Strategies

Summary

A comprehensive, yet efficient approach is proposed to sequence the genes of Zea mays (corn). Corn is both a classical genetic model and a major row crop, and the sequence of the corn genome will have a fundamental impact on corn genetics and improvement. The central component of the proposal is to generate a draft sequence of the maize gene space by: 1.) shotgun sequencing of the hypomethylated fraction of the corn genome, which is known to contain most of the genes. This will allow us to focus on the 15-20 percent of the corn genome that will be most useful rather than on the largely repetitive genome as a whole. The hypomethylated fraction of the maize genome will be produced with the GeneThresher technology from Orion Genomics. 2.) shotgun sequencing of high Cot selection libraries produced by Jeff Bennetzen.

In addition to filtered shotgun sequencing, we will evaluate the filtered shotgun methods for gene hit rates, gene coverage and method specific biases.  These activities will provide the research community with a powerful resource for gene discovery and manipulation in corn. Finally, to facilitate community access to corn genes and clone resources, we will build web-based bioinformatics resources that will provide data views that combine basic sequence analysis with comparative and structural analyses. Furthermore, all sequences generated will be submitted to the HTGS (high-throughput genome sequencing) or GSS (genome survey sequences) divisions of GenBank, which will serve both to archive the data and enhance public access.

SPECIFIC AIMS

1. Generate a draft sequence of the corn "genespace" in 2 years using methyl filtration technology and high Cot selection.
2. Determine the gene hit rate and gene coverage for each technology. Determine the overall gene hit rate and gene coverage for the combined resource.
3. Determine the approprite mix of GeneThresher® vs. high Cot reads to yield the highest information content.