POC Conf. Call 9-10-13

POC meeting, Skype Conference Call; Date: Tuesday Sept 10th, 2013 10am PST/1pm EST

In attendance: Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Brian Atkinson (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Barry Smith, Marie Alejandra Gandolfo (Cornell)

Absent: none

- please see the Items_for_future_meetings page, will be moved here before the meeting

multi-tissue plant structure development stage (PO:new)

• Needs a parent term: multi-tissue plant structure development stage (PO:new), then the definitions can be re-written, currently a direct child of plant structure development stage (PO:0009012). This would also be the parent for seed development and plant organ development (see below)

Accepted, will post proposed definition on SF tracker

leaf development stage (PO:0001050)

• See Google Doc for revisions in progress.
• Need to look into non-vascular leaf development and see if it applies there as well, or if we will need separate terms for vascular and non-vascular leaves.

• leaf development stage (PO:0001050): A phyllome development stage (PO:0025579) that has as a primary participant a leaf (PO:0025034).

Current structure: All these will be renamed "vascular leaf...."

• Links to Relevant References
  • Genetic Control of Leaf Development- Plant Cell
  • The developmental dynamics of the maize leaf transcriptome
  • Uchida et al (2010) Coordination of leaf development via regulation of KNOX1 genes. Journal of Plant Research 123: 7–14
  • Comparative plant development: the time of the leaf?
  • Independent recruitment of a conserved developmental mechanism during leaf evolution

vascular leaf development stage and child terms

Proposed new term and definition:

• vascular leaf development stage (new PO:0025570): A leaf development stage (PO:0001050) that begins with the onset of vascular leaf initiation stage (PO:0001051) and ends with the termination of the vascular leaf senescence stage (PO:0001054).

We will also need: * non-vascular leaf development stage (new PO:id): A leaf development stage (PO:0001050) that begins with the onset of non-vascular leaf initiation stage and ends with the termination of the non-vascular leaf senescence stage.

• Need to do more research on the development of the non-vascular leaf

see also: moss phyllides, moss info and Background_info_on_Physco_biology_and_culture.

PJ: We should have a parallel "generic" branch of leaf development to group the stages such as leaf expansion across both non-vascular or vascular leaves.

Add comment on how every stage can end in accidental death. Also mention something death being the canonical end point

New/revised child terms under vascular leaf development stage (PO:0025570)

• Note: Use "during which" rather than "when" and "ends with the beginning of the..."
• Each definition should have a consistent format (ie. begin with the termination/ends with the initiation).
• Add a comment on the top level term about how all PSDS's may be terminated before reaching senescence stage.

vascular leaf initiation stage (PO:0007040)

vascular leaf initiation stage (PO:0007040): A vascular leaf development stage (PO:0025570) when localized cells of the peripheral zone (PO:0000225) in the shoot apical meristem (PO:0020148) transition from indeterminate growth to determinate growth and ends with the beginning of the vascular leaf expansion stage (PO:0001052). Comment: Cells in the primordium are not yet differentiated.

DWS: Should omit transition from indeterminate growth -> determinate growth. The peripheral meristem is always in the shoot apical meristem.

The cells in the SAM transition from anticlinal divisions to periclinal divisions, leading to a leaf primordium or bump. Usually in L2 or L3, rarely in L1.

Later mitosis ceases leaving the marginal or submarginal meristems and the leaf expansion stage is mainly cell expansion

Leaf development in Monocots need to be looked at as they have a basal intercalary meristem.

What are "localized cells"? The cell divisions are localized

revised Def'n: vascular leaf initiation stage: A vascular leaf development stage (PO:0025570) which begins with the onset of localized periclinal division in the peripheral zone (PO:0000225) and ends with the beginning of the vascular leaf primordium formation stage (PO:0001019).

PJ- we should add a note that the concentration of auxin is highest under the spot where the primordium will form- the vascular leaf anlagen (PO:0025431).

Note that this comment is already there on the vascular leaf anlagen (PO:0025431) term

can we leave out "in the SAM"?

This is when the analagen forms- later develops into the primordium

Create a 'vascular leaf primordium development stage'- move existing term

followed by a stage called 'vascular leaf surface polarity determination stage (synonym "pre-expansion stage)

DWS: Need to look at the organization of the SAM in ferns- Do they have the equivalent of a peripheral zone?: cup-shaped zone, runs from protoderm to protoderm, under the apical cell. DWS will look into it.

DWS: Need to look at the development of phyllode leaves (PO:0025335), such as those in Acacia and other desert plants. They expand perpendicularly to the pattern of normal leave, have strong adaxial meristems, rather than marginal meristem. Flattened in a proximal -

This might go under the new 'vascular leaf surface polarity determination stage'

Def'n: An adult ensiform leaf with a lamina that develops in a median plane, rather a transverse plane, throughout the length of the leaf and is a result of increased activity of the adaxial meristem early in development. [source: PMID:18978364, PO_REF:00006, PO_REF:00007]

Comment: Common in legumes of the genus Acacia. Similar development occurs in other ensiform leaves in some monocots, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:0025336, transition phyllode leaf). Phyllodes are generally xeromorphic.

