A view to a-maize

AMES, Iowa -The maize genome sequence is now complete, thanks to a decoding effort so challenging even the epic aptitudes of secret agent 007--James Bond--would have come up short.

Iowa State University (ISU) Plant Sciences Institute (PSI) researchers developed methods for the assembly of sequence data and conducted much of the ongoing functional analysis work as part of a multi-institutional, $29.5 million, National Science Foundation-funded effort led by the Genome Center at Washington University School of Medicine, St. Louis, and included the University of Arizona, Tucson, and Cold Spring Harbor Laboratory, New York.

PSI researcher Patrick Schnable, Baker Professor of agronomy and lead author for the maize genome sequence publication, coordinates a team of researchers now using these data to address multiple biological questions.

The first discoveries are published along with the sequence itself in the 20 November issue of Science. A set of companion papers accompany this feat and a separate set of companion papers will appear in the open access online journal Public Library of Science (PLoS) Genetics.

These accomplishments have been awarded the coveted cover spot in both journals. Additionally, the Science issue includes a specially designed maize poster intended to serve biology readers with a Cliffs Notes© version of the merits of maize as an experimental organism and its value as a crop.

What the effort has so far revealed is a genome nearly as large as that of the human, containing about the same number of genes but substantially more complex. Its dramatic complexity tested the resolve of the genome assemblers as never before due to an unprecedented number of long strings of repetitive sequence and highly conserved transposable elements-restless chunks of DNA that jump around within the genome during normal cell division. They restructure the genome, generate genetic diversity and influence gene expression patterns. Eighty-five percent of the genome consists of these repetitive pieces that provide clues to the mysteries of genetic variability and gene function.

The maize line selected for sequencing is B73, an Iowa State-originated inbred line that was highly prized for making hybrids that are used for food, feed, and a variety of industrial feedstocks, including fuel.

B73, released in 1972, was the product of breeding efforts by ISU agronomy professor emeritus Wilbert Russell. The line and its descendents are now present in half the parentage of nearly all hybrid corn grown around the globe. These high-performing commercial hybrids have led to unprecedented corn yields for farmers.

"Inbred B73 dramatically increased corn yields in hybrid combinations during the 70's, and became a key ancestral female line in today's global germplasm pool. Understanding the genes that may have contributed to B73's unique heterotic contributions will provide a critical base for future yield improvement in corn," says Ted Crosbie, Vice President of Global Plant Breeding at Monsanto Company.

The sequence in hand is but a starting point for plant scientists, yet speaks volumes for the possibilities it stores. Within this tome lie secrets for improving agronomic efficiency that will save growers on input costs and also has potential to improve water quality. It also equips researchers with an important model for understanding the biology of dedicated biofuel grasses.

"The real value of a sequenced genome is that it provides us with a reference from which to assess whether naturally occurring sequence variability among individuals is responsible for differing abilities to adapt to environments. Once we recognize and understand these patterns, we will have the ability to rapidly develop diverse maize hybrids that can fit the management practices and environmental scope that corn producers experience," says William Beavis, George F. Sprague Endowed Chair of Population Genetics and interim director of ISU's Plant Sciences Institute.

Accompanying the sequence paper in Science, Schnable, Dan Nettleton, Lawrence H. Baker Chair in Biological Statistics, and their Plant Sciences Institute colleagues add another piece to the complex and incomplete informational mosaic of genetic control in hybrids.

Hybrids are widely grown commercially because they typically agronomically outperform inbreds due to the phenomenon of hybrid vigor or heterosis. First described in 1908, its mechanism of action still remains a mystery.

Comparing offspring from B73 and another important maize inbred Mo17, Schnable's group discovered that the paternally transmitted copies of genes (regardless of whether it was B73 or Mo17) preferentially control gene expression in hybrid progeny.

While it does not explain heterosis, it shows that "paternally contributed copies of genes are capable of sculpting the transcriptome," explains Schnable. "This finding suggests that epigenetic factors may influence the performance of hybrids. This knowledge will modify our approaches to crop improvement."

Three additional papers by Schnable's team appear in PLoS Genetics. Iowa State University researchers along with teams from the University of Minnesota, the University of Florida and Roche NimbleGen, Inc., again comparing the genomes of two inbred maize lines, B73 and Mo17, report 180 intact single-copy genes that are present in one line but completely missing in the other.

The researchers believe this may explain the astonishing diversity of maize phenotype from the structural to the molecular, suggesting new plot lines to follow in pursuit of understanding heterosis.

Although the data reinforce the view that maize is highly diverse genetically, they also show that there are many large genomic regions that have little or no variation. This information raises potential concerns about our ability to continue to improve maize.

A second paper takes a stab at explaining how one transposable element discovered by ISU professor emeritus Donald Robertson, the Mu transposon, chooses its moves within the maize genome.

Combining next generation sequencing technology with some powerful statistical analyses, the researchers have confirmed that Mu insertions are not randomly distributed and Mu elements preferentially seek out regions on the chromosomes where chromatin is less tightly packed. Mu insertion patterns follow classic recombination patterns seen in meiosis (during organismal reproduction), suggesting a new venue for more efficient genetic manipulation to support plant breeding efforts.

A third paper reports on a mechanism by which gene and transposon activity is controlled. The mechanism, involving small RNA molecules and their interactions with chromatin, has already been shown to regulate transposons. It has now been shown to influence gene activity as well.

"In the future, we can expect to routinely sequence transcriptomes and genomes of several maize lines and other crop species using billions of short reads from next generation sequencers. We are in the midst of a revolution in computational methods to facilitate this, and high performance computing will play a key role due to the enormity of data and complexity of analysis needs," says ISU team member Srinivas Aluru, Ross Martin Mehl and Marylyne Munas Mehl Professor of Computer Engineering.