An ear of corn on the stalk in a field ready for harvesting.

A four-year, multi-institutional effort co-led by three Cold Spring Harbor Laboratory (CSHL) scientists culminated today in publication of a landmark series of papers in the journal Science revealing in unprecedented detail the DNA sequence of maize (Zea mays). Maize, or corn, as it is commonly called by North American consumers, is one of the world’s most important plants and the most valuable agricultural crop grown in the United States, representing $47 billion in annual value.

The sequence spans 2.3 billion DNA base-pairs and contains some 32,500 genes, or about one-third more than the human genome, according to the team that assembled it over the last four years. This version of the maize genome — taken from a variant called B73 — is important, in part, because it is regarded by the scientific and agricultural communities as a “reference” version. It represents a significant filling-in of gaps in a draft maize sequence announced a year and a half ago, but more importantly, comes with what amounts to a detailed reference manual, a set of comprehensive annotations.

A scientific and practical landmark

“Both the sequence itself and the annotations are a landmark,” says Doreen Ware, Ph.D., a co-principal investigator of the project whose CSHL lab focused primarily on the annotation and evolutionary analysis. Principal investigator of the Maize Genome Project of the National Science Foundation, which provided funding with the U.S. Department of Agriculture (USDA) and the U.S. Department of Energy, is Richard Wilson, Ph.D., of Washington University, St. Louis. Other co-principal investigators include scientists from the University of Arizona and Iowa State University.

In a parallel effort, Ware’s CSHL team also helped generate the first so-called “HapMap” of maize in collaboration with Edward Buckler, a USDA scientist. The HapMap, a shorthand for haplotype map, gauges diversity in the maize genome by comparing 27 distinct genetic lines of the plant with the reference version. A human HapMap, prepared in conjunction with the Human Genome Project, has revealed important linkages between genetic variations and risk for major diseases in ethnically and geographically distinct human populations.

“What’s important about the maize project,” says W. Richard McCombie, Ph.D., CSHL Professor, co-principal investigator on the maize genome project, and a pioneer in genome sequencing efforts, “is that it provides a reference DNA sequence for the most important agricultural crop in the U.S., making it much easier for people to look at the many variants of different strains or ‘accessions’ of maize.” New sequencing technologies, just now becoming commercially viable, will now “analyze other maize strains by comparing them to this one — albeit at dramatically lower costs and accelerated speeds,” McCombie notes.

Another of the CSHL co-project leaders, Professor Robert Martienssen, Ph.D., puts the maize sequencing project into historical perspective. Martienssen, a world leader in research on transposons — bits of DNA that copy and insert themselves randomly across the chromosomes — noted that transposable elements are found in all organisms, “but were discovered in maize more than 60 years ago,” by CSHL’s Barbara McClintock, who was honored with a Nobel Prize for the discovery in 1983. “It is a remarkable achievement to now be able to visualize transposons in such detail in the maize genome sequence,” Martienssen says.

“Wonderful diversity” and its evolutionary implications

Transposons play a particularly dramatic role in the maize genome, as the sequence clearly shows. Nearly 85 percent of the genome is composed of hundreds of families of transposable elements, distributed unevenly across the 10 maize chromosomes. This is one aspect of the maize genome’s complexity; another is its variability between different “individuals.” Maize plants from two different strains are, on average, more genetically different than humans are different from chimpanzees.
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