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ARS Home » Midwest Area » Madison, Wisconsin » Cereal Crops Research » Research » Publications at this Location » Publication #177132

Title: Validation of Rice Genome Sequence by Optical Mapping

Author
item ZHOU, SHIGUO
item BECHNER, MICHAEL
item PLACE, MIKE
item CHURAS, CHRIS
item Leong, Sally
item FORREST, DAN
item RUNNHEIM, ROD
item GOLDSTEIN, STEVE
item LEVY, MIRION
item SCHWARTZ, DAVID

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/15/2007
Publication Date: 8/15/2007
Citation: Zhou, S., Bechner, M., Place, M., Churas, C., Leong, S.A., Forrest, D., Runnheim, R., Goldstein, S., Levy, M., Schwartz, D. 2007. Validation of Rice Genome Sequence by Optical Mapping. Biomed Central (BMC) Genomics. Available at: http://www.biomedcentral.com/1471-2164/8/278.

Interpretive Summary: A new way of viewing the organization of the rice genome and its chromosomes was implemented. The nuclear DNA was spread as single molecules on glass slides and subjected to cutting with an enzyme that recognizes a specific DNA sequence. The resulting pieces of DNA still aligned with one another were visualized in the microscope and the size of the pieces was determined. The resulting whole-genome optical map of rice chromosomes was compared with the map prepared from the genome sequence. Both maps showed a good correspondence and missing parts of and errors in the DNA sequence were identified. The optical map thus provides important new information about the complete rice genome including its overall size and that of each chromosome.

Technical Abstract: Rice is the most important food crop in the world today, supplying sustenance for almost half of the world's population, which thankfully bears the simplest genome analyzed to date within the grass family. These features, in part, make it a model system for the study of other cereals including maize, wheat, barley, sorghum, and sugarcane. Although draft genome sequences of rice (Oryza sativa L. ssp. japonica and indica) are available, many gaps await closure, and purely independent means are required to fully validate sequence build data. To facilitate on-going sequencing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome--variety Nipponbare. The map consists of 17 contigs, covering 12 rice chromosomes, with a total genome size of 374.83 Mb, making it the largest optical map to date; this value is about 13% smaller than original estimations. Seven out of the 17 optical map contigs are finished, covering the entire chromosomes 2, 3, 4, 5, 7, 8 and 10- including centromeres and telomeres, while the 10 remaining optical map contigs span the rest. As such, the comprehensive alignment of optical vs. in silico restriction maps of sequence builds afforded the genome-wide tabulation of gaps and misassemblies that may point the way to their rectification. Finally, major advances in the optical mapping system render it now fully integrated and largely automated; we envision its use a platform for comparative genomics that would leverage sequence and annotation information across a broad range of rice subspecies and varieties.