"The maize genome is a true maze — full of confusing repeats and dead-ends that have troubled would-be sequencers for years," says Schwartz.
Publication of the genome is expected to advance knowledge of corn's ancestry, and also guide breeders trying to extract even more productivity from a crop that is expected to produce more than 200 million tons of grain from more than 87 million acres in the United States this year.
Producing the genome sequence required input from a unique optical mapping facility in the Laboratory for Molecular and Computational Genomics at UW-Madison.
Unlike traditional gene sequencers, who examine DNA letter by letter, the optical mapping system looks at bigger pieces, and that has positioned the lab's research as a key complementary component for working with the data produced by gene sequencers.
The first step in optical mapping system is to stretch out long, string-like DNA molecules and stick them to electrically charged glass plates. These molecules are sliced up into a series of consecutive chunks, marking them in the same way as a grocery bar code, and then painted with a fluorescent dye.
When the bar-coded molecules are exposed to a blue laser, the amount of fluorescent light they emit reveals the length of each barcode feature. The microscopes in the optical mapping system are fully automated, so millions of bar-coded molecules can be pieced together to reveal the structure of a genome.
The optical map supplies a scaffold, or big-picture view, of the structure of the DNA under study, says Schwartz. "Traditional sequencing must work 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, accuracy and cost."
Scientists say the speed-ups and cost reductions now affecting DNA analysis are akin to those once seen in the computer industry, and it is only a matter of time before it's routine to analyze an individual case of cancer. Because cancer has so many genetic variations, such analyses will likely lead to a period of "personalized medicine" in which the treatment is matched to the genetic makeup of a particular tumor, not by the averaged response gathered from broad-based studies.
"The maps we make tell us a lot about us, touch the food we eat, and the organisms that can make you sick," says Schwartz. "I believe this system is going to help deliver cost-effective personal genomics, and that will allow more effective diagnosis, earlier detection of cancer, and unclog the pipelines for new drugs. This work points the way toward new tools for exploring personal genomics."
Dave Tenenbaum, 608-265-8549, email@example.com
David C. Schwartz | EurekAlert!
Climate change, population growth may lead to open ocean aquaculture
05.10.2017 | Oregon State University
New machine evaluates soybean at harvest for quality
04.10.2017 | University of Illinois College of Agricultural, Consumer and Environmental Sciences
University of Maryland researchers contribute to historic detection of gravitational waves and light created by event
On August 17, 2017, at 12:41:04 UTC, scientists made the first direct observation of a merger between two neutron stars--the dense, collapsed cores that remain...
Seven new papers describe the first-ever detection of light from a gravitational wave source. The event, caused by two neutron stars colliding and merging together, was dubbed GW170817 because it sent ripples through space-time that reached Earth on 2017 August 17. Around the world, hundreds of excited astronomers mobilized quickly and were able to observe the event using numerous telescopes, providing a wealth of new data.
Previous detections of gravitational waves have all involved the merger of two black holes, a feat that won the 2017 Nobel Prize in Physics earlier this month....
Material defects in end products can quickly result in failures in many areas of industry, and have a massive impact on the safe use of their products. This is why, in the field of quality assurance, intelligent, nondestructive sensor systems play a key role. They allow testing components and parts in a rapid and cost-efficient manner without destroying the actual product or changing its surface. Experts from the Fraunhofer IZFP in Saarbrücken will be presenting two exhibits at the Blechexpo in Stuttgart from 7–10 November 2017 that allow fast, reliable, and automated characterization of materials and detection of defects (Hall 5, Booth 5306).
When quality testing uses time-consuming destructive test methods, it can result in enormous costs due to damaging or destroying the products. And given that...
Using a new cooling technique MPQ scientists succeed at observing collisions in a dense beam of cold and slow dipolar molecules.
How do chemical reactions proceed at extremely low temperatures? The answer requires the investigation of molecular samples that are cold, dense, and slow at...
Scientists from the Max Planck Institute of Quantum Optics, using high precision laser spectroscopy of atomic hydrogen, confirm the surprisingly small value of the proton radius determined from muonic hydrogen.
It was one of the breakthroughs of the year 2010: Laser spectroscopy of muonic hydrogen resulted in a value for the proton charge radius that was significantly...
17.10.2017 | Event News
10.10.2017 | Event News
10.10.2017 | Event News
20.10.2017 | Information Technology
20.10.2017 | Materials Sciences
20.10.2017 | Interdisciplinary Research