DWS will send us a diagram; need to think about how to encompass them. Also in some moss plants

Note: Will have the new preceded_by relation added to order them

Children of vascular leaf initiation stage (PO:0007040)

• formation of vascular leaf founder cells (PO:0001003): A vascular leaf initiation stage (PO:0007040) when the cells of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).

Comment: The leaf primordium is not yet distinguishable.

vascular leaf expansion stage (PO:0001052)

• vascular leaf expansion stage (PO:0001052): A vascular leaf development stage (PO:0025570) that begins with cell differentiation and cell expansion forming the leaf lamina (PO:0020039) and ends with the onset of the leaf fully expanded stage (PO:0001053).
  • new comment: The majority of leaf expansion is due to cell enlargement. The leaves of some plants may not have a conspicuous midrib or rachis.

May be due to cell division or cell enlargement. During vascular leaf expansion stage the vasculature is forming as well- need to encompass that as well.

Children of vascular leaf expansion stage (PO:0001052)- revised names and definitions:

• formation of vascular leaf primordium stage (PO:0001019): A vascular leaf expansion stage (PO:0001052) when the shoot apical meristem (PO:0020148) forms a vascular leaf primordium (PO:0000017) on the peripheral zone (PO:0000225).

this term should move up to be a child of vascular leaf initiation stage- how does this fit in with the 'formation of vascular leaf founder cells" stage

• formation of vascular leaflet primordia stage (PO:0004500): A vascular leaf expansion stage (PO:0001052) at which a leaflet primordium (PO:0025481) is initiated on the leaf rachis (PO:0020055) of a compound leaf (PO:0020043).

need to review this in terms of leaflet discussion, should move up to VL initiation stage as well, most likely

• formation of ligule primordium stage (PO:0001021): A vascular leaf expansion stage (PO:0001052) when conical P3 leaf completely encloses SAM, and the ligule (PO:0020105) primordium is visible.

check "ligule (PO:0020105) primordium"- PO:id should be after the term, need to create a term ligule primordium ligule PO:0020105 is not a leaf- it is a cardinal organ part, formation of ligule primordium stage would be part of leaf development, not is_a

Discussion on these terms were tabled for the next meeting:

• hood-shaped primordium stage (PO:0001020: A vascular leaf expansion stage (PO:0001052) when a hood-shaped primordium is formed, partially enclosing P1 and SAM, as in Poaceae.
• rapid elongation of vascular leaf lamina stage (PO:0001023): A vascular leaf expansion stage (PO:0001052) during which a rapid elongation of the leaf lamina (PO:0020039) occurs.
• rapid elongation of leaf sheath stage (PO:0001024): A vascular leaf expansion stage (PO:0001052) during which a rapid elongation of the leaf sheath (PO:0020104) occurs.

vascular leaf post-expansion stage (PO:0001053)

• vascular leaf post-expansion stage (PO:0001053): A vascular leaf development stage (PO:0025570) that begins when the vascular leaf (PO:0009025) is fully expanded and cell expansion has ceased and ends with the onset of the vascular leaf senescence stage (PO:0001054).

Use the "begins with.... and ends with..." template. Perhaps change term to "vascular leaf mature stage", or maybe keep the "leaf fully expanded stage". Examples of leaves with indeterminate growth, ferns, viney leaves, some Mahongany plants, but they are the exceptions. Could add as a comment (get names from DWS).

vascular leaf senescence stage (PO:0001054)

• vascular leaf senescence stage (PO:0001054): A vascular leaf development stage (PO:0025570) that begins with the formation of a abscission zone at the base of a vascular leaf (PO:0009025) and ends with leaf separation and death.

Would omit formation of a abscission zone. Perhaps say ends with death of vascular leaf. Need to add the references to the GO terms.

Need to look at this more- abscission zone (PO:0000146) starts in the petioles (are part of the leaf), starts with cell senescence, should refer to 'point of attachment'. Don't need to specify where the abscission zone forms. Note all leaves abscise, end with death of the vascular leaf

Need to review leaf senescence- see plant cell resource

OBO Foundry Review of Plant Ontology

Content of the review has been moved to a gdoc

NSF PI meeting Sept 4th-6th in DC

• PJ and DWS attended

Any news?

Upcoming meetings and Presentations 2013-2014:

• The Plant Genomics Congress USA, St Louis, September 23rd & 24th, 2013

No one from PO is planning to attend

• PAG 2014 January 11-15, 2014 - San Diego, CA, USA

• • PJ has been contacted by PAG organizers; Suggest slightly new focus "Plant Ontologies and Systems Biology"
  • Ideas for speakers- someone from GO and others?>>

• • Registration is now open: PAG 2014. Early reg'n till Nov. 1st

Next meeting scheduled for Tuesday, Sept 24th, 2013 at 10am Pacific/1pm Eastern

-MAG has requested the meeting be moved to 10:30am Pacific/1:30 pm Eastern- would that works for the others in the group?

Works for most, BS may have a conflict once a month