Ames, Iowa
March 17, 2003

Researchers led by an Iowa State University professor have uncovered a genetic pattern in cotton that is likely to have implications for other crops, including corn and soybeans.

"We don't really understand what those implications are, but they are astonishing and possibly far- reaching," botanist Jonathan Wendel said. The study by Wendel, ISU research associates Keith Adams and Ryan Percifield, and Richard Cronn of Oregon State University, is in this week's Proceedings of the National Academy of Sciences.

Grants from the U.S. Department of Agriculture, the National Science Foundation and Iowa State's Plant Sciences Institute supported the work.

Cotton is a polyploid; it has two copies of every gene instead of one, one pair of genes from each of two cotton species that evolved separately on two continents, then somehow crossed 1 million to 2 million years ago. As a result, it has double the number of genes humans and animals have. Corn and soybeans also are polyploids.

"The question is, are both those genes turned on or turned off at the same time, or are there alternatives," Wendel said. "One theory is that one gene would be free to change, to play around and promote evolution. That gene would acquire a new function or it would die.

"What we didn't expect was that immediately upon polyploid formation Š these duplicate genes would
change their form of expression in a most surprising way."

Wendel and his fellow researchers theorized that if a gene were active in both of the parent species, it would be expressed in the polyploid descendant.

The group tested for 40 randomly chosen cotton genes. "What we found was an incredible level of
alteration in gene expression," Wendel said. "More than a quarter of the genes expressed changed the way they were expressed" from the parents. If those results were extrapolated over all 30,000 cotton genes, about 7,500 would have patterns different from the parent plants.

"Here's the cool part," Wendel said. In one part of the plant's flower, the gene pair from parent 1 was
turned off while the gene pair from parent 2 was expressed. But in another part of the flower, the gene pair from parent 1 was expressed and the gene pair from parent 2 was turned off - just the opposite mode.

"You get reciprocal silencing of the duplicates," Wendel said. "This was totally unexpected." Gene silencing, or genes becoming inactive, varied depending on the plant organ and gene under study.

The researchers found the phenomenon in both a modern cotton strain and in a natural strain 1 million to 2 million years old. Wendel said that means the expression changes likely happened when the two genomes merged to make cotton a polyploid, or happened soon after the merger.

"The paradigm is evolution happens through slow, tick-tock changes" - random mutations that survive or fail - or through sudden changes in conditions, Wendel said.

"This is true, but superimposed on this is this whole new way of thinking" - change that happens when
genomes merge to make polyploids, Wendel said.

Wendel believes the unusual pattern will be found in other polyploids, such as corn and soybeans. The study may mean that gene function responds even more to small changes in the genome - the complete set of genetic instructions - than previously thought, he said.

"How you harness this to improve plants is a question I can't answer," Wendel said, though he believes it will be useful someday.

The researchers will continue the work by studying the expression of thousands of genes.