Plant scientists are entering the home straight in their bid to map the genome of maize (corn, Zea mays). Weighing in at 2.5 billion base pairs, the genome is about the same size as the human version, and will be the biggest plant genome yet mapped. The data are already accelerating the discovery of useful traits, but could also provide a springboard for a more ambitious effort: the detailed sequencing of the entire maize genome.

Current work is focusing on two maps. A high-resolution genetic map, analogous to a series of signposts showing the relative positions of different genes, was made available last November. A physical map, composed of overlapping cloned gene fragments to give the distances between the genes, is nearly complete and is being combined with the genetic version to create a scaled map of gene positions.

“We have assembled about 95% of the physical map and about half of it has been anchored to the genetic map,” says Ed Coe, a geneticist with the US Department of Agriculture and a director of the Maize Mapping Project. Funded by a five-year, US$11-million grant from the National Science Foundation (NSF), the project involves scientists at the University of Missouri-Columbia, where Coe is based, and the universities of Arizona and Georgia.

Project scientists predict that the integrated map will be complete in September, but it has already helped researchers. “The map has had an impact on me,” says Vicki Chandler, who studies gene control at the University of Arizona. “I now know exactly what the physical distance is between my genetic markers and where my gene is,” she says.

For many crop scientists, the sequence of the maize genome is the next logical step. Others disagree, pointing out that the rice genome, which is already sequenced, is similar to that of maize. They argue that the rice sequence, together with the integrated maize map, will provide a good guide for geneticists.

But certain aspects of maize biology, such as the unusual vigour of some hybrid strains, need the genome sequence to be fully understood, some researchers contend. Gene order and the number of genes vary greatly between different strains, and this may contribute to hybrid vigour. “We can't use the rice genome as a reference sequence for understanding the diversity of maize,” says Joachim Messing, a maize geneticist at Rutgers University in Piscataway, New Jersey.

Some experts think it would be impractical to sequence maize and other large, repetitive cereal genomes to the same standard as rice. Last September, to address these concerns, the NSF provided $10 million for a programme to test a gene-enriching strategy for sequencing the maize genome. The project aims to develop a method for filtering out gene-poor areas of the genome, and to uncover ways in which the integrated map can be used to anchor data from sequencing of the gene-rich areas.

It remains to be seen what the private sector will contribute to the maize effort. Several firms, such as DuPont, based in Wilmington, Delaware, have sequenced parts of the maize genome. “At least two of the major players are interested in partnering with us,” says Coe.