protoderm

[planteome-user]

Protoderm PO:0006210 should be is_a meristem, part_of apical meristem.

Current def: The undifferentiated surface cell layer of the primary plant body, which gives rise to epidermis.
New def: A meristem that is part of the apical meristem and gives rise to a portion of epidermis.

Reported by: rlwalls2008

Original Ticket: obo/plant-ontology-po-term-requests/125

[planteome-user]

It might be better to say that the protoderm develops from the outer layer of the apical meristem, rather than say that it is part of the apical meristem. Could use develops from meristem L1 (PO:0009020) for shoots, but I think not for roots.

Slightly revised new def: A meristem that develops from the outer layer of an apical meristem and gives rise to a portion of epidermis.

Original comment by: rlwalls2008

[planteome-user]

We need to define the primary and secondary plant bodies.

Primary: derive from apical meristem, both root and shoot
Secondary: derived from lateral meristems: vascular cambium and phellogen

Original comment by: dws409

[planteome-user]

At POC conference call 6-23-10, decided to keep part_of apical meristem.

We will make SF tracker items for primary and secondary plant body, and deal with them separately.

Original comment by: rlwalls2008

[planteome-user]

New definition: protoderm: A meristem that that develops from the outer layer of an apical meristem and gives rise to a portion of epidermis. Part_of apical meristem.

Original comment by: rlwalls2008

[planteome-user]

This term was accepted at the 6-23-10 conference call and was closed.

Original comment by: cooperl09

[planteome-user]

it actually gives rise to all of the epidermis, not just a portion. The epidermis is continuous over the whole plant.

Original comment by: dws409

[planteome-user]

this is where prefixing "portion of.." can actually make things clearer

* every portion of protoderm can give rise to a portion of epidermis

• the whole protoderm can give rise to the whole epidermis

we don't need to prefix the term so long as we're clear that we are talking about portions from the definitions and the hierarchy

Original comment by: cmungall

[planteome-user]

A protoderm can also be present in a plant embryo, therefore I suggest that we modify this definition.

New proposed def.:
protoderm (PO:0006210): A portion of meristem tissue (PO:ID) that develops from the outer layer of an apical meristem (PO:ID) or the outer layer of a plant embryo (PO:ID) and gives rise to a portion of epidermis (PO:ID).

Comment: Protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also call it an epidermis in a meristematic state.

New exact synonym: portion of protoderm tissue

Original comment by: rlwalls2008

[planteome-user]

propose slightly modified revised definition:

protoderm (PO:0006210): A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo (PO:0009009), and gives rise to a portion of epidermis (PO:0005679).

Note: changed "develops from the outer layer" to "is the outer layer"

I am not absolutely sure about this, but it seems more clear- According to our revised definitions, it forms in the first embryo dev stage (globular), so I think it works.

The confusion arises with the child terms, as they are defined using the "is_a"

e.g.:
adaxial protoderm (PO:0006083):
was: A portion of protoderm (PO:0006210) tissue that is the outermost layer of the shoot apical meristem (PO:0020148) and gives rise to the leaf adaxial epidermis (PO:0006018).

comments?

Original comment by: cooperl09

[planteome-user]

I see that there was some discussion about the wording of this earlier. Either way is fine with me, but I think they should be consistent.

Original comment by: cooperl09

[planteome-user]

I need to remember why we said it develops from the outer layer of the SAM. I think it has something to do with the development of protoderm marking the transition from SAM to a primordium. However, I agree that it doesn't make sense with the child term definition. I'll try to look into this more.

Original comment by: rlwalls2008

[planteome-user]

I think we might be better to say it is the outer layer of the embryo or SAM, at a particular stage. Using "develops from the outer layer" makes it sounds like the outer layer is a structure which could be related to the protoderm through 'develops_from'. In reality, though the outer layer is sort of a vague region.

Original comment by: cooperl09

[planteome-user]

Seems to me that the original is fine as is.

Dennis

From: Ramona Walls <rwalls@users.sf.netmailto:rwalls@users.sf.net>
Reply-To: "[obo:plant-ontology-po-term-requests]" <125@plant-ontology-po-term-requests.obo.p.re.sf.netmailto:125@plant-ontology-po-term-requests.obo.p.re.sf.net>
Date: Wednesday, December 3, 2014 6:38 PM
To: "[obo:plant-ontology-po-term-requests]" <125@plant-ontology-po-term-requests.obo.p.re.sf.netmailto:125@plant-ontology-po-term-requests.obo.p.re.sf.net>
Subject: [obo:plant-ontology-po-term-requests] #125 protoderm

I need to remember why we said it develops from the outer layer of the SAM. I think it has something to do with the development of protoderm marking the transition from SAM to a primordium. However, I agree that it doesn't make sense with the child term definition. I'll try to look into this more.

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[plant-ontology-po-term-requests:#125]http://sourceforge.net/p/obo/plant-ontology-po-term-requests/125 protoderm

Status: open
Group: plant anatomy
Labels: Request: Existing term-related
Created: Tue Jun 15, 2010 06:17 PM UTC by Ramona Walls
Last Updated: Tue Dec 02, 2014 10:05 PM UTC
Owner: Ramona Walls

Protoderm PO:0006210 should be is_a meristem, part_of apical meristem.

Current def: The undifferentiated surface cell layer of the primary plant body, which gives rise to epidermis.
New def: A meristem that is part of the apical meristem and gives rise to a portion of epidermis.

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Original comment by: dws409