The genomes of different maize plants have revealed key differences between varieties. Credit: Science/AAAS

Plant biologists have something special to be thankful for this US Thanksgiving Day. The genome of maize (corn) — a staple crop first introduced by Native Americans to the European settlers centuries ago — has finally been sequenced. The genetic secrets of maize, one of the world's most widely grown grains, should accelerate efforts to develop improved crop varieties to meet the world's growing hunger for food, animal feed and fuel.

The genome "is really a tremendous resource", says John Doebley, a maize geneticist at the University of Wisconsin–Madison who was not involved in the project. "It gives us a tool for mapping genes that we didn't have before."

The four-year, US$31-million project to sequence maize (Zea mays) was led by a US-based consortium of researchers who decoded the genome of an inbred line of maize called B73, an important commercial crop variety. The 2.3-billion-base sequence — the largest genetic blueprint yet worked out for any plant species — includes more than 32,000 protein-coding genes spread across maize's 10 chromosomes. Sections of DNA called transposable elements, which can move around the genome and cause mutations, are the most abundant parts of the sequence, spanning almost 85% of the genome.

"What we have here is a crucial part of the instruction manual for how you breed a better corn plant," says Richard Wilson, director of the Genome Center at Washington University in St Louis, Missouri, who led the maize-genome project. "You can now find where genes that underlie certain traits are located, and, thus, you have the tools for how you go off and breed those desired traits into new generations of plants."

Joachim Messing, director of the Plant Genome Initiative at Rutgers University in Piscataway, New Jersey, who was not involved in the sequencing, says he was surprised by how well previous analyses based on small snippets of the genome predicted some of the overall trends. "Practically all the things that we had forecast before could be validated with the entire sequence," he says.

The newly minted genome was published today in Science1, together with 13 companion analyses in Science and the Public Library of Science Genetics.

Metal master

After sequencing their first maize genome, researchers then tackled other corn varieties for comparison. Luis Herrera-Estrella and his colleagues at the Research and Advanced Studies Center of the National Polytechnic Institute (CINVESTAV) in Irapuato, Mexico, sequenced a maize variety from the Mexican highlands called Palomero. This ancient strain, ideal for making popcorn, diverged from B73 about 9,000 years ago — around the time that maize was first domesticated from the grass teosinte.

What we have here is a crucial part of the instruction manual for how you breed a better corn plant. Richard Wilson , Genome Center at Washington University, St Louis, Missouri

The team report that the Palomero genome is around 400 million nucleotides smaller and contains about 20% less repetitive DNA than B732. "You can contain three Arabidopsis genomes or one rice genome in the size difference between those two maize genomes," notes Virginia Walbot, a molecular biologist who studies maize at Stanford University in Palo Alto, California, and is an author of one of the Public Library of Science Genetics papers3. "These size differences that have arisen in the time of domestication and plant breeding are really major."

Herrera-Estrella's team also found more than a dozen genes related to heavy-metal detoxification and environmental-stress tolerance that were conserved in B73 and Palomero, but that were absent from teosinte, suggesting that these genes were involved in the domestication process2. Peering back into the geological record, the researchers realized that there were frequent volcanic eruptions 8,500–10,500 years ago in the Trans-Mexican Volcanic Belt — a region close to the cradle of maize domestication — that dumped heavy metals into the local soils. The conservation of the metal-detoxification and stress-tolerance genes in the derived strains "strongly suggests that environmental changes caused by volcanic activity represented an important driving force that acted early in maize domestication", Herrera-Estrella says.

Breeder's trove

Another team, led by Edward Buckler, a maize geneticist with the US Department of Agriculture's Agricultural Research Service who is based at Cornell University in Ithaca, New York, sequenced part of the gene-rich region of 27 maize varieties to map haplotypes — groups of genes that tend to stick together and probably share a common function or origin.

This 'HapMap' revealed thousands of genes around the centres of the chromosomes, where they were unlikely to be shuffled around during recombination, the process in which paired strands of DNA are separated and swapped around during cell division4.

Recombination is necessary for plant breeders to unite favourable genes from different crop varieties in a single plant. So, without much recombination, "effectively, there are thousands of genes that are recalcitrant to breeding efforts", says Buckler. He notes that this could explain why farmers often need to cross-breed, or hybridize, different inbred lines to produce the superior corn varieties that we tend to eat.

The higher quality of hybrids can also be chalked up to different corn varieties harbouring non-overlapping and complementary sets of genes, says maize geneticist Patrick Schnable, an author on the genome paper1. In a separate study, Schnable and his colleagues at Iowa State University in Ames compared the genome structures of B73 with those of another inbred line called Mo17. They found hundreds of genes that appeared only once in one or other of the two genomes5. This suggests that crossing the two varieties could produce hybrids containing a higher number of beneficial genes.

The maize HapMap also promises to make combining desirable genes easier, notes Buckler. That's because researchers can test seeds for DNA markers that flag up the presence of particular haplotypes, rather than having to grow entire plants to assess whether the traits conferred by those haplotypes are present.

The resource can also be used to produce heartier corn varieties by systematically scanning the genome for genes that underlie key traits, such as those that allow the plant to thrive with reduced fertilizer and nutrient input, or that boost the plant's drought tolerance, he adds.

Over centuries and millennia, maize breeders have made great strides in producing bigger, better and tastier corn, says Schnable. "This genome will allow us to develop tools to make their jobs a little easier."