A delayed response on "POC observations so far"

[Vincent, Leszek]

Sue (& possibly others),

The "bottom line" (elevator pitch) is that the Zea mays Plant Structure
ontology has attempted to represent the biological reality of monoecy
via incorporating ontogenetic data & reflecting phylogenetic theory &
satisfies the 'true path rule'- check it out.

- Leszek

> -----Original Message-----
> From: owner-po-dev at brie4.cshl.org 
> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Sue Rhee
> Sent: Wednesday, October 08, 2003 4:54 PM
> To: po-dev at plantontology.org
> Subject: Re: A delayed response on "POC observations so far"
> 
> 
> give me the bottom line in three sentences or less.
> 
> thanks,
> sue
> 
> On Wed, 8 Oct 2003, Vincent, Leszek wrote:
> 
> > Hi POC colleagues,
> >
> > Here's some 'bedtime reading'.
> >
> > Recently there was discussion about the representation of unisexual 
> > florets in a taxon which bears both functionally male & 
> female florets 
> > in separate flowering structures e.g. adequate representation of 
> > monoecy in taxa such as Zea mays. Furthermore concern was 
> raised about 
> > querying an ontology, involving a monoecious taxon, for the term 
> > gynoecium - that such a search should be able to retrieve 
> > gynoecium-related info. associated with the tassel as well 
> as the ear 
> > as in Zea mays.
> >
> > Pankaj & possibly some others may recall that some of us 
> visited this 
> > area sometime last year & the synthesis of that dialogue 
> was recorded 
> > in the current ontology for Zea mays (freely available from 
> > plantontology.org). But to show you an example of the tentative 
> > solution to the challenge I've reproduced a portion of the 
> > representation below:
> >
> > organ
> >   %tassel (functionally male inflorescence)
> >     <pedicellate spikelet of tassel
> >       <lower floret of pedicellate spikelet of tassel
> >         <gynoecial tissue (abortive) of lower floret of pedicellate 
> > spikelet of tassel
> >         <lodicules of lower floret of ....
> >         <palea of lower floret of .....
> >         <stamens of lower floret of ....
> >       <lower glume of pedicellate spikelet of tassel
> >       <upper glume of .....
> >     <sessile spikelet of tassel
> >       etc.
> >   %lateral branch
> >     <ear (functionally female inflorescence)
> >       <pedicellate spikelet of ear
> > etc....
> >
> > Yes, it is a little complex (view it via DAG-Edit for a clearer 
> > representation than that provided here) but it is my/our 
> best attempt 
> > yet at capturing the biological complexity such that the true path 
> > rule is met for this biological reality in Zea mays. 
> Furthermore, it 
> > should satisfy the query needs referred to above. Of course 
> there may 
> > be other considerations that have since transpired...
> >
> > For me, as a botanist & plant systematist, I think it is a good 
> > solution because it captures the ontogenetic detail for these 
> > structures and it is also consistent with phylogenetic argument 
> > concerning these structures - and consequently should be 
> applicable to 
> > taxa, other than Zea, where monoecy & dioecy is found.
> >
> > It is true that some folk may not (at first) appreciate the 
> biological 
> > relevance of including both the androecium & gynoecium in both the 
> > tassel & ear. My attempt to cover that 'base' is provided in the 
> > definition for "floret". In this definition I spell out the 
> > ontogenetic reality of both the androecium & gynoecium 
> being initially 
> > present in both the tassel & ear florets - hence their need to be 
> > included in both the tassel & lateral branch/ear nodes. It 
> also draws 
> > attention to the putative phylogenetic necessity for such a 
> > representation. Implicitly what I'm practicing is that 
> ontogenetic & 
> > phylogenetic information are both extremely important for 
> inclusion in 
> > the application of the 'true path rule'.
> >
> > Here's the definition for floret (yes, it is detailed):
> > "The floret is the individual flower of the Zea mays plant. In the 
> > grass family (Poaceae, alt. Gramineae) each floret is typically 
> > bisexual (perfect), possessing both an androecium and a gynoecium. 
> > Each floret typically has a pair of bracts, the lemma and 
> palea, which 
> > subtend the floret. It is important to note that In Zea mays the 
> > florets of the 'tassel' are functionally male (the female component 
> > (gynoecium) having aborted early on in development). The florets of 
> > the 'ear' are functionally female (the male components (androecium) 
> > having aborted early on in development). The possession of 
> > functionally male and functionally female florets (or 
> flowers) on the 
> > same plant is a condition called monoecy. While Zea mays is 
> > functionally monoecious, the presence of both androecial 
> and gynoecial 
> > tissue in the early stages of floret ontogeny is phylogenetically 
> > significant. Consequently, the androecium is represented in the 
> > florets of the ear and the gynoecium is represented in the 
> florets of 
> > the tassel, even though either of these whorls is absent in the 
> > functional florets. The inclusion of both whorls in the floret 
> > ontology for the florets of ears and spikelets is based on this 
> > phylogenetically significant ontogeny. East and Hayes (1911, p.
> > 134-135) provided the following: "Perhaps it should be mentioned in
> > passing that the immature sex organs, so called, of maize 
> seem endowed
> > with the power of becoming either stamens or carpels. One 
> often finds a
> > normal ear ending in stamens, and nearly every plant 
> produces lateral
> > branches which have carpels and stamens mixed together
> > indiscriminantly." Studies of mutants have explored these 
> occurrences
> > and similar occurrences in tassels, corroborating the 
> inherent bisexual
> > nature of the floret meristem prior to the subsequent 
> development of the
> > monoecious condition." (the length of this defn. possibly provides
> > argument for the inclusion of some sort of comment field closely
> > associated with the definition?).
> >
> > I've also been using the Derived/Develops_from relationship 
> in the Zea 
> > ontology. This relationship accommodates the temporal & 
> spatial needs 
> > associated with ontogeny e.g. the development of primordia.
> >
> > You'll note, when browsing the ontology via DAG-Edit, that I still 
> > need to provide definitions for some terms - an ever pressing need.
> >
> > Let me have your candid comments/thoughts.
> >
> > Leszek
> >
> > ===========================
> > P. Leszek D. Vincent Ph.D., FLS
> > Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall, 
> University of 
> > Missouri-Columbia, Columbia, MO 65211-7020, USA.
> > Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850;
> > Ph/Fax (Home): (573) 441-1228;
> > Email: Leszek at missouri.edu
> > Yahoo! Messenger: leszekvincent
> > Plant Systematist on the Plant Ontology Consortium
> > Associate Curator, Dunn-Palmer Herbarium (UMO)
> > Research Associate, Missouri Botanical Garden, USA
> > CEO - PhytoSynergy, LLC
> > =======================
> >
> >
> 
> --------------------------------------------------------------
> ---------------
> Sue Rhee                         	rhee at acoma.stanford.edu
> The Arabidopsis Information Resource	URL: www.arabidopsis.org
> Carnegie Institution of Washington	FAX: +1-650-325-6857
> Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
> 260 Panama St.
> Stanford, CA 94305
> U.S.A.
> --------------------------------------------------------------
> ---------------
> 
>