Award Abstract #0527192
Sequencing the Maize Genome

NSF Org:	IOS Division of Integrative Organismal Systems
Initial Amendment Date:	November 15, 2005
Latest Amendment Date:	February 11, 2009
Award Number:	0527192
Award Instrument:	Cooperative Agreement
Program Manager:	Diane Jofuku Okamuro IOS Division of Integrative Organismal Systems BIO Directorate for Biological Sciences
Start Date:	November 15, 2005
Expires:	October 31, 2009 (Estimated)
Awarded Amount to Date:	$29450001
Investigator(s):	Richard Wilson rwilson@watson.wustl.edu (Principal Investigator) Patrick Schnable (Co-Principal Investigator) Rod Wing (Co-Principal Investigator) W. Richard McCombie (Co-Principal Investigator) Doreen Ware (Co-Principal Investigator)
Sponsor:	Washington University School of Medicine 660 South Euclid Avenue Saint Louis, MO 63110 314/747-4134
NSF Program(s):	PLANT GENOME RESEARCH RESOURCE, PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):	BIOT, 9109, 7577, 1329
Program Element Code(s):	7577, 1329

ABSTRACT



PI: Richard K. Wilson, Ph.D., Washington University

Co-PIs: Dr. Sandra Clifton, Ph.D., Washington University St. Louis

Dr. Rod Wing, Ph.D.,University of Arizona

Dr. Patrick Schnable, Ph.D.,Iowa State University

Dr. Srinivas Aluru, Ph.D.,Iowa State University

Dr. Lincoln Stein, M.D. Ph.D., Cold Spring Harbor Laboratory

Dr. Doreen Ware, Ph.D., Cold Spring Harbor Laboratory

Dr. W. Richard McCombie, Ph.D., Cold Spring Harbor Laboratory

Dr. Robert Martienssen, Ph.D., Cold Spring Harbor Laboratory



Maize is an important biological research system with a long and rich history. Over the past century, an active research community has grown up around the available extensive genetic tools and diverse germplasm. In this time, maize has become a leading system for addressing fundamental questions in genetics such as the impact of domestication on genome structure, the molecular basis of heterosis (hybrid vigor), and role of transposons in genome evolution. Research on maize has led to major advances in our understanding of fundamental life processes in plants such as reproduction, seed formation, germination, photosynthesis, and biosynthesis of primary metabolites including amino acids, carbohydrates and fatty acids. A genome sequence is a logical next step to enable the best use of maize as an experimental system and in order to translate research advances into improved crops.

At 2.6 billion base pairs, the maize genome is about the same size as the human genome. However, its organization is far more complex. More than 80% of the genome is made up of a complex mixture of repetitive DNA that includes several classes of retrotransposon. Only about 20% of the genome comprises the genes and these are scattered throughout the 10 chromosomes in small islands. A detailed physical map that is linked to the genetic map has been developed that covers more than 90% of the genome. Based on this detailed knowledge about the genome structure and organization, the maize research community has developed a description of the "gold standard" for a genome sequence (http://www.maizegdb.org/genome/goldstandard.pdf). The gold standard maize genome is defined as containing the complete sequence and structures of all maize genes and their locations (in linear order) on both the genetic and physical maps of maize, using B73 as the reference genome.

This project is designed to provide a maize genome sequence as close to the gold standard as possible with the currently available technology. Bacterial Artificial Chromosome (BAC) clones of known location along the physical map will be sequenced to 6x coverage, and integrated with the available sequence information obtained through prior sequencing of Expressed Sequence Tags (ESTs), transposon insertion sites, gene-enriched genomic DNA and whole genome shotgun libraries. The resulting genome sequence will contain high quality sequence (fewer than one error per 100,000 bases) of the non-repetitive regions that include the genes and regulatory elements, anchored to the genetic and physical maps. The sequence will be annotated for gene models, predicted exon/intron structures, EST and full-length cDNA data, gene ontologies, and homologies with sequences from other organisms.

Educational activities that focus on maize and the genome sequence and aimed at K-12 students and their parents will be developed at Washington University St. Louis Genome Sequencing Center in collaboration with the St. Louis Science Center. Training resources, tutorials and workshops for end-users of the maize sequence appropriate for researchers, students, and breeders will be developed and made available through Gramene (http://www.gramene.org) located at the Cold Spring Harbor Laboratory.

All primary and assembled sequences over 2,000 base pairs in length will be deposited in GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) within 24 hours of generation. Trace files will be deposited in the NCBI Trace Repository (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi) within one week of production. Assembled, finished BAC clone sequences will be deposited in GenBank as soon as the finished sequence has passed all quality analysis tests and has been approved for submission by the quality analysis team. Project information and data will be available through a web site accessible through the Washington University Genome Sequencing Center (http://www.genome.wustl.edu). Maize sequence assemblies and maize genetic resources will be incorporated into Gramene (http://www.gramene.org) and MaizeGDB (http://www.maizegdb.org) on a quarterly basis.

Maize (corn) is one of the most economically important plants in the US. In 2004, 80.9 million acres of corn were planted with a production value of over $22 billion. While corn is grown in the U.S. for food and feed, it is also converted into a myriad of processed food products and serves as an important material for many industrial products. The maize genome sequence will be a key resource for continued use of maize as an experimental system for advancing fundamental biology as well as for the development of new and improved maize varieties in the public and private sector.

This project was funded as part of the Maize Genome Sequencing Project: An NSF/DOE/USDA Joint Program.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

, S., Narechania, A., Stein, J.C., and Ware, D. "A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes," BMC Genomics, v.9, 2008, p. 517.

Wicker, T., Narechania, A., Sabot, F., Stein, J., Vu, GT., Graner, A., Ware, D. and Stein, N.. "Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats," Genomics, v.9, 2008, p. 518.

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