The complex corn genome—coming in at a hearty two billion base pairs (compared with the human genome's 2.9 billion base pairs)—has been mapped by more than 150 researchers, who worked for years to decipher the grain's genetic code. It's the most complicated plant genome to be deciphered to date and promises to increase the efficiency of the crop itself.

"It sets up our ability to start using three million to five million years of diversity" rather than a few hand-selected traits to improve production, says Ed Buckler of Cornell University and a collaborator on the research. "That's going to allow us to make lots of improvements," he says.

The four-year project, which was supported by various government agencies (including $30 million from the National Science Foundation) and prompted in the 1990s by the National Corn Growers Association, promises to contribute a veritable cornucopia of new insights useful to many industries, including agriculture, energy and even manufacturing. The results were published online November 19 in a series of papers in Science and PLoS Genetics.

Deep into the maize
Getting to the bottom of this staple's DNA, however, was no small task. The corn genome actually has 12,000 more genes than humans do and manages to stuff them onto 10 chromosomes (as opposed to humans' 23). All of this data, and the repetitiveness of corn's code, made the task a daunting one. The team used a combination of physical and optical mapping to arrive at the findings.

After locating and characterizing the cereal's 32,000 genes, researchers now anticipate a new bounty of genetically tuned varieties. "Having the genome sequence is like having part of the instruction manual," says study author Richard Wilson of Washington University in Saint Louis (W.U.), echoing the famous 2000 comment of then Human Genome Project leader Francis Collins, who called knowledge of our genome a "glimpse of our instruction book."

A better understanding of the plant's biochemical pathways may even be able to inspire totally new uses. "We're really excited that we've been able to generate a large number of markers that people can work with," says Buckler, who is also part of the U.S. Department of Agriculture's Agricultural Research Service. "We're going to be able to do genome-wide association studies very rapidly, which have already taken off in humans." The findings may also help researchers solve the mystery of hybrid vigor, the as-yet unsolved puzzle as to why a hybrid offspring proves to be a better grower than what would be expected from the sum of its parents' genetic assets.

This information will certainly speed up the development time of new corn varieties. Both academic and corporate researchers will now be able to do genetic tests on seeds to see if they are exhibiting desired traits rather than wait through a full growing season, Wilson explains. Buckler notes one breeding program that is already underway to increase the vitamin A content in corn after discovering a relevant allele last year. "Once we find a good gene with good alleles, we can breed with it immediately," he says.

Digging into corn's genetic past
The new picture that has emerged of the plant also helps researchers better understand its evolution and history. The crop was domesticated from a Central American grass called teosinte some 10,000 years ago. Much of the genetic diversity of maize, however, reaches nearly five million years back, Buckler says. Others had previously pointed to a few genes that were likely integral in domestication (such as those for ear size or kernel tenderness), but the new map suggests at least 100 to 200 genes have been involved in the domestication and selective breeding of the plant, Buckler notes. And as it turns out, "a lot of the genes have to do with making it a big ear," he says, citing the growth from the historical few inches to today's grocery store varieties that can regularly reach more than a foot in length.

Researchers selected the B73 variety of hybrid corn to map, which was developed in the 1970s at Iowa State University in Ames. It is "a favorite lab strain" in which a lot of the groundwork research had already been done, Wilson notes.

Unlike mammals, mated corn varieties can have fairly vast genetic differences and still produce viable offspring. A partial sequencing of 27 other varieties revealed some striking variances. The Mo17 variety, for example, did not have at least 180 genes that appear in B73. "Any two maize varieties are as diverse from each other as humans are from chimpanzees," Buckler says.

An abundance of genes
It may seem strange that the number of DNA bases in humans should tally up nearly negligibly higher than they do in corn, but as Wilson points out, it's important "to not get hung up on the numbers." If we based our understanding of sophistication purely on these rankings, he says, "we pale in comparison to the pine tree." It's how the genomes are organized that is important. "Human genes are so much more complicated," points out Wilson, who is the director of The Genome Center at W.U.'s medical school.

Other theories about the relative complexity of some plants to vertebrates call on genetic efficiencies. Advanced animals can usually move out of a suboptimal environment (or in the case of humans, even change it). On the other hand, "a plant essentially has to stand there and take it," Buckler says. "In certain aspects that's more complex—you can't run away from the pathogens that are attacking you, so you have to create a diversity of options to deal with those things."

Despite its fruitful adaptations, the crop has gotten its share of flack for consuming precious water and nutrient resources, especially as its acreage has increased to meet biofuel and animal feed demands. Many behind the project, however, assert that this new knowledge will help create varieties that will be more environmentally sound and even more specially tuned for each location (being more drought tolerant or requiring less nitrogen, for example). And more corn could mean more big business in the U.S., which already grows some 44 percent of the world's supply (and is also the cereal's biggest consumer). This year alone, the country's 87 million acres of corn are expected to produce about 13 billion bushels, which could bring in more than $3 billion.

Aside from potential for fueling the economy, corn could play an important role in feeding the growing global population. An extra 2.3 billion people could mean a 70 percent jump in food demand by 2050, according to United Nations estimates. Having now surmounted the corn challenge gives researchers confidence to tackle even more complex crop genomes, such as wheat and barley—other potential weapons in fighting global hunger.

Clues from the corn project may have implications for medical research. Wilson, who is a geneticist, also examines human DNA. "Cancer genomes are difficult to figure out in some of their complexities, as well," he says. "I think there are a lot of mini tour de forces in the corn genome that we can use for looking at human disease."