PO:Growth stage ontology objectives and rationale

Plant Ontology Consortium

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Growth Stage Ontology: Objectives and Rationale
Introduction
Ontology design rationale
Organization of the ontology
Adaptability to other plants
Frequently asked questions (FAQs)

Introduction

Comparison of plant genomes at a variety of levels are facilitatedby ontologies being developed by the Plant Ontology Consortium and Gene Ontology Consortium. While the latter allows comparison at the cellularlevel, the former through the use of its anatomy ontology, allows usersto do comparative searches of genes associated to the same anatomicalparts of different species. To understand the link between genotype andphenotype, comparison at the gross morphological state of a plant isnecessary. Historically, species-specific terminologies were used todescribe the various stages of a growing plant, but this makescross-species comparisons difficult. Here we attempt to standardizethese terms and to develop an ontology that describes plant growthstages as progressive events visible to the naked eye. This ispresented here as the 'whole plant growth stage ontology'. A first stepin producing this ontology was the integration of three existingspecies-specific ontologies, namely maize, Arabidopsis, and rice.

Objectives of POC for developing an ontology for whole plantgrowth stages

1) To enable querying of comparable growth stages across plantspecies.
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 Triticeaeontologies from Grameneand 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 phenologicallysimilar growth stages of all flowering plants. Preliminary work onintegration of growth stages of crop plants had been done by thissystem. Thus there is a already a foundation for correlating growthstages across monocots and dicots, with much of the initial workextracting and integrating ideas from published literature having beenaccomplished by BBCH. Moreover this scale is based on Zadoksscale which is widely used for cereals in the United States. It wasalso adapted for the model plant Arabidopsis.Hence, building on the BBCH scale is immediately promising forintegrating the descriptions of growth stages across Arabidopsis andthe monocots, rice and maize. It also lends itself well for ontologicalstructuring, which is important for the Plant Ontology Consortium.

Modifications

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

Ontology design rationale

Temporal relationship: The growth stage ontology istemporal and follows the sigmoid plant growth curve. The time stagingis not chronological, it is strictly artificial and marks onlyprogressive landmark events during growth. The term to term relationships used inthe ontology are "is_a" and "part_of". The overlapping events of plantgrowth and development would require several relationship types thatwould complicate our ontology and are avoided here.
Generic terms: Unambiguous terms are used to describe thebiological events of plant growth. Care was taken to ensure that theterms and definitions were applicable to most flowering plants. Forexample, 'flowering'(PO:0007016) is defined as "the stage at which any flower(s) on theplant are open".
Species-specific terms as synonyms: The above term 'flowering'(PO:0007016) has synonyms; 07-anthesis in wheat, 09-flowering insorghum, 5 flowering in maize, 5.2 silking in maize and so on.The synonyms may link back to the species-specific database for furtherinformation.

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:0007033)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 throughoutthis phase are often annotated. Reproductive stages are frequentlyinitiated 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, 'panicleinitiation'.

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 genericstage, and has two instances, 'booting' (PO:0007014) and 'inflorescenceemergence from flag leaf sheath' (PO:0007041). Flowering stagesare described under 'flowers open' (PO:0007026) as thenumber/proportion of flowers open, fruit formation stages are describedin terms of increase in percent fruit size, and ripening stages are described asrelative to the whole process of ripening, e.g., 'earlystage of ripening' (PO:0007001).
The ontology includes measures of growth such as percent increase insize, valuable to breeders who have prior knowledge of the size/numberof fruits and flowers produced by a given species under a certain setof conditions. However, such measures may not work very well forgeneral biologists, and in future, measures of broader acceptance willbe added.

C.Senescence (PO:0007017) is defined as the processes that occur near the end of aplant'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 stagebelong to Triticeae.

Adaptability to other plants

Presently this ontology includes the reference plants rice, maizeand Arabidopsis. However, other plant's growth stages can be added withrelative ease. Thus 'oneleaf visible' (PO:0007094), has a synonym e.g. unifoliolate leavesunfolded in soybean (SOY:0000015). The soybean terms from SoyBase canthus be integrated into the generic ontology. We hope to include otherspecies from Fabaceae, Solanaceae, etc.

Note

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