DeKALB – Part of Thomas Sims’ job is to work with mutants on a daily basis.
Sims isn’t a sci-fi superhero. He is a biologist researching the genetic sequence of petunias.
Sims is an associate professor of biological sciences at Northern Illinois University, and for more than 30 years, he has been using the petunia plant as a model in his research of plant reproduction.
“Plants can recognize and discriminate their own pollen from other plants and other individuals of the same species,” Sims said. “Plants prevent inbreeding through genetics and biochemistry, whereas humans and animals use behavior. To understand this phenomena of self-incompatibility, I use the petunia as a system for my research. My interest is how a plant knows and makes the recognition between self and non-self.”
Sims first read papers published by the University of Minnesota about self-incompatibility and the petunia plant while he was a doctoral student at UCLA. Before starting research on the topic, Sims said he knew next to nothing about petunia plants as a species.
“It turns out that petunias were the best system to work on to study the phenomena of self-incompatibility,” Sims said. “It’s a combination of a very specific, practical and lucky choice.”
Through his research, Sims became involved with and attended World Petunia Days, held every 18 months. WPD promotes international collaboration among Petunia scientists and breeders. During a WPD meeting six years ago, the genomic sequence of petunias was discussed, and advances in technology and decreases in cost made it possible to create a project, the Petunia Genome Project, to better understand the petunia’s DNA sequence.
Nearly 30 institutions in 10 countries helped form the Petunia Genome Project. It took two years to raise the money needed to begin the research of the whole-genome sequencing of the petunia plant.
When the project’s original leader, Tom Gerats, became ill, he asked Sims to take over leadership of the project. As director, Sims invited other biologists to join the project, including fellow NIU professor Mitrick Johns. Sims and Johns first met as graduate students at the University of Oregon, when Sims was studying corn and Johns studied fruit flies. Their paths crossed again when they both were professors at NIU.
After working on sequencing with researchers, including Lukas Mueller from Cornell University and Alvaro Hernandez from the University of Illinois, the project combined the work they had already done with Cris Kuhlemeier from the University of Bern’s sequencing technology, which made it easier to put together large genomes. Finding the mistakes and errors in the new technology and combining that sequencing with the first approach allowed the researchers to create one DNA sequence for each of the parent species: Petunia axillaris and Petunia inflata.
The history of the petunia
Petunia is genus of 35 species of plants, in the same Solanaceae family as tobacco, tomatoes, potatoes, eggplants and peppers. The name petunia comes from a French word from tobacco, “pétun.”
The most common petunia, Petunia hybrida, is a hybrid plant created when European botanists crossed two parent species of petunia when they went to Brazil in 1830. The Petunia Genome Project’s goal was to find and sequence the DNA of the mother and father, or progenitor, plants. The first plant, Petunia axillaris, has white flowers that open at night and are pollinated by moths. The second plant, Petunia integrifolia, is closely related to Petunia inflata. Petunia inflata has dark purple flowers that open during the day and are pollinated by bees. Both Petunia axillaris and Petunia inflata live in the same habitat in Brazil, but they never cross in the wild because of the different flowering times and pollinators; they can only be crossed by botanists.
“Petunia axillaris and Petunia inflata are the most likely progenitors, but there were probably multiple parents,” Sims said. “Once the European botanists crossed the two petunias to make Petunia hybrida, the plant was adopted and bred like crazy. As a geneticist, the hybrids are an absolute mess because they have been bred and manipulated so much for traits like their color and scent.”
By knowing the DNA sequences of the two parent plants, researchers can find particular genes and variants. Each of the parent genomes have 14 chromosomes, seven from each parent, and about 1.2 billion individual bases of DNA. There are four types of bases found in a DNA molecule: adenine (A), cytosine (C), guanine (G) and thymine (T).
“By looking at the genes and the gene sequences, you can find patterns of ACGT,” Johns said. “We have been working the last two years comparing what the genes look like in the species and individually. The first step was to have that initial blueprint, and now we are generating more and more information comparing the petunia to other plants in its family, figuring out how variations and dominant and recessive traits work.”
Ball Horticultural in West Chicago created a new variety of petunia that has black flowers, the Black Velvet Petunia. In this particular mutation, chlorophyll is not broken down within the flower and absorbs colors of light across the spectrum, turning the flowers black. By comparing the mutated plant’s DNA sequence to other petunias and flowers, researchers will begin to understand what genes and mutations cause the petunia flowers and other flowers, including dahlias and impatiens, to turn black.
Petunias’ ties to ending world hunger
Sims and Johns said their ultimate goal is to understand what makes a petunia a petunia and apply that information to closely related plants, including calibrachoa, and other plants in the Solanaceae family that people eat, including tomatoes, peppers and potatoes.
“We know the specific genetic changes of the commercial potato and tomato and dozens of other species of green and red fruit,” Sims said. “By crossing traits of wild species with commercial varieties, we can incorporate useful traits. It can be done, but it’s a slow and difficult process.”
“The whole goal of science is to improve our lives,” Sims said. “When most people look at petunias, they see a bunch of pretty flowers. Petunias are closely related to tomatoes and potatoes, and people are very fortunate to walk into a grocery store and see mounds of food. The world’s population is expanding, and we need to understand how plants relate and work to make it possible to keep up with the demand of food supply.”
Johns said that because of changes in climate, habitats and temperature, the world is changing faster than evolution and breeding can keep up with.
“Most of our land is already used, and it’s shrinking as we build and pave over cornfields,” Johns said. “We have to figure out how to increase food production and use smaller amounts of land. … We don’t have hundreds or thousands of generations to change what is very necessary. We have to use our fundamental knowledge and build on it. We’re still working and learning. It’s a life-long learning process.”