North Carolina State University and Philip Morris USA in late 2002 reached an agreement under which the tobacco company will provide $17.6 million over 4½ years to fund a project to map the genome of tobacco.

The Tobacco Genome Initiative will take advantage of a rapidly emerging expertise in genomic sciences, said Dr. Steven Lommel, assistant vice chancellor for research. The contract is the largest ever signed for a research effort in the College and among the largest for the university.

“This initiative marks a milestone in N.C. State’s emergence as a national leader in genomic research and opens a new chapter in our understanding of the tobacco genome,” said N.C. State Chancellor Marye Anne Fox. “By placing all new information from this study into the public domain, scientists, farmers, businesses and students worldwide will benefit from N.C. State’s discoveries.”

“N.C. State University is particularly solid and good at looking at plant diseases and disease control,” said Lommel. “This database will be valuable in understanding plant disease in general and will be a Holy Grail for plant disease research on campus and nationally. It will collectively take plant disease research to the next level.”

“The idea is to make a physical map of the tobacco genome and to sequence as many genes as possible,” said Dr. Charles Opperman, professor of plant pathology and genetics, who will lead the project.

“Tobacco is an important model system. It’s used to study other plants that may be more difficult to work with,” Opperman added. “The data derived from this project will be important to plant scientists working with a number of other plants, studying how other species develop, yield, resist pests and pathogens, and many other areas.”

Lommel echoed Opperman, saying, “Tobacco is a beautiful plant model system. It is a keystone solanaceous plant.”

“Solanaceous” refers to the family that includes not only tobacco, but crops such as tomato, potato, pepper, eggplant — a family of commodities important to the economy of North Carolina.

“What we learn in tobacco will be important to all of them,” said Lommel.

What is learned may also lead to the development of alternative products from and uses for tobacco.

“Tobacco presents very important and interesting biosynthetic pathways,” Lommel said.

The project is likely to provide information that may lead to genetic engineering of tobacco for alternative uses. Tobacco is thought to be a promising candidate for molecular farming. It may be possible to change the genetic makeup of tobacco plants, either by introducing foreign genes or by altering the plant’s existing makeup, so that tobacco contains valuable chemicals or drugs. The plants would then be harvested and processed for these chemicals or drugs.

Lommel credited Dr. Johnny Wynne, associate dean of the College and director of the N.C. Agricultural Research Service, with having the vision to pursue funding for the project — one that Wynne believes is in the right place at the right time.

“Right now we have, in my opinion, the best research program in flue-cured tobacco in the world,” said Wynne. “This initiative will accelerate our current genetics programs in tobacco, both the traditional and new alternatives research programs, while this project will also provide data for our bioinformatics group. The tobacco plant is a perfect model for data that could be used in the bioinformatics area.”

With completion of the project, tobacco will be among a handful of plants whose genomes have been mapped. The genomes of rice and a plant called Arabidopsis have been mapped, and mapping the genome of corn is well under way, Lommel said. Arabidopsis is a weed that is a member of the mustard family. It is often used as a model plant.

“We hope to sequence over 90 percent of tobacco’s genes,” said Opperman. “This does not mean we’ll know what all the genes do, although in some cases we will be able to determine gene function.”

It’s not clear how many genes a tobacco plant has, Opperman added, although it is thought tobacco has between 25,000 and 50,000 genes.

“The genome map hands you the keys to do a whole range of experiments,” Opperman said. He added that knowing where a gene lies in the genome often provides clues as to how the gene works and what it does.

“And we’ll probably discover novel genes during the project,” he said, adding that the project may aid in understanding how plants and other organisms evolve.

Already, Lommel said, “Other faculty are lining up to use the data we’ll be generating. The results will flow out throughout the research. Value and discovery will be occurring during the entire project.”

From the academic perspective, he said, “This is a real boon to our graduate programs in genomics and bioinformatics. These students will be working on these projects, so it will be a great boon to the training and education of graduate students.”

While the Tobacco Genome Initiative will be headquartered in Opperman’s laboratory, it will take advantage of relatively new facilities in the College of Agriculture and Life Sciences, such as the Genome Research Laboratory, a 4,000-square-foot, $3 million lab on N.C. State’s Centennial Campus that makes available to college researchers the latest genomic technology.

Opperman added that Orion Genomics, a St. Louis, Mo., company, will also play a key role in the project. N.C. State has contracted with Orion for use of the company’s proprietary Gene Thresher technology, which identifies gene-rich regions of a genome. Only about 1 percent of the tobacco genome is thought to contain genes, so the technology will help narrow the search for genes.

The signing of the agreement comes at the conclusion of a year-long pilot study.

“We developed some of the tools we’ll need for the project,” said Opperman. “We tried out sequencing strategies, developed some physical infrastructure and data analysis tools. The first year was basically a feasibility study. Could we scale up and do this? The answer was ‘yes.’”