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Corn Genomics Pops Wide Open

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Science  07 Mar 2008:
Vol. 319, Issue 5868, pp. 1333
DOI: 10.1126/science.319.5868.1333

The sequencing of maize genomes and the development of new strains are enabling faster exploitation of this key crop's natural diversity.

The sequencing of maize genomes and the development of new strains are enabling faster exploitation of this key crop's natural diversity

Field tech.

Bar-coding tools speed maize genetics research.

CREDIT: KARIN HOLMBERG/CORNELL UNIVERSITY (ARS/USDA)

A decade ago, sequencing the maize genome was just too daunting. With 2.5 billion DNA bases, it rivaled the human genome in size and contained many repetitive regions that confounded the assembly of a final sequence. But last week, not one but three corn genomes, in various stages of completion, were introduced to the maize genetics community. In addition, researchers announced the availability of specially bred strains that will greatly speed tracking down genes involved in traits such as flowering time and disease resistance. These resources are ushering in a new era in maize genetics and should lead to tougher breeds, better yields, and biofuel alternatives. “We're sitting on very exciting times,” says Geoff Graham, a plant breeder at Pioneer Hi-Bred International Inc.

The world's biggest crop, maize (Zea mays) comes in all shapes and sizes. Indeed, the genomes of any two varieties can be as different as chimp and human DNA. Cataloging, understanding, and harnessing this variation to improve crop yields have been longtime goals for researchers.

Toward that end, in 2005, the U.S. National Science Foundation (NSF) and the U.S. departments of Agriculture (USDA) and Energy (DOE) provided $30 million to a consortium headed by Richard Wilson at Washington University in St. Louis, Missouri, to tackle the genome of a well-studied maize strain called B73. Rod Wing of the University of Arizona, Tucson, provided 15,000 mapped segments of the corn's DNA for sequencing, and at a meeting* last week in Washington, D.C., Wilson described B73's draft genome. About 6500 of the segments Wing provided are completely finished and most of the rest are well under way. Even at this stage, “we believe the quality and coverage will enable new discoveries,” says Wilson.

Maize researchers agree. B73's full sequence “is going to underpin all the research that we do in maize genomics,” predicts Patrick Schnable of Iowa State University in Ames.

Take the quest to improve the potential of corn and perennial grasses as biomass for biofuels. A key goal is to increase sugar content and sugar's availability for conversion to biofuels. “We need to greatly increase mass per acre,” says Nicholas Carpita, a plant cell biologist at Purdue University in West Lafayette, Indiana. He and his colleagues have compared the rice and Arabidopsis genomes with the B73 DNA already deposited in the public database GenBank. They found more than 1400 corn genes involved in building plant cell walls—the ultimate energy sources—and are homing in on those that affect biomass quantity and quality. “The maize genome allowed us to get to [those] genes,” he says.

And the B73 genome isn't the only one in the works. With $9.1 million from the Mexican government, Jean-Philippe Vielle-Calzada of the National Laboratory of Genomics for Biodiversity in Irapuato and his colleagues have decoded a native “popcorn” strain grown at elevations above 2000 meters. Although still in more than 100,000 pieces, the sequence has revealed many new genes, he reported. This variety's genome “will be of tremendous value in terms of understanding the evolution of [maize] domestication,” he says.

In addition, Daniel Rokhsar of DOE's Joint Genome Institute in Walnut Creek, California, and his colleagues have begun to decipher the DNA of a well-studied maize strain called Mo17, using new, cheaper sequencing technologies. If the effort proves cost-effective, NSF and DOE may support the sequencing of additional strains.

But genome sequences aren't the only big news for maize researchers. As part of the Maize Diversity Project, USDA plant geneticist Edward Buckler of Cornell University and his colleagues have bred almost 5000 lines of maize, revealing the full range of the plant's diversity. These lines were derived from crosses between B73 and 25 other inbred maize lines from all over the world; each marriage has given rise to about 200 lines. For the past 2 years, teams have planted these lines in 11 fields across the United States and measured many different traits—height, cob size, flowering time, and so on—for each line.

Using those lines, Buckler's team has also put together a detailed genetic map of the maize genome, which is helping researchers home in on target genes by means of an approach called nested association mapping. “It's an incredible resource … on equal par to having the sequence,” says Cornell's Thomas Brutnell.

Using the map, researchers can easily pinpoint the spots on the genome that underlie variation in a particular trait, then use the genome sequence to figure out which gene is at that spot. “It holds [great] power,” says Jay Hollick of the University of California, Berkeley. “Virtually any trait can be measured.”

Already, Buckler reported, his team has pinned down 50 genes that dictate flowering time. Some lines flower as much as 45 days apart, but no single gene region shifted flowering time by more than 3 days.

Another resource introduced at the meeting will help Buckler and others sort out how genes interact. The agribusiness giant Syngenta announced it was making available 7500 lines of corn, each representing a B73 genome with a single piece of DNA bred into it from one of the 25 strains of the Maize Diversity Project. Taken together, the lines incorporate all the genetic diversity of those strains but make it easier to understand the activity of particular genes. The community has long awaited these tools, says Brutnell: “They are really going to revolutionize the way we do genetics.”

  • *“The 50th Annual Maize Genetics Conference,” 27 February-2 March, Washington, D.C.

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