POC Conf. Call 10-28; 11-5 2013

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POC meeting, Skype Conference Call; Date: Tuesday Oct 29th, and Nov 5th 2013 10:30am PDT/1:30pm EDT

In attendance: Laurel Cooper (OSU), Marie Alejandra Gandolfo (Cornell)


Root meristems

Discussion continued from POC_Conf._Call_10-15-13#root_apical_meristem_PO:0020147_and_child_terms -

We need to revise root: (since shoot-borne roots are also roots)

  • root (PO:0009005):: A plant axis (PO:0025004) that is part of a root system (PO:0025025).

Comment: Commonly thought of as one of the three basic parts of the seed plant body. A plant structure that is usually underground and does not bear leaves and only rarely shoots, is usually more or less positively geotropic, is endogenous in origin, indeterminate in growth and often with secondary thickening.

related tracker: ISSR requests for root terms from Rich Zobel

Revised def'n: A plant axis (PO:0025004) that is usually positively geotropic and found below ground, lacks shoot axis nodes (PO:0005004) and does not bear leaves (PO:0025034).

- "Usually descending axis, normally below ground, serves to anchor the plant and absorb and conduct water and minerals into it (Raven 5th edition)"

-"The four major functions of roots are 1) absorption of water and inorganic nutrients, 2) anchoring of the plant body to the ground, and supporting it, 3) storage of food and nutrients, 4) vegetative reproduction. In response to the concentration of nutrients, roots also synthesise cytokinin, which acts as a signal as to how fast the shoots can grow. Roots often function in storage of food and nutrients. The roots of most vascular plant species enter into symbiosis with certain fungi to form mycorrhizas, and a large range of other organisms including bacteria also closely associate with roots. (wikipedia)"

-"That portion of the plant axis lacking nodes and leaves and usually found below ground. (Harris and Harris)

Propose revised definition: root (PO:0009005): A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004), grows indeterminately and is usually positively geotropic.

Revised Comment: Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the ground, and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually found underground, although there are many exceptions, such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034).

  • root system (PO:0025025): A collective plant organ structure (PO:0025007) that produces root apical meristems (PO:0020147) and the plant structures that arise from them.

This may or may not include the shoot-borne roots, depending on how the RAM is defined.

Revised def'n: root system (PO:0025025): A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof.

This wording is necessary to include the parts of the root system that do not arise directly from the root meristems- for example: the products of secondary growth from the root vascular cambium PO:0025438, root procambium (PO:0006307), quiescent center (PO:0020149), or the root cork cambium (PO:0025436).

  • shoot system (PO:0009006): A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them.

Revised def'n: A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013), the plant structures (PO:0009011) that arise from them.

    • Problem is this would also include the shoot-borne roots. Perhaps should refer to the shoot system meristem (PO:0006079)??

Actually, this term is somewhat redundant- it should either be inclusive of all the meristems of the shoot system, or it should be obsoleted.

root apical meristem PO:0020147 and child terms

  • apical meristem (PO:0020144): A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root system (PO:0025025).

Revised def'n: A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025).

  • Issue with child terms root apical meristem PO:0020147: should these be "gives rise to a xxxx root- not part of a xxxx root.?
  • root apical meristem (PO:0020147): A root meristem (PO:0006085) formed at the apex of a root (PO:0009005), including those originating from an lateral root apical meristem (PO:0006020).

Revised def'n: root apical meristem (PO:0020147): A root meristem (PO:0006085) located at the root tip (PO:0000025), behind the root cap (PO:0020123).

All roots have a root cap, even the aerial roots.

Should be: A root apical meristem (PO:0020147) gives rise to a primary root (PO:0020127).

Should be: A root apical meristem (PO:0020147) gives rise to a lateral root (PO:0020121).

adventitious root apical meristem (PO:0006021) and associated terms

  • Currently: adventitious root apical meristem (PO:0006021): A root apical meristem (PO:0020147) that is part of an adventitious root.

Revised name and def'n: shoot-borne root meristem (PO:0006021): A root apical meristem (PO:0020147) that gives rise to a shoot-borne root (PO:0000042).

-Added missing SF xref: OBO_SF2_PO: 163 added -part_of relation to shoot-borne root (PO:0000042)

broad synonym: adventitious root (not problem with existing definition of root, below)

We should remove the phrase 'in the post