POC Conf. Call 11-8-11

POC meeting, Webex Conference Call; Date: Tuesday Nov 8th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_11-1-11?

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podarium

Comment from Traitnet: is synonym to tubercle

Rebman and Pinkava, Florida Entemologist (2001) describes podaria and tubercles (as synonyms) as a swelling of the stem (cladode) fused with the base of a leaf:

"Tubercles (or podaria) are swellings below the conic leaves of the pad (long-shoot). The upper part of the conic leaf is the blade, which abscises in a week or two at a notch. The leaf base, or petiole, and adjacent stem tissues are fused together forming the tubercle. The tubercle may elongate and swell such as in species of pincushion cacti (Mammillaria spp.). If the raised tubercles align vertically around the stem they can coalesce with those directly above and below forming ribs, like those of the saguaro."

Beentje's definition of podarium: (in cacti or other succulents): a modified leaf base functioning as the photosynthetic organ.

Beentje's definition of tubercle: (in ball- or barrel- shaped cacti), cone-shaped protuberances that are enlarged modified leaf bases fused with adjacent stem tissue (also lists two other definitions for tubercle).

Gibson and Nobel (1986, A Cactus Primer) describe a tubercle as developing form a leaf base, but they never clearly define it. -

Gibson and Nobel's description is based on work by Boke (AJB 1941 and 1944), who also does not clearly define tubercle. Boke: "The surface of the plant consists of spirally arranged protuberances which represent persistent leaf bases and on the adaxial sides." Then later, after describing the development of the leaf base: "The writer prefers to regard the leaf base as a part of the stem." He never actually uses the words tubercle or podarium.

Useage of the word tubercle by Papafotiou et al. (2001, Plant Cell, Tissue and Organ Culture)suggests that they are referring to the leaf base: "explants of the normal form were single tubercles excised (with part of the branch tissue at their base)"

Butterworth et al. (2002, Systematic Botany): "Zimmerman (1985) states that ribs and tubercles are mutually exclusive terms, although a number of intermediates are found. He recommends the use of the term podarium, suggesting that in reality ribs are series of podaria joined end-to-end. Tubercles, however, represent free or distinct podaria. This terminology allows for intermediacy between ribs and tubercles. The size and shape of tubercles range from long and leaf-like (as in Leuchtenbergia Hooker, Obregonia Fric, and some species of Ariocarpus Scheidweiler) to broad with shallow axils, as in Turbinicarpus."

(Zimmerman, A. D. 1985. Systematics of the genus Coryphantha (Cactaceae). PhD. thesis, University of Texas, Austin.)

Tubercle seems to be more widely used than podarium (no hits for podarium on Web of Science, 9 hits for tubercle and cactus).

proposed def. tubercle: A conical shaped swollen leaf base that is fused with adjacent shoot axis tissue.

Comment: Found in cacti and other succulents. May elongate and swell, as in species of pincushion cacti (Mammillaria spp.). Tubercles align may merge with those directly above and below to form ribs, as in saguaro (Carnegiea). The upper part of a leaf from which a tubercle develops is usually shed early in development.

is_a leaf base

synoyms: podarium, podaria (plural)

ref.: Systematic Botany 27(2):257-270. 2002 Molecular Systematics of Tribe Cacteae (Cactaceae: Cactoideae): A Phylogeny Based on rpl16 Intron Sequence Variation

Get diagram images from Troll.

cladode and phylloclade

These are related terms. Suggest we add them for use in cacti. Also will need them for FNA mappings.

From Beentje:

cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf

phylloclade: portion of stem or branch (several nodes an dinternodes) flattened and expanded to serve the functions of a leaf.

FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.

proposed definitions:

cladode: A shoot axis that is flattened and expanded.

comment: Has an increased area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.

synonyms: phylloclade, cladophyll

diaspore

definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.

We could add this term as a kind of upper level bin term (similar to trichome)

Problem is that the definition is based on function (reproduction) rather than structural, positional, or developmental information.

A plant structure that is a dispersed for reproduction. Examples: seed, fruit, spore, bulbil, gemma, tureon

Collaborations and other items

Wood anatomy and Forest trees

Wood anatomy: PO will work with a group of scientists to develop ontology terms to describe wood anatomy.

From Jill Wegrzyn at UC Davis: The forest tree community (and in particular the conifers), are interested in collaborating with the Plant Ontology project to develop terms specific to our communities. I currently coordinate efforts on the TreeGenes database (http://dendrome.ucdavis.edu) and will be leading efforts to integrate ontologies into our existing database.

We should start by looking at wood anatomy books and online resources from the IAWA (International Association of Wood Anatomists). They have two main glossaries - one for gymnos and one for angiosperms. They want to have categories for wood structures.

We need to start on this now by dealing with basic terms like tracheary element. These really need work in the PO, so we need to get them in order before we can describe wood anatomy.

FNA

See last week's minutes for details of the mappings (POC_Conf._Call_11-1-11#FNA).

Next steps:

• add 364 synonyms to existing terms
• fix several errors that were discovered while doing the mappings
• add 143 unique new terms, plus their synonyms

-FNA provides definitions, so this will be relatively easy

• work with FNA to create an official mapping file

-will need to get unique IDs for duplicate FNA terms

-will need to figure out how to handle FNA terms that map to >1 PO term

-discuss how to map terms that are too general for PO (101 character terms)

• begin work on phenotype/character terms, inlcuding the 101 from this list plus all of the FNA character terms

PGDSO revisions

sub-types of whole plant development stage: vegetative, reproductive, senescent, and dormant stages

Continued from POC_Conf._Call_11-1-11.

other sporophyte stages

proposed definition, sporophyte dormant development stage: A sporophyte development stage that has as a participant a sporophyte/occurs during the interval between a suspension of physiological activity and the reactivation of physiological activity.

What about embryonic phase? Is it a vegetative development stage, or does it precede it?

proposed definition, embryo development stage: A sporophyte development stage (or a sporophyte vegetative development stage) that has as a participant a sporophyte/occurs during the interval between the first cell division of a zygote and ...

From our definition of plant embryo (PO:0009009): An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryonic phase ends when organs (roots, shoot axes, or leaves) begin to form.

We can work on more specific subdivisions of the embryonic stage later.

proposed definition, sporophyte vegetative development stage: A sporophyte development stage that has as a participant a sporophyte/occurs during the interval between seed germination and initiation of reproductive structures. proposed definition, sporophyte reproductive development stage: A sporophyte development stage that has as a participant a whole plant during the interval between the initiation of reproductive structures and something (onset of dormancy, senescence, or resumption of vegetative stage). Has as part a sporangium?

other gametophyte stages

proposed definition, gametophyte dormant development stage: A gametophyte development stage that has as a participant a whole plant during the interval between a suspension of physiological activity and the reactivation of physiological activity.

proposed definition, gametophyte vegetative development stage: A gametophyte development stage that succeeds spore germination and ends with the formation of gametangia.

proposed definition, gametophyte reproductive development stage: A gametophyte development stage that is initiated with the development of a gametangium and terminated with fertilization.

Comment: Some gametophytes may die before fertilization.

Plant structure development stages (other than whole plant)

Need to get these in order so we can deal with user requests.

Need to look at seed and leaf dev stages, see where trichomes will fit in; add tuber dev stages (under plant organ dev stage).