Award Abstract #0221536
Consortium for Maize Genomics

NSF Org:	IOS Division of Integrative Organismal Systems
Initial Amendment Date:	September 18, 2002
Latest Amendment Date:	September 23, 2005
Award Number:	0221536
Award Instrument:	Cooperative Agreement
Program Manager:	Jane Silverthorne IOS Division of Integrative Organismal Systems BIO Directorate for Biological Sciences
Start Date:	September 1, 2002
Expires:	December 31, 2005 (Estimated)
Awarded Amount to Date:	$5928755
Investigator(s):	Karel Schubert kschubert@danforthcenter.org (Principal Investigator) Roger Beachy (Co-Principal Investigator) John Quackenbush (Co-Principal Investigator) Catherine Whitelaw (Co-Principal Investigator)
Sponsor:	Donald Danforth Plant Science Center 975 N. Warson Rd. St. Louis, MO 63132 314/587-1041
NSF Program(s):	PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):	BIOT, 9109
Program Element Code(s):	1329

ABSTRACT



Maize is both a classical genetic model for plant research and an economically important crop. Having a sequence of the genes of maize will have a fundamental impact on maize genetics and crop improvement. However, the maize genome is large and complex, comprising a sea of highly repetitive DNA containing islands of genes. Current estimates indicate that the gene islands only make up 15-20% of the genome. Selective sequencing of just the gene islands would thus be a rapid and cost-effective alternative to sequencing the whole genome.

The overall goal of this project is to develop and evaluate high-throughput and robust strategies to isolate and sequence maize genes. Two promising approaches will be tested. The first, termed "methylation-filtering", is based on the finding that the highly repetitive DNA is modified (methylated) while the genes are largely free of such modification. The second, termed "high Cot selection", exploits the relatively low abundance of the gene sequences, which are present in a small number of copies in the genome. Each method yields a fraction of the genome highly enriched for the genes. Libraries of these DNA fragments will be sequenced and the sequences assembled and annotated to give a first picture of the sequence and organization of maize genes. All sequence information will be released immediately into GenBank and project data analyses will be available through web-based resources.

The outcomes of this project will provide the research community with a powerful resource for maize genetics, biology, and breeding. They will also facilitate determination of the best strategy for attempting large-scale sequencing of maize genes.

Deliverables:

Maize Libraries

Contact Karel Schubert at the Danforth Center (www.danforthcenter.org) for information on the libraries. Contact Dr. Rod Wing at AGI (www.genome.arizona.edu) for access to the clones from the methylation filtered and high CoT libraries of maize.

Maize Sequencing Results:

Sequence reads will be submitted to the HTGS division of GenBank and the trace files submitted to the NCBI trace database on a weekly basis. Concomitant with submission to NCBI both the sequence data and trace files will accessible from the Donald Danforth Plant Science Center maize website for use by the broader Maize research community.

Bioinformatics:

At a minimum, assemblies of the sequence will be released every three months, with the goal of providing monthly updates. Assembled sequences will be available from the TIGR website.

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