'Panning for gold' in the maize genome

New approaches yield gene-rich regions, accelerate sequencing

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.

NSF Plant Genome Research Program Officer:
Jane Silverthorne, 703-292-8470, [email protected]

Related NSF web sites:

FY 2003 Awards, NSF Plant Genome Research Program:
http://nsf.gov/bio/pubs/awards/genome03.htm

Previous news releases on plant genomes:
http://www.nsf.gov/od/lpa/news/03/pr03114_priors.htm

NSF Directorate for Biological Sciences Plant Genome Project site:
http://www.nsf.gov/bio/dbi/dbi_pgr.htm

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ARLINGTON, Va.-Studies of the unique landscape in the Dry Valleys of Antarctica provide new insights into the origin of similar features on Mars and provide one line of evidence that suggests the Red Planet has recently experienced an ice age, according to a paper in this week's issue of the journal Nature.

The distribution of hexagonal mounds and other features on the Martian surface at mid-latitudes similar to those in the Dry Valleys also supports previous scientific assertions that a significant amount of ice lies trapped beneath the Red Planet's surface.

David Marchant, a Boston University researcher who has studied the Dry Valleys for 17 years, co-authored the paper with James W. Head (lead author), John Mustard and Ralph Milliken, at Brown University, and Mikhail Kreslavsky of Kharkov National University in Ukraine.

The National Science Foundation (NSF) supported Marchant's work in the Dry Valleys, which helped underlie the assertions in the Nature paper. NSF is an independent federal agency that supports fundamental research and education across all fields of science and engineering. NSF manages the U.S. Antarctic Program, which supports and coordinates virtually all U.S. scientific research on the southernmost continent.

Head, Mustard and Milliken were supported by NASA.

The floor of Antarctica's Beacon Valley, in particular, is covered with hexagonal mounds that, from the air, resemble the patterns of cracked mud on a dry lakebed. The Dry Valleys mounds, however, often measure meters in diameter.

Although these polygon-shaped features occur throughout the Arctic and Antarctic, an unusual variety found in the western Dry Valleys region has received particular attention because it forms only in perennially frozen soils with significant ice content. These polygons form as sub-freezing temperatures fluctuate, causing the underlying ice to contract in a hexagonal pattern. As the ice contracts, fine sediments sift down into the cracks, leaving a coarse-grained deposit covering the ice.

The research reported in Nature shows that similar mounds and other formations that appear in the mid-to-high latitudes on Mars could indicate ice buried near the planet's surface as well. Using new information on the global distribution of surface landforms on Mars, together with data gathered from NASA's Mars Global Surveyor and Mars Odyssey missions, Head and other researchers were able to piece together a history of recent ice ages on Mars.

"The last ice age on Mars began about 2.1 million years ago and ended as recently as 400,000 years ago," according to Head.

Like ice ages on Earth, Martian ice ages are driven by variations in the planet's orbit, particularly the tilt of the planet's axis. But Martian ice ages, unlike ice ages on Earth, appear to begin as the polar regions warm, rather than cool.

Warming of the Martian Poles causes the planet's ice caps to partially vaporize and release water vapor into the Martian atmosphere. Winds transport the water vapor, along with ubiquitous Martian dust, toward the equator and deposit it in a meters-thick layer as far as 30 degrees north and south latitude. There, it drapes over existing terrain, smoothing the Martian surface.

Head and his co-authors report that emplacement of this meters- thick layer of snow and dust at 30 degree latitudes represents an "ice age" on Mars. The small number of impact craters seen in these features, along with the known patterns of changes in Mars' orbit and tilt, are used to estimate the age of these Martian ice ages.

The Nature findings complement a paper recently published in the journal Geology, in which Head and Marchant argue that features on the surface of the Red Planet are remarkably like glacial features found only in the Dry Valleys.

The findings not only have implications for the search for microbial life on Mars, but also may help scientists better understand the unique Polar desert environment of the Dry Valleys, and in particular the ancient climate record that may be stored in the landscape.

"These extreme changes on Mars provide perspective for interpreting what we see on Earth. Landforms on Mars that appear to be related to climate changes help us calibrate and understand similar landforms on Earth. Furthermore, the range of microenvironments in the Antarctic Dry Valleys helps us read the Mars record," said Marchant.

If the analogy between the geologic processes on Mars and those in the Dry Valleys holds true, then scientists may conclude that Mars may be more hospitable to microbial life than previously suspected.

Biologists continue to make discoveries that push back the boundaries at which conditions are too extreme to support life. NSF-funded researchers, for example, have offered evidence that microbes can survive in extremes of cold and darkness between ice crystals at the South Pole.

Although the Dry Valleys were thought to be a virtual dead zone when first explored a century ago, new evidence suggests that the lakes and other landscape features support microscopic life.

Images/B-Roll: For Betacam SP B-roll of the Antarctic Dry Valleys, please contact Dena Headlee, [email protected], 703-292-7739

NSF Program Officer: Scott Borg, 703-292-8030, [email protected]

Principal Investigator: David Marchant, 617-353-3236, [email protected]

The National Science Foundation is an independent federal agency that supports fundamental research and education across all fields of science and engineering, with an annual budget of nearly $5 billion. National Science Foundation funds reach all 50 states through grants to nearly 2,000 universities and institutions. Each year, NSF receives about 30,000 competitive requests for funding, and makes about 10,000 new funding awards. The National Science Foundation also awards over $200 million in professional and service contracts yearly.

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