safety, with simultaneous reduction of risk to health by chemical pollution. To enable sequencing the larger maize genome, this project seeks to provide sets of overlapping cloned DNA fragments, about 150 kb in size that are placed on the genetic map of maize. This placement will be greatly facilitated by zip code-like sequences of these cloned DNA fragments. These zip codes are in particular valuable since a certain percentage is conserved in sequence and order between maize and the closely related rice genome (synteny). Since the rice genome sequence is aligned to the rice genetic map, ordering the sets of overlapping maize DNA fragments will be greatly enhanced in regions of synteny. The resulting map of DNA fragments will be used to generate contiguous genomic sequence. This will show whether the larger size of the maize genome, largely due to non-genic, repeat sequences, will require a different method for obtaining the gene content of maize. A few examples of long stretches of maize genomic DNA provide biologists for the first time information about the variability in gene density and a correlation of the genetic and physical map over several centiMorgans. Such genetic distances are already long enough to demonstrate to breeders how genes are discovered based on linkage of traits to DNA.
