Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

’Panning for gold’ in the maize genome

19.12.2003


New approaches yield gene-rich regions, accelerate sequencing



Decoding of a variety of plant genomes could accelerate due to two complementary methods that remove from analysis vast stretches of DNA that do not contain genes.

The approaches, applied jointly in efforts to determine the gene sequences in maize, are described in the Dec. 19 issue of the journal Science. The evaluation of these methods and the assembly of the resulting sequences were undertaken by two groups led by researchers from The Institute for Genomic Research (TIGR) in Rockville, Md., and Cold Spring Harbor Laboratory in New York.


The research was funded by the National Science Foundation’s Plant Genome Research Program.

Only about a quarter of the maize genome codes for genes, and these are found in small clusters scattered through a mixture of non-coding DNA and transposons (mobile DNA segments). Two different methods tested by the TIGR group successfully captured parts of the maize genome containing genes. The gene-sequences are of most interest because they provide the specific blueprint for an organism’s development, structure and physiology.

With so much non-gene sequence to deal with, it has not been feasible to sequence and assemble the whole maize genome with current technologies. Thus, it is a major shortcut to capture only the portion of the maize sequence containing its genes without having to sequence the entire genome.

"Collecting the maize genes for sequencing is like panning for gold," said Jane Silverthorne, program director for NSF’s plant genome program. "Just as gold can be separated from the surrounding rock because it is denser, maize genes can be separated from the surrounding DNA by their chemical and sequence properties."

The first method tested, called methylation filtration, removes sequences that contain a chemical modification (methylation) found on most of the repeated sequences and transposons, leaving behind the proverbial gold of genes. It was developed by a team led by Robert Martienssen and W. Richard McCombie at Cold Spring Harbor Laboratory.

The second method, developed by researchers at the University of Georgia, removes the repeated sequences by separating the DNA into "high-copy," gene-poor segments and "low-copy," gene-rich segments.

Led by Cathy Whitelaw, the research team at TIGR compared sequences obtained by the two methods. About one fourth of the genes in each collection matched known gene sequences. About 35 percent of the genes were represented in both collections.

Each method was found to enrich for distinct but complementary regions of maize’s 10-chromosome genome. Combined, the methods could cut the amount of sequencing necessary to find all of the maize genes to about one-fourth of what it would take to sequence the entire genome.

As both methods yielded short stretches of sequence, a major challenge was to reassemble these into complete genes. To do this, the Cold Spring Harbor group lined up the sequence pieces from maize along the rice genome sequence, a deep draft of which was completed in 2002 by an international consortium. The researchers then reassembled selected sets of sequence fragments into complete genes. This approach will be an important part of assembling the short pieces of DNA yielded by the two enrichments methods into complete gene clusters.

According to Silverthorne, "Together, these findings suggest that scientists could be able to sift out the approximately 450 million base pairs of DNA containing the genes from the maize genome and then reassemble the sequence. Such a comprehensive genomic resource would provide growers and breeders a wealth of tools to improve maize, as well as other cereal crops."


Other collaborators in the study included the Donald Danforth Plant Science Center and Orion Genomics, both of St. Louis, Mo.

Sean Kearns | NSF
Further information:
http://nsf.gov/bio/pubs/awards/genome03.htm
http://www.nsf.gov/od/lpa/news/03/pr03114_priors.htm
http://www.nsf.gov/bio/dbi/dbi_pgr.htm

More articles from Life Sciences:

nachricht Decoding the genome's cryptic language
27.02.2017 | University of California - San Diego

nachricht New risk factors for anxiety disorders
24.02.2017 | Julius-Maximilians-Universität Würzburg

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Safe glide at total engine failure with ELA-inside

On January 15, 2009, Chesley B. Sullenberger was celebrated world-wide: after the two engines had failed due to bird strike, he and his flight crew succeeded after a glide flight with an Airbus A320 in ditching on the Hudson River. All 155 people on board were saved.

On January 15, 2009, Chesley B. Sullenberger was celebrated world-wide: after the two engines had failed due to bird strike, he and his flight crew succeeded...

Im Focus: Breakthrough with a chain of gold atoms

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

Im Focus: DNA repair: a new letter in the cell alphabet

Results reveal how discoveries may be hidden in scientific “blind spots”

Cells need to repair damaged DNA in our genes to prevent the development of cancer and other diseases. Our cells therefore activate and send “repair-proteins”...

Im Focus: Dresdner scientists print tomorrow’s world

The Fraunhofer IWS Dresden and Technische Universität Dresden inaugurated their jointly operated Center for Additive Manufacturing Dresden (AMCD) with a festive ceremony on February 7, 2017. Scientists from various disciplines perform research on materials, additive manufacturing processes and innovative technologies, which build up components in a layer by layer process. This technology opens up new horizons for component design and combinations of functions. For example during fabrication, electrical conductors and sensors are already able to be additively manufactured into components. They provide information about stress conditions of a product during operation.

The 3D-printing technology, or additive manufacturing as it is often called, has long made the step out of scientific research laboratories into industrial...

Im Focus: Mimicking nature's cellular architectures via 3-D printing

Research offers new level of control over the structure of 3-D printed materials

Nature does amazing things with limited design materials. Grass, for example, can support its own weight, resist strong wind loads, and recover after being...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Booth and panel discussion – The Lindau Nobel Laureate Meetings at the AAAS 2017 Annual Meeting

13.02.2017 | Event News

Complex Loading versus Hidden Reserves

10.02.2017 | Event News

International Conference on Crystal Growth in Freiburg

09.02.2017 | Event News

 
Latest News

New pop-up strategy inspired by cuts, not folds

27.02.2017 | Materials Sciences

Sandia uses confined nanoparticles to improve hydrogen storage materials performance

27.02.2017 | Interdisciplinary Research

Decoding the genome's cryptic language

27.02.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>