POC Conf. Call 10-1-13

POC meeting, Skype Conference Call; Date: Tuesday Oct 1st, 2013 10:30am PDT/1:30pm EDT

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

Absent:Barry Smith (OBO)

vascular leaf development stage and child terms

• Continued from POC_Conf._Call_9-24-13
• See Google Doc for revisions in progress.

Proposed new term and definition:

• vascular leaf development stage (new PO:0025570): A leaf development stage (PO:0001050) which begins with the onset of the vascular leaf initiation stage (PO:0001051) and ends with the termination of the vascular leaf senescence stage (PO:0001054).
  • No comment currently

-def'n accepted, OK. Need to add the references to the GO terms

vascular leaf initiation stage (PO:0001051) and child terms:

• vascular leaf initiation stage (PO:0001051):

• Old def'n: The earliest histological evidence of leaf initiation, i.e, a change in the orientation of cell division both in the epidermis and in internal layers of the shoot meristem occurs at this stage (Poethig S, 1997, Plant Cell 9:1077-1087).

• Revised def'n: A vascular leaf development stage (PO:0025570) which begins with the onset of the vascular leaf anlagen formation stage (PO:0001003) and ends with the termination of the vascular leaf primordium polarity determination stage (PO:0001052).

• Revised Comment: Localized cell divisions in the peripheral zone (PO:0000225) transition from anticlinal to periclinal divisions.

-def'n accepted, OK; Need to add the references to the GO terms.

-Need to add a comment that in some plants, the leaf developmental stages may occur in the same leaf simultaneously. For example, leaves maize (or other grasses) have various zones where stages are occurring. Done

vascular leaf anlagen formation stage (PO:0001003)

• Old name and def'n: formation of the leaf founder cells stage (PO:0001003): The initial stage of leaf development when cells in the SAM are already determined to form a leaf primordium, but the primordium itself is not distinguishable morphologically.

• Revised name and def'n: vascular leaf anlagen formation stage (PO:0001003): A vascular leaf initiation stage (PO:0007040) during which the cells of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).

• Revised comment: The initial stage of leaf development when cells in the shoot apical meristem (PO:0020148) are already determined to form a vascular leaf primordium (PO:0000017), but the primordium is not yet morphologically distinguishable .

Added Revised synonym (exact): vascular leaf founder cell formation stage.

Question: Are the leaf founder cells the same as the leaf analgen? It would appear so.

• Definition from Nature Review: Tsiantis1 & Hay, 2003:

LEAF FOUNDER CELLS: A group of cells that encompasses several layers of the shoot apical meristem and from which a leaf primordium is derived. Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.

There are about a dozen anlagen terms in the PO:

vascular leaf anlagen (PO:0025431): A phyllome anlagen (PO:0025430) that will give rise to a vascular leaf primordium (PO:0000017) and is part of a peripheral zone (PO:0000225) of a vegetative shoot apical meristem (PO:0008016). [source: PMID:14732442, POC:curators]

Comment: This is the region where you have the maximum concentration of auxin in the SAM (at least in a few species that have been studied).

phyllome anlagen (PO:0025430): A portion of meristem (PO:0009013) tissue that is part of a part_of peripheral zone (PO:0000225) and will give rise to a phyllome primordium (PO:0025128).

comment: The phyllome anlagen is only detectable by gene expression, not morphology.

After extensive discussion, we decided to revert to the name "vascular leaf anlagen formation stage (PO:0001003)" and to create new terms to describe the founder cells, which make up the anlagen. Will add "anlagen cell as a synonym.

Should add a comment: The anlagen is made up of one or more founder cells. Since the number of FC will vary across species.

