Fall 2002 -- Vol. 20, No. 1

NSF Grant Allows Floral Genome Project to Blossom at Penn State

The Floral Genome Project has been established at Penn State with a 5-year research grant totaling more than $7.4 million from the National Science Foundation. The project, which is the first of its kind to analyze a large group of genes from a large group of plants, involves researchers at four universities in the United States and several collaborators in Europe and will generate an enormous data set that can be used by researchers worldwide for comparative studies of plant development, evolution, and gene function. “Flowering plants first appeared in the fossil record about 125 million years ago and quickly became the dominant land plants as a result of their reproductive innovations such as flowering and fruiting,” says Claude dePamphilis, associate professor of biology, a participant in Penn State’s Life Sciences Consortium, and the project’s principal investigator. “How flowers originated and diversified at the genetic level is a fundamental mystery in plant biology that we are aiming to solve.”

Scientists have not yet discovered all the genes that control the development of a flower and they do not yet know how these genes interact with each other. Such knowledge is important because flowers not only are essential for the reproduction of most plants but they also have major economic importance for their blossoms, seeds, and fruit. The overall goals of the project are to isolate several thousand floral genes from each of 13 species of economically and evolutionarily important flowering plants and to isolate a similar number of reproductive genes from non-flowering seed plants, the gymnosperms, which are the closest relatives of flowering plants. “The analysis of these gene sequences and their expression patterns, along with the comparison of these genes, should provide new insights into the evolution of the flower and the evolution of flowering plants,” says Hong Ma, professor of biology, who will assist dePamphilis as the co-investigator for the Penn State component of the project.

“We are going to generate the first comparative collection of gene-expression patterns for a large number of genes across a diverse collection of flowering-plant species,” Ma says. Previous projects have focused on a single gene or a small group of genes and a single species or a small group of species—typically one of the “model” species such as the Arabidopsis weed that are widely studied in research laboratories. “Most of the economically important species of flowering plants are not closely related to the model species used in previous genetic research, and we do not know how generally applicable to crop plants are the discoveries made with these laboratory plants,” Ma says. One of the project’s goals is to compare model plants with other plants in order to make use of existing research knowledge by applying it to plants of economic and evolutionary importance. Another goal is to develop new methods and tools for doing evolutionary-functional-genomics research on a wider variety of plants.

“We designed the Floral Genome Project to lay the ground work for practical applications. Knowledge of the general architecture of reproductive genes and their functions across flowering plants should improve our ability to take direct control over breeding in a large variety of plants of economic importance,” dePamphilis says. Details learned about flowering in the poppy plant, for example may lead to specific approaches scientists could use to prevent flowering or fruiting specifically in the heroin poppy but not in other plants.

The researchers say the immense quantity of data and the analytical tools that the project is expected to produce will assist scientists working on many other fundamental questions in the genomics, development, phylogenetics, and molecular evolution of plants. The project also is expected to produce new and more efficient techniques for plant biologists and their students, such as high-volume hybridization methods for evaluating the precise expression patterns of hundreds of genes in numerous species and for summarizing those patterns in 3-dimensional computer images of the developing flowers.

The gene sequences and gene-expression data produced by the Floral Genome Project will be publicly available through the GenBank database of the National Institutes of Health and through the project's Virtual Flower web site, an interactive database (http://floralgenome.org). "We will be adding some 100,000 new partial gene sequences and several thousand fully sequenced expressed genes to the public genetic databases,” dePamphilis says. “Already, we’ve made significant progress in developing databases and new software tools for understanding expressed gene sequences.” The Floral Genome Project’s web site will provide annotated links to genomic and functional information in Arabidopsis, rice, and maize, and to expressed gene studies in tomato, maize, and many other important crop species.

In addition to dePamphilis and Ma, other project scientists at Penn State include Jim Leebens-Mack, research assistant professor of biology, who will serve as the project manager; Webb Miller, professor of computer science and engineering, and Dawn Field, adjunct assistant professor of biology, who are the project’s co-investigators for bioinformatics; John Carlson, associate professor of molecular genetics and a co-investigator for sequencing and woody species; and Nina Federoff, Evan Pugh Professor of Life Sciences and the Verne M. Willaman Chair in Life Sciences. Penn State statistics faculty participating in the project include Francesca Chiaromonte, assistant professor; Bruce Lindsay, distinguished professor; and Naomi Altman, associate professor. “Penn State’s expertise is strong in all three areas of this project: sequence analysis and molecular evolution, expression studies and flower development, and bioinformatics, plus the support of the Penn State Life Sciences Consortium and the Eberly College of Science gives us a major advantage for tackling such a complex project,” dePamphilis says.

The project’s co-investigators at universities other than Penn State include Steven Tanksley and Jeff Doyle at Cornell University; Douglas Soltis and Pamela Soltis at the University of Florida; and David Oppenheimer at the University of Alabama. In addition, European collaborators include Michael Frohlich at the British Museum of Natural History in London, Victor Albert at the Norwegian Museum of Natural History in Oslow, Gunter Theissen at the University of Jena in Germany, and Steve Ferris at Sweden’s Natural History Museum in Stockholm.

Barbara K. Kennedy

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