MAIZE MISSOURI 17 CHROMOSOME 10 PROJECT

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: NRI COMPETITIVE GRANT
• Reporting Frequency: Annual
• Accession No.: 0205513
• Grant No.: 2006-35300-16556
• Cumulative Award Amt.: $1,500,000.00
• Proposal No.: 2005-05302
• Project Start Date: Nov 1, 2005
• Project End Date: Oct 31, 2008
• Grant Year: 2006
• Program Code: [52.1]- (N/A)

Recipient Organization
UNIVERSITY OF CALIFORNIA, BERKELEY
(N/A)
BERKELEY,CA 94720

Performing Department
REGENTS OF THE UNIVERSITY

Non Technical Summary
The high-quality annotated sequence of chromosome 10 of Missouri 17 Zea mays will provide a resource for the study of variation in maize that will accelerate molecular and genetic research into the function and regulation of cereal genes, advancing agriculture and energy research and development, plant biotechnology, and our understanding of basic plant physiology, diversity, and genetics. Application of this knowledge will benefit the agricultural and energy industries and consumers. Results will be distributed via GenBank, MaizeGDB, and the websites at JGI and Georgia. This project will also provide workshops on maize genomics and interdisciplinary training to postdoctoral researchers.

Animal Health Component

(N/A)

Research Effort Categories

Basic

50%

Applied

(N/A)

Developmental

50%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1510	1080	100%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1510 - Corn;

Field Of Science
1080 - Genetics;

Keywords

maize

genomics

genome sequence

variation

Goals / Objectives
We will produce a high-quality reference sequence for chromosome 10 of the Zea mays Missouri 17 inbred line that is integrated with enhanced maize physical and genetic maps. Our target is to finish the gene space according to the standards established by the human genome project. We will adopt a whole genome shotgun strategy for this 180 million base pair chromosome. Although the maize genome is highly repetitive, preliminary data show that most repeats are sufficiently diverged to ensure the success of the whole chromosome shotgun approach that we propose.

Project Methods
To achieve our goal, a total of 7X shotgun coverage of chromosome 10 will be generated starting from flow-sorted material, assembled along with other available datasets, and annotated at the Joint Genome Institute to generate a high-quality draft sequence. Targeted finishing of at least 40 million base pairs of annotated gene space will be carried out at the Stanford Human Genome Center. Protein coding genes will be identified based on known expressed sequences from maize, sorghum, rice, and other plants, augmented by ab initio gene prediction methods tuned for maize. The Plant Genome Mapping Laboratory at the University of Georgia will anchor the genome sequence to the physical and genetic maps, taking advantage of synergy with other grass mapping data.

Progress 11/01/05 to 11/01/06

Outputs
This is to report on Year One progress on "Maize Missouri 17 Chromosome 10 Project", whose aim is to provide information about the genome structure and sequence of the Missouri 17 inbred line. The proposed plan was to flow sort the smallest chromosome of Mo17 and shotgun sequence it to assess the feasibility of this approach to complex cereal genomes. It was noted, however, that the technical feasibility of this approach was in question, and the initial milestone was to assess whether sorting would be possible. Further analysis showed that the confident flow sorting of this chromosome in amounts suitable for use in shotgun sequencing was not feasible. This result was reported to the Maize Genome Project advisory committee. The committee recommended revising the plan with alternative sequencing efforts aimed at measuring sequence variation across maize inbred lines, with a possible broader focus on additional maize inbred lines beyond Mo17. Since the original proposal, the desire to resequence human genomes has let to the availability of new sequencing technologies that could be directed at resequencing complex plant genomes like maize. We are developing a plan for applying the Solexa technology to "resequence" Mo17 relative to B73, either through reduced representation methods (e.g., using restriction digests to reduce the complexity of the sample before sequencing) or by directed resequencing of exons or introns. This plan is being discussed with members of the Maize Genome Project advisory board and the Maize Genetics Executive Committee as recommended by the advisory board. We note that one of the original goals of the proposal -- the demonstration that a complex cereal genome could be sequenced and assembled using a whole genome shotgun method -- has been met through the sequencing and assembly of the ~750 Mb Sorghum bicolor genome. An initial draft of this sequence, including a provisional annotation, is available at www.phytozome.net/sorghum . Comparative analysis of sorghum with available maize sequences demonstrated high levels of collinear gene order and conserved gene structure, providing a framework for using sorghum annotations to aid in the structural annotation of the maize genome.

Impacts
An improved characterization of the genomic-level variation of diverse maize inbred lines will contribute a dense set of genetic markers for the improvement of maize as a crop for food or bioenergy, allow for the characterization of quantitative trait loci for an increased understanding of fundamental processes in plant biology, enhance our understanding of the fundamental principles by which genomic variation arises in plants.

Publications

• No publications have been prepared at this stage of the project. 2006