We will destroy the new term of the same name: vascular leaf anlagen formation stage (PO:0025586). done

We should add a comment that the anlagen may consist of one or more founder cells (new po:id).

references for anlagen and founder cells

"The development of a leaf begins with a regional shift in the polarity and rate of cell division and expansion within a group of leaf founder cells on the flank of shoot apical meristem." Smith and Hake 1992

See image: founder-cell population (FC) that will give rise to the next leaf primordium

Goh et al, 2012 Development

PO-dev Feb.06

vascular leaf primordium formation stage (PO:0001019)

-was formerly a child of leaf expansion, moved to leaf initiation stage

• Old name and def'n: formation of leaf primordium stage PO:0001019: Stage of leaf development when leaf primordium is formed as a small protrusion on the flank of SAM. [source: TAIR:Katica_Ilic]

• Revised name and def'n: vascular leaf primordium formation stage (PO:0001019): A vascular leaf initiation stage (PO:0001051) during which a vascular leaf primordium (PO:0000017) forms in the peripheral zone (PO:0000225) of the shoot apical meristem (PO:0020148).

We decided that this should this be "vegetative shoot apical meristem (PO:0020148)"

Revised comment: The vascular leaf primordium (PO:0000017) develops from the vascular leaf anlagen (PO:002543).

Accepted as revised. Probably need to add GO terms to this as well.

vascular leaf primordium polarity determination stage (new PO:0025572)

* vascular leaf primordium polarity determination stage (PO:0025572): A vascular leaf initiation stage (PO:0001051) during which the vascular leaf primordium (PO:0004725) develops an adaxial side (PO:0004726) and an abaxial side (PO:0004725).

Comment: The vascular leaf primordium adaxial side (PO:0004726) is the closest side to the meristem. This stage leads to the development of a bifacial vascular leaf.

Revised comment: The vascular leaf primordium adaxial side (PO:0004726) is the side which is proximal to the meristem.

This term refers to the following two terms (children of phyllome primordium (PO:0025128); both have also been revised:

• Old name and def'n: adaxial side of leaf primordium (PO:0004726): "A portion of phyllome primordium tissue that is the adaxial/inner side of the leaf primordium develops into the adaxial/upper leaf blade.

• New name and def'n: vascular leaf primordium adaxial side (PO:0004726): "A portion of vascular leaf primordium (PO:0000017) that faces the shoot apical meristem (PO:0020148) and develops into the adaxial (upper) side of the leaf lamina (PO:0020039).

add narrow synonym: vascular leaf upper side; suggestion to use "vascular leaf lamina, but that term does not exist. It is a part_of the leaf and so we decided not to add all those terms.

• Old name and def'n:abaxial side of leaf primordium (PO:0004725): A portion of phyllome primordium tissue that is the abaxial/outer side of a leaf primordium and develops into the abaxial/lower leaf blade.

• New name and def'n: vascular leaf primordium abaxial side (PO:0004725): A portion of vascular leaf primordium (PO:0000017) that faces away from the shoot apical meristem (PO:0020148) and develops into the abaxial (lower) side of the leaf lamina (PO:0020039).

Comments: The vascular leaves (PO:0009025) of some plants may not have an obvious adaxial or abaxial side such as the leaves of many xerophytic (arid-adapted) species. The adaxial and abaxial side may appear considerably more rounded and this could be due to early activity of the vascular leaf adaxial meristem (PO:0025401) and/or leaf abaxial meristem (PO:0025401).

See also: Eshed et al,

We decided to use the terms: "proximal" and "distal" rather than "closer to" or "farther away from". May be obscured in leafs that are resupinate, like in an Alstromeria. Forms the dorsal and ventral sides. Need to make it clear that we are referring to the side of the meritsem.

Note the confusion in the literature about dorsal and ventral sides: Dorsoventral patterning in plants. Recommendation is to use abaxial and adaxial to avoid confusion.

Discussion of shoot node (PO:0005004): A cardinal organ part of a shoot axis where one or more spikelet, flower, floret, branch, bud, or leaf may arise.

Digression into whether or not we should refer to the shoot node rather than the meristem? I think this is later in the development, and there is no leaf node. Will flag for future attention.

