Whole Plant Development Stages

Introduction
Ontology design rationale
Organization of the whole plant development stage branch
Adaptability to other plants
Frequently asked questions (FAQs)

Introduction

Comparison of plant genomes at a variety of levels are facilitated by ontologies being developed by the Plant Ontology Consortium and the Gene Ontology Consortium. While the latter allows comparison at the cellular level, the former, through the development of terms for plant anatomical entities, allows users to do comparative searches of genes associated to comparable anatomical parts in different species. To understand the links between genotype and phenotype, comparison at the developmental state of a plant is also necessary. Historically, species-specific terminologies were used to describe the various stages of a growing plant, but this makes cross-species comparisons difficult. The PO standardize the terms that describes whole plant growth and development stages as progressive events visible to the naked eye. This is presented as the whole plant development stage branch of the PO.

A first step in producing this ontology was the integration of three existing species-specific ontologies for maize, Arabidopsis, and rice. Later, this effort was expanded to encompass all plants. This was done primarily by adding new upper-level terms for sporophyte and gametophyte developments stages, such as sporophyte vegetative stage or gametophyte dormant stage. Specific terms for development stages found in only non-seed plants, such as thallus vegetative whole plant development stage, were also added.

The whole plant development stage branch of the PO is part of the plant structure development stage branch.

Objectives for developing ontology terms for whole plant development stages

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

Species-specific ontologies

The maize growth stage ontology from MaizeGDB, rice and Triticeae ontologies from Gramene, and the 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 development stages of all flowering plants. Preliminary work on integration of whole plant development stages of crop plants had been done with this system. Thus there is a already a foundation for correlating development stages across monocots and dicots, with much of the initial work of extracting and integrating ideas from published literature having been accomplished by the 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 was immediately promising for integrating the descriptions of development stages across Arabidopsis and the monocots rice and maize. It also lends itself well to ontological structuring, which facilitated conversion to an ontology.

Effective use in genomics required many changes 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 time staging of whole plant development stages is not chronological; it is strictly artificial and marks only progressive landmark events during growth. The primary relationships used in this branch of the PO are "is_a" and "part_of". However, these relationships do not provide information on the order of development stages. In the future, temporal relations such as 'precedes' or 'preceded_by' may be added to the PO.
Generic terms: Unambiguous primary names are used to describe the biological events of plant development. Care was taken to ensure that the names and definitions were applicable to all plants in which a given stage occurs. For example, 'flowering stage' (PO:0007016) is defined as "the stage at which any flower(s) on the plant are open" and can be used for any angiosperm.
Species-specific terms as synonyms: The above term ('flowering stage' (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 whole plant development stage branch

Whole plant development stage (PO:0007033), has three subclass:

gametophyte development stage (PO:0028003)
sporophyte development stage (PO:0028002)
life of whole plant (PO:0025337)

Gametophyte development stage and sporophyte development stage describe the two major phases in any plant's life cycle. Similar to the anatomical term for whole plant, the term life of whole plant is unlikely to be used much for annotation of gene expression, but it was included for completeness. There are only two types of life of whole plant, because every life of whole plant is either a maximal gametophyte stage or a maximal sporophyte stage.

The gametophyte development stage and sporophyte development stage are further divided into subclasses for vegetative, reproductive, dormant, and senescent stages, plus additional classes for the plant zygote stage (for sporophytes) and the plant spore stage (for gametophytes). For example, the subclasses of sporophyte development stage are:

plant zygote stage (PO:0001097)
sporophyte vegetative stage (PO:0007134)
sporophyte reproductive stage (PO:0007130)
sporophyte senescent stage (PO:0007017)
sporophyte dormant stage (PO:0007132)

Vegetative growth is a broad term and genes expressed throughout the sporophyte vegetative stage are often annotated. The sporophyte vegetative stage (PO:0007134) has as subclasses plant embryo stage (PO:0007361), coleoptile emergence stage (PO:0007045), seed germination stage (PO:0007057), main shoot growth stage (PO:0007112), and formation of axillary shoot stage (PO:0007073). Each of these classes (other than coleoptile emergence stage), in turn has its own subclasses. For example, the subclasses of main shoot growth stage are leaf production stage, rosette growth stage, and stem elongation stage. These terms were defined based on the knowledge that the number of visible leaves is a widely used parameter across many plants, that measurement of the diameter of rosette is specific to Arabidopsis, and that th node number serves as a measure of stem elongation for workers on Triticeae. The three classes were created to avoid redundancy of a single top node, while at the same time retaining language familiar to users of species-specific terms. 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'.

The sporophyte reproductive stage (PO:0007130) has as subclasses inflorescence detectable stage (PO:0007047), flowering stage (PO:0007016), fruit formation stage (PO:0007042), and ripening stage (PO:0007010). 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 the future, measures of broader acceptance will be added.

The sporophyte senescent stage (PO:0007017) is defined as "A sporophyte development stage during which a sporophyte participates in multicellular organism senescence," refering to the GO term for multicellular organism senescence (GO:0010259).

The sporophyte dormant stage (PO:0007132) is defined as "A sporophyte development stage during which a sporophyte participates in a dormancy process," refering to the GO term for dormancy process (GO:0022611). At present, all the synonyms to this stage belong to Triticeae.

Adaptability to other plants

Although many of the low-level subclasses of whole plant development stage reference rice, maize, and Arabidopsis, all of the upper-level terms in this branch of the PO are defined to be general enough for any plant in which the development stage can occur. For example, the term sporophyte dormant stage (PO:0007132) can be used for any plant that undergoes dormancy during the sporophyte development stage. At lower-levels, other plants' growth stages can be added with relative ease, either as synonyms of existing terms or as new subclasses. For example, one leaf visible (PO:0007094), has a synonym '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 terms specific to economically important species from the 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.