Maize manual now in-hand

Team success advances understanding of maize genome and facilitates future sequencing efforts of additional maize races.
Team success advances understanding of maize genome and facilitates future sequencing efforts of additional maize races.

Just two years ago, a team from Iowa State joined the $32 million effort to sequence the corn genome led by The Genome Sequencing Center at Washington University School of Medicine in St. Louis. In February, the completion of the first draft sequence of the inbred B73 line of Zea mays L. was announced.

The Iowa State team led by Srinivas Aluru, Stanley Chair in Interdisciplinary Engineering and professor in the Department of Computer and Electrical Engineering, and Patrick Schnable, associate director of the Plant Sciences Institute and Baker Professor in the Departments of Agronomy, and Genetics, Development and Cell Biology, worked on refining and analyzing the genomic sequences generated in St. Louis.

“One of the biggest challenges we faced was to make sense of the multiple types of data that came in,” says Aluru. “Even when the computational method is right it is still a challenge to make it work to solve biological problems—to fine tune it correctly.”

Capitalizing on techniques perfected through the Human Genome Project that have since been adapted to plants, the St. Louis team used Bacterial Artificial Chromosomes (BACs) to generate the genetic code. This has become the preferred method for rapidly generating enough DNA in small enough pieces for the sequencing instruments to read.

The Iowa State team received a variety of information to make sense of including the raw sequence from about 15,000 BACs, parent clone information, the maize genetic map and the BAC map. These all served as sources of evidence to help the Iowa State team confirm what they were deciphering.

As is the nature of a `first run' sequence, “it comes with a certain error rate which adds to the uncertainty in sorting,” explains Aluru.

The sequence itself further complicated matters because of long strings of repetitive sequence—identical puzzle pieces that were challenging to fit into the overall draft.

What has been determined from this initial draft is that the corn genome is big—about the size of the human genome but containing nearly twice as many genes, about 50,000.

Some of these 50,000 genes are duplicated elsewhere in the genome. “They encode the same protein but are expressed at different times, in different tissues, or when responding to environmental signals,” says Schnable.

About 350 genes discovered by the ISU team through their analysis appear to be unique—not found in any other organism, thus far.

Many of the long repetitive segments that created so many assembly hurdles for the team are retrotransposons, segments of DNA that can jump around the genome. They often alter gene function depending upon where they settle, reshuffle the genome and add to variability or diversity between individual corn plants.

Now the functional genomics part of maize research begins in earnest.

“One of the amazing findings over the last decade is the high degree of genetic similarity that exists among cereals, grasses and other species,” says Schnable. “Our analysis and those of the world-wide maize genetics research community will continue well beyond the official completion of the project.”