New and inexpensive genomics method takes off

March 20, 2012 By Amanda Garris

(PhysOrg.com) -- Genotyping-by-sequencing (GBS), a powerful new technique developed at Cornell, is leveling the playing field in genomics research. Less than a year after publication, it is being applied to answer questions about diverse species, including hops, fox, turf grass, maize, cow, tomato and raspberry.

The GBS protocol, published in May 2011 in the journal , allows researchers to generate huge amounts of . Identifying differences between the DNA of individuals is the first step toward unlocking the for their differences in appearance or behavior.

What sets GBS apart from other equally powerful methods is, in part, a lower price tag. One cent buys about 50,000 data points, which is up to 50 times cheaper than other methods.

"Funding for agricultural has always lagged behind that of ," said Rob Elshire, the technique's developer and the sequencing technology lead in the lab of Ed Buckler, a research geneticist with the U.S. Department of Agriculture Agricultural Research Service and adjunct professor of and genetics. "GBS is an enabling technology -- it's cracking the door open for many underfunded research areas."

The technique's cost effectiveness has been a strong selling point, but the method was also designed to be easy and robust compared with other DNA typing methods.

"In developing GBS, we ... eliminated as many steps as possible," Elshire said.

The method allows users to collect data on up to 384 individuals in a single sequencing lane, using a protocol with only four basic steps from DNA to data. Because of this efficiency, GBS can generate sufficient data for a thesis, a breeding program or an ecological study in a matter of weeks.

"GBS can generate terabytes of data," said Sharon Mitchell, Institute for Genomic Diversity's (IGD) research and laboratory manager and co-author on the PLoS One paper. "To help users, we have held several workshops mostly dedicated to the pipeline for data analysis and hands-on practice with it."

She added that "Interest in GBS has been snowballing." To keep up with the daily demand for information and assistance for users of the technique, additional staff are being hired, Mitchell said, "and nearly a year after publication, the article remains one of the top 10 most viewed genomics articles on PLoS One."

A Feb. 16-17 workshop on campus, for example, was filled to capacity and attracted participants -- primarily plant breeders, geneticists, animal scientists and evolutionary biologists -- from as far away as New Zealand.

"The aspect of GBS that is most appealing is that it produces tens to hundreds of thousands of genetic markers," said Mitchell. "Most plant and animal breeders are interested in using this plethora of markers to speed up the breeding process in a big way."

To meet the continued demand for training, the workshop will soon be available as a video on the IGD website, and workshops will be offered in India and Africa in the coming year.

The IGD is a nonprofit institute affiliated with the Cornell Institute for Biotechnology and Life Sciences Technologies. Since its establishment in 1998, it has helped organize molecular breeding workshops in Mali, Venezuela, Costa Rica, South Africa, Ghana, Nigeria and Kenya.

Explore further: Progress made on group B streptococcus vaccine

Related Stories

Progress made on group B streptococcus vaccine

October 30, 2009

Scientists supported by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, have completed a Phase II clinical study that indicates a vaccine to prevent Group B Streptococcus ...

Genomic tools can help researchers develop crops quickly

February 22, 2011

(PhysOrg.com) -- Using powerful genome sequencing tools created for human genetics, researchers can now exploit the genetic diversity of crops to improve productivity, sustainability and nutrition, a Cornell researcher reported ...

Recommended for you

How bees naturally vaccinate their babies

July 31, 2015

When it comes to vaccinating their babies, bees don't have a choice—they naturally immunize their offspring against specific diseases found in their environments. And now for the first time, scientists have discovered how ...

New insights into the production of antibiotics by bacteria

July 31, 2015

Bacteria use antibiotics as a weapon and even produce more antibiotics if there are competing strains nearby. This is a fundamental insight that can help find new antibiotics. Leiden scientists Daniel Rozen and Gilles van ...

Out of the lamplight

July 31, 2015

The human body is governed by complex biochemical circuits. Chemical inputs spur chain reactions that generate new outputs. Understanding how these circuits work—how their components interact to enable life—is critical ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.