Navigation Links
Sweet corn story begins in UW-Madison lab

MADISON 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."


Contact: David C. Schwartz
University of Wisconsin-Madison

Related biology news :

1. Cancers sweet tooth may be weakness
2. Recent news reports of sweetener reformulations raise questions about motivations
3. Purple sweet potato means increased amount of anti-cancer components
4. The bitter side of sweeteners
5. Quality and purity of popular stevia sweetener strengthened by new reference standards
6. Red pandas reveal an unexpected (artificial) sweet tooth
7. Liking sweets makes sense for kids
8. Spun-sugar fibers spawn sweet technique for nerve repair
9. New standard for popular stevia-based sweetener to assure products quality
10. Sweetened beverage consumption increases in the US
11. Honey adds health benefits, is natural preservative and sweetener in salad dressings
Post Your Comments:
(Date:10/29/2015)... 2015 NXTD ) ("NXT-ID" ... on the growing mobile commerce market and creator ... a leading marketplace to discover and buy innovative ... wallet on StackSocial for this holiday season.   ... "Company"), a biometric authentication company focused on the ...
(Date:10/26/2015)... India , October 26, 2015 ... --> adds ... 2015 to 2021 as well as ... 2015-2019 research reports to its collection ... . --> ...
(Date:10/22/2015)... BEDFORD, Mass., Oct. 22, 2015  Aware, Inc. (NASDAQ: AWRE ... financial results for its third quarter ended September 30, 2015.  ... third quarter of 2015 was $4.0 million, a decrease of 33% ... income in the third quarter of 2015 was $2.2 million, or ... per diluted share, in the same period a year ago.  ...
Breaking Biology News(10 mins):
(Date:11/24/2015)... ... 2015 , ... Copper is an essential micronutrient that all ... copper is also toxic to cells. With a $1.3 million award from the ... a systematic study of copper in the bacteria Pseudomonas aeruginosa (P. aeruginosa), a ...
(Date:11/24/2015)... ... 24, 2015 , ... This fall, global software solutions leader SAP and AdVenture ... develop and pitch their BIG ideas to improve health and wellness in their schools. ... to win the title of SAP's Teen Innovator, an all-expenses paid trip to Super ...
(Date:11/24/2015)... /PRNewswire/ - Aeterna Zentaris Inc. (NASDAQ:  AEZS) (TSX: ... 11,000 post-share consolidation (or 1,100,000 pre-share consolidation) Series ... Warrants") subject to the previously disclosed November 1, ... which will result in the issuance of 365,518 ... issuance of such shares, there will be approximately ...
(Date:11/24/2015)... LAVAL, QC , Nov. 24, 2015 /CNW Telbec/ - ... the "Corporation") announced today that Mr. Pierre Laurin , ... a corporate presentation at the upcoming Piper Jaffray 27 th ... York Palace Hotel, on December 1-2, 2015. ... be available for one-on-one meetings throughout the day. The presentation ...
Breaking Biology Technology: