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Sweet corn story begins in UW-Madison lab
Date:11/19/2009

ork on small chunks at a time, but the maize genome is incredibly complex, full of repeats, and that's confusing. It's like buying a 10,000-piece jigsaw puzzle; from looking at one piece, it's hard to know if you are looking at the dwarf's foot, or Snow White's face. Our optical maps, just like the box cover, give the big picture that allows the sequencers to link up their smaller pieces into a complete genome."

Shiguo Zhou, Schwartz's colleague who did much of the heavy lifting in the optical map of maize, says the optical mapping system was "incredibly cost-effective and invaluable in dissecting the infamously complex maize genome."

Zhou and Schwartz were the principal authors of a companion article in PLoS Genetics, which explained how they made the optical map of corn.

At the center of the Schwartz system is a series of automated microscopes that run 24 hours a day, seven days a week. "For the maize genome, we looked at about 2 million molecules. If you had to do that by hand, hunched over a microscope, you would grow dizzy from boredom," says Schwartz.

Once the optical information is obtained, it is correlated with the letter-by-letter information coming from the gene sequencers. That statistic-intensive process is handled by hundreds of networked computers, running software that were created by Schwartz's collaborators Michael Waterman and his student, John Nguyen, and enabled to run on Miron Livny's computer cluster in the department of computer sciences.

"The maize optical map is by far the most complex example of genome analysis via single molecules," says Schwartz, who with Zhou recently mapped the plant disease that caused the deadly Irish potato blight, and continues to affect potato and tomato farmers today. "It was created using completely new techniques which greatly surpass conventional sequencing and all available next-generation sequencing methods and platforms in terms of completeness, speed, accurac
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Contact: David C. Schwartz
dcschwartz@wisc.edu
608-265-0546
University of Wisconsin-Madison
Source:Eurekalert

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