Suggestion to use 'vascular leaf lamina', rather than leaf lamina (PO:0020039), but that is not a term in the ontology

vascular leaf differentiation stage (new PO:0025574)

40:56 on recording

This term was proposed during last POC conference call to emphasize the importance of cell and tissue differentiation.

Proposed new term and def'n vascular leaf differentiation stage (new PO:0025574): A vascular leaf development stage (PO:0025570) that begins with the formation of cambial initial cells (PO:0000295) and epidermal initial cells (PO:0000349) and ends with the formation of the leaf epidermis (PO:0006016) and the leaf vascular system (PO:0000036).

Proposed comment: tba

We should be referring to procambium (PO:0025275) and protoderm (PO:0006210) rather than cambial initial cells (PO:0000295) and epidermal initial cells (PO:0000349).

* cambial initial cell (PO:0000295): An initial cell (PO:0004011) that is part of the vascular cambium (PO:0005598) or cork cambium (PO:0005599), and by periclinal divisions, produces cells to the outside or inside of the cambial axis.

• • phloem mother cell PO:0000400
  • fusiform initial cell PO:0000079
  • ray initial cell PO:0000082

* epidermal initial cell (PO:0000349): An initial cell (PO:0004011) that is part of an epidermis (PO:0005679) and gives rise to specialized cell types of the epidermis.

• • stomatal initial cell (PO:0000062)

Gonzalez et al 2012, Trends in Plant Science

vascular leaf expansion stage PO:0001052

old name and def'n: 2 leaf expansion stage (PO:0001052): Stage of leaf development which begins when cell differentiation and cell expansion occurs and finishes when the leaf reaches its full size.

Proposed revised name and def'n vascular leaf expansion stage (PO:0001052): A vascular leaf development stage (PO:0025570) during which vascular leaf size increases primarily through cell expansion.

Proposed comment: During this stage leaf shaping (GO:0010358) occurs which is defined as the developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed.

• Note: The majority of cell division occurs early in leaf development and cell expansion is the major agent of leaf expansion link or see above image.

From Esau 1965: It appears that leaf differentiation occurs during the intercallary growth of the leaf. The difference between palisade and spongy mesophyll/cells is a matter of individual growth or elongation.

Refer to the GO term: cell growth GO:0016049: The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. synonym: cell expansion.

Revised comment: During this stage, the process of cell growth (GO:0016049) occurs, defined as the process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. synonym: cell expansion.

Suggested revisions to leaf shaping (GO:0010358); Proposed new name: multidimensional leaf expansion: The developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed.

vascular leaf post-expansion stage (PO:0001053):

old name and def'n: 3 leaf fully expanded stage (PO:0001053): Stage of leaf development when leaf is fully expanded.

Proposed new Name and def'n: vascular leaf post-expansion stage: A vascular leaf development stage (PO:0025570) that begins when the vascular leaf (PO:0009025) is fully expanded and ends with the onset of the vascular leaf senescence stage (PO:0001054).

from 9-10-13: 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 Mahogany plants, but they are the exceptions. Could add as a comment (get names from DWS).

vascular leaf senescence stage (PO:0001054)

Tabled for next week's discussion

• Links to Relevant References- vascular leaf development
  • Genetic Control of Leaf Development- Plant Cell teaching tools
  • 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? Tsiantis & Hay, 2003 Nature Reviews Genetics
  • Li, Brutnell et al (2010) The developmental dynamics of the maize leaf transcriptome. Nat Genet 42: 1060–1067
  • Leaf adaxial–abaxial polarity specification and lamina outgrowth: evolution and development, Plant and Cell Physiology, 2012
  • Gleissberg 2002
  • FERNS: The evolution, morphology, and development of fern leaves, Vasco et al 2013
  • Independent recruitment of a conserved developmental mechanism during leaf evolution
  • Gonzalez et al, Trends in Plant Science 2012

Upcoming meetings and Presentations 2013-2014:

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

• • Slightly new focus: "Integration of Ontologies and Systems Biology"

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

The deadline for Early Pre-Registration is November 1, 2013