Growth Stages Ontology Principles

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Key organizing principles and rules of Growth Stages Ontology

Contents

Introduction

Comparison of plant genomes at a variety of levels are facilitated by ontologies being developed by the Plant Ontology Consortium and Gene Ontology Consortium. While the latter allows comparison at the cellular level, the former through the use of its anatomy ontology, allows users to do comparative searches of genes associated to the same anatomical parts of different species. To understand the link between genotype and phenotype, comparison at the gross morphological state of a plant is necessary. Historically, species-specific terminologies were used to describe the various stages of a growing plant, but this makes cross-species comparisons difficult. Here we attempt to standardize these terms and to develop an ontology that describes plant growth stages as progressive events visible to the naked eye. This is presented here as the 'whole plant growth stage ontology'. A first step in producing this ontology was the integration of three existing species-specific ontologies, namely maize, Arabidopsis, and rice.

Objectives of POC for developing an ontology for whole plant growth stages

1) To enable querying of comparable growth stages across plant species.
2) To enable annotation to growth stages from a common platform.
3) Standardize plant growth stage nomenclature.

Species-specific ontologies

Maize growth stage ontology from MaizeGDB, rice and Triticeae ontologies from Gramene and Arabidopsis growth stage ontology from TAIR were used for integration.

Adaption of BBCH model of growth stages

The BBCH-scale is a system for a uniform coding of phenologically similar growth stages of all flowering plants. Preliminary work on integration of growth stages of crop plants had been done by this system. Thus there is a already a foundation for correlating growth stages across monocots and dicots, with much of the initial work extracting and integrating ideas from published literature having been accomplished by BBCH. Moreover this scale is based on Zadoks scale which is widely used for cereals in the United States. It was also adapted for the model plant Arabidopsis. Hence, building on the BBCH scale is immediately promising for integrating the descriptions of growth stages across Arabidopsis and the monocots, rice and maize. It also lends itself well for ontological structuring, which is important for the Plant Ontology Consortium.

Modifications

Effective use in genomics required many changes to be done to the BBCH system, which was essentially designed for use by agronomists alone. The principal stages of the BBCH scale were largely maintained with some changes in organization and numbering.

Ontology design rationale

Temporal relationship: The growth stage ontology is temporal and follows the sigmoid plant growth curve. The time staging is not chronological, it is strictly artificial and marks only progressive landmark events during growth. The term to term relationships used in the ontology are "is_a" and "part_of". The overlapping events of plant growth and development would require several relationship types that would complicate our ontology and are avoided here.

Generic terms: Unambiguous terms are used to describe the biological events of plant growth. Care was taken to ensure that the terms and definitions were applicable to most flowering plants. For example, [/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0007016 'flowering' (PO:0007016)] is defined as "the stage at which any flower(s) on the plant are open".

Species-specific terms as synonyms: The above term [/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0007016 'flowering' (PO:0007016)] has synonyms; 07-anthesis in wheat, 09-flowering in sorghum, 5 flowering in maize, 5.2 silking in maize and so on. The synonyms may link back to the species-specific database for further information.

Organization of the Ontology

  • Whole plant growth stages (PO:0007033)
    • A. Vegetative growth (PO:0007134)
    • B. Reproductive growth (PO:0007130)
    • C. Senescence (PO:0007017)
    • D. Dormancy (PO:0007132)

A. Vegetative growth (PO:0007134) has three instances, "Germination" (PO:0007057), "Main shoot growth" (PO:0007112), and "Formation of axillary shoots" (PO:0007073). "Main shoot growth" (PO:0007112) itself has three instances, "Leaf production", "Rosette growth" and "Stem elongation". The number of visible leaves is a widely used parameter across many plants. Measurement of the diameter of rosette is specific to Arabidopsis. Node number serves as a measure of stem elongation for workers on Triticeae. The three instances were created to avoid redundancy of a single top node, at the same time retaining language familiar to users of species-specific terms. Vegetative growth is a broad term to which genes expressed throughout this phase are often annotated. Reproductive stages are frequently initiated when the plant is still apparently in a vegetative stage, e.g. in main shoot development, the stage "stem elongation begins" (PO:0007079), has as a synonym, "panicle initiation".

B. Reproductive growth (PO:0007130) has "inflorescence visible" (PO:0007047), "flowering" (PO:0007016), "fruit formation" (PO:0007042) and "ripening (PO:0007010)" stages. "Inflorescence visible (sensu Poaceae)" (PO:0007012) is distinct from the generic stage, and has two instances, "booting" (PO:0007014) and "inflorescence emergence from flag leaf sheath" (PO:0007041). Flowering stages are described under "flowers open" (PO:0007026) as the number/proportion of flowers open, fruit formation stages are described in terms of increase in percent "fruit size", and ripening stages are described as relative to the whole process of ripening, e.g., "early stage of ripening" (PO:0007001).

The ontology includes measures of growth such as percent increase in size, valuable to breeders who have prior knowledge of the size/number of fruits and flowers produced by a given species under a certain set of conditions. However, such measures may not work very well for general biologists, and in future, measures of broader acceptance will be added.

C. Senescence (PO:0007017) is defined as the processes that occur near the end of a plant's active life.

D. Dormancy (PO:0007132) is defined as a suspension of physiological activity that can be reactivated once it is broken.. At present, all the synonyms to this stage belong to Triticeae.

Adaptability to other plants

Presently this ontology includes the reference plants rice, maize and Arabidopsis. However, other plant's growth stages can be added with relative ease. Thus "one leaf visible" (PO:0007094), has a synonym e.g. "unifoliolate leaves unfolded in soybean" (SOY:0000015). The soybean terms from SoyBase can thus be integrated into the generic ontology. We hope to include other species from Fabaceae, Solanaceae, etc.

Note

Plant development occurs at several levels of organization. It has been helpful to divide plant growth into a series of stages even though many events overlap. Biologists have resorted to this reductionist approach, which allows simplified interpretations of what could otherwise be a continuous and complex series of events. Thus stages are not to be thought of as discrete and isolated steps, but as landmarks in a continuous developmental process; they are tools with which to analyze the subtle differences in plant growth.

Frequently Asked Questions

Please consult the FAQ for the Growth Stages Ontology.

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IN DISCUSSION