The Floral Genome Project

Variations in floral architecture are of major evolutionary and economic importance, impacting various plant processes such as pollination and gene flow, as well as fruit production and seed dispersal. However, despite the central role of flowers in plant reproduction and agriculture, questions about the origin and diversification of the flower remain fundamental problems in plant biology. Recent studies in plant developmental genetics and genomics have identified dozens of genes with specific roles in flower development in Arabidopsis and other model organisms. Still, many (if not most) genes with critical roles remain undiscovered, largely because of functional redundancy. Because most economically important species are not closely related to model plant species, novel approaches are needed to build upon existing genome projects and transfer knowledge to nonmodel organisms.

The Floral Genome Project will investigate the origin, conservation, and diversification of the genetic architecture of the flower, and develop conceptual and real tools for evolutionary functional genomics in plants. A set of plant 'exemplars' was selected, based on recent phylogenetic studies, to include the basal angiosperm groups where most flower diversity is found, plus key eudicot lineages where many crop species occur. The Floral Genome Project will generate large EST datasets, capturing thousands of sequences of genes expressed during early flower development in each species. New sampling approaches will be used to improve the chance of obtaining rare transcripts and of obtaining comparable gene sets from each species. Finished sequencing for up to 300 unique genes per species will allow study of the evolution of key genes and gene families expressed in flowers, and test leading hypotheses about the origin of the flower The Floral Genome Project will examine the site and timing of gene expression for the unique genes detected in each species using a combination of microarray analysis and new methods of high throughput in situ hybridization. Expression patterns will be evaluated for hundreds of genes in each species, and summarized in 3-D virtual reconstructions of developing flowers. This project would generate the first comparative data set of expression patterns for a large number of genes across diverse angiosperms.

These experiments will generate an enormous dataset of gene sequences and their expression in different species, and will require new informatic tools for the comparative analysis of gene history, gene function, and molecular evolution. Informatics efforts will include the generation of software for improved phylogenetic analysis of gene families and an automated data pipeline to enable researchers to move efficiently from traces to trees in an exploratory fashion. A phylogenetic database, integrated with web-based tools for flexible inquiry, will be created as a public resource to relate sequence information from expressed gene studies in a phylogenetic framework. This database 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. The Floral Genome Project will provide a key resource for generating hypotheses about common gene functions in plants and the potential sources of variation among diverse species.

FGP Consortium:
PI: Claude dePamphilis (Penn State) cwd3@psu.edu
Co-PIs: Hong Ma (Penn State), John Carlson (Penn State), Webb Miller (Penn State), Steven Tanksley (Cornell U.), Jeff Doyle (Cornell U.), Douglas Soltis (U. Florida), Pamela Soltis (U. Florida), David Oppenheimer (U. Florida), Naomi Altman (Penn State), Jim Leebens-Mack (Penn State),
Former Co-PIs (now residing in Europe): Victor Albert (U. Oslo; phylogenetics), Michael Frohlich (British Museum of Natural History and Penn State; methods development of library methods, gene curation, Mostly Male Theory), Dawn Field (Oxford C.E.H., bioinformatics), Günter Theißen (Jena U., MADS box and floral genes)
Additional Collaborators: Francesca Chiarmonte (Penn State, statistical analysis of microarray experiments), Steve Farris (Stockholm; phylogenetics),  Mike Havey (University of Wisconsin; Asparagus genomics), Rafael Perl-Treves (Bar-Ilan University; Cucumis floral development), Jeannine Rowland (USDA; Vaccinium genomics)