Submitted to: Plant Physiology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/1/2006
Publication Date: 9/1/2006
Publication URL: http://hdl.handle.net/10113/80046
Citation: Pujar, A., Jaiswal, P., Kellogg, E., Ilic, K., Vincent, L., Avraham, S., Stevens, P., Zapata, F., Reiser, L., Rhee, S., Sachs, M.M., Schaeffer, M.L., Stein, L., Ware, D., McCouch, S. 2006. Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology. 142:414-428. Interpretive Summary: Because plant genome databases use diverse vocabularies to describe anatomy, morphology and growth stages, it is difficult to query multiple databases for all genome information about a particular topic, for example root growth. We have integrated these diverse vocabularies into a networked hierarchy or ontology for several plant species, which include a model plant, thale cress and the cereal grains: corn, rice, wheat, barley, oats, and rye. A browser installed at http://www.plantontology.org accesses annotations on whole-plant growth stages in three different plant genome databases. The growth stage ontology is meant to link genetic and molecular information of plant growth in different species, from germination to senescence in developmental time and space. An immediate result of the work is to leverage developmental information gained in any of the plant species using the ontology to the understanding of similar developmental stages in other plants, in particular the crop plants. In the long term, maximizing plant growth stage knowledge will enhance productivity and reduce costs to the consumers for food and other plant-based products.
Technical Abstract: Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth and development. Each species or family specific community developed distinct terminologies for describing whole-plant growth stages. This semantic heterogeneity made it impossible to use growth stage description contained within plant biology databases to make meaningful computational comparisons. The Plant Ontology Consortium (http://www.plantontology.org) was founded to develop standard ontologies describing plant anatomical as well as growth and developmental stages that can be used for annotation of gene expression patterns and phenotypes of all flowering plants. In this article, we describe the development of a generic whole-plant growth stage ontology that describes the spatiotemporal stages of plant growth as a set of landmark events that progress from germination to senescence. This ontology represents a synthesis and integration of terms and concepts from a variety of species-specific vocabularies previously used for describing phenotypes and genomic information. It provides a common platform for annotating gene function and gene expression in relation to the developmental trajectory of a plant described at the organismal level. As proof of concept the Plant Ontology Consortium used the plant ontology growth stage ontology to annotate genes and phenotypes in plants with initial emphasis on those represented in The Arabidopsis Information Resource, Gramene database, and MaizeGDB.