Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

The Role Of Plant Ontology In Comparative Plant Genomics And Gene Discovery

Chih-Wei Tung¹ , Pankaj Jaiswal¹ , Katica Ilic² , Anuradha Pujar¹ , Elizabeth Kellogg³ , Felipe Zapata^3,4 , Peter Stevens^3,4 , Shuly Avraham⁵ , Mary Schaeffer^6,7 , Leszek Vincent⁷ , Martin Sachs^6,8 , Sue Rhee² , Doreen Ware⁵ , Lincoln Stein⁵ , Susan McCouch¹

¹  Department of Plant Breeding, Cornell Universty, Ithaca, NY 14853, USA

²  Carnegie Institution of Washington, Stanford, CA 94350, USA

³  Department of Biology, University of Missouri at St. Louis, St. Louis, MO 63121, USA

⁴  Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, MO 63110, USA

⁵  Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA

⁶  Agriculture Research Services, United States Department of Agriculture, USA

⁷  University of Missouri-Columbia, Columbia, MO 65211-7020, USA

⁸  Maize Genetics Cooperation-Stock Center, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA

The increasing availability of data from several plant genome sequencing projects and comparative genomic approaches provide a promising direction for investigating genes and their functional and sequence homologs involved in plant development. However, when associating their structures (anatomy) and growth stages, varied terminology is used for diverse plant species. This makes it difficult to draw conclusions from the predicted or known experiments involving cross-species comparisons. Therefore, developing the controlled vocabularies (ontologies) to describe plant morphological, anatomical and growth and developmental stages was necessary. In 2003, the Plant Ontology Consortium (POC) (www.plantontology.org) was formed to meet this need and to provide a semantic framework for meaningful cross-species queries across multiple databases, such as Gramene, TAIR, MaizeGDB and other model plants. The result was the Plant Ontology (PO).
In the past three years, plant biologists were able to consistently use these PO terms in the annotation of tissue and/or growth stage specific expression of genes, proteins, and phenotypes that were supported by experimental evidence. So far, over 6,300 gene annotations have been documented in the POC database, and can be used in conjunction with other useful information (such as their biochemical characterization from their source databases) to predict phenotypes, determine functions of gene products, and possibly initiate gene discovery through comparative genomics analysis. The current and near-future development efforts for POC are focused on the introduction of species-specific terms into the PO to accommodate annotations from legumes (Medicago and soybean), Solanaceae (tomato), poplar (Populus) and Triticeae (wheat, oat and barley). We expect PO development to be an ongoing activity as we seek to create a robust resource that is responsive to new discoveries in our understanding of plant biology.