Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Sweet corn story begins in UW-Madison lab

23.11.2009
This week, scientists are revealing the genetic instructions inside corn, one of the big three cereal crops. Corn, or maize, has one of the most complex sequences of DNA ever analyzed, says University of Wisconsin-Madison genomicist David Schwartz, who was one of more than 100 authors in the article in the journal Science.

"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, djtenenb@wisc.edu

David C. Schwartz | EurekAlert!
Further information:
http://www.wisc.edu

Further reports about: DNA DNA molecule UW-Madison genetic variation maize genome single molecule sweet

More articles from Agricultural and Forestry Science:

nachricht Alkaline soil, sensible sensor
03.08.2017 | American Society of Agronomy

nachricht New 3-D model predicts best planting practices for farmers
26.06.2017 | Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

All articles from Agricultural and Forestry Science >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

A Map of the Cell’s Power Station

18.08.2017 | Life Sciences

Engineering team images tiny quasicrystals as they form

18.08.2017 | Physics and Astronomy

Researchers printed graphene-like materials with inkjet

18.08.2017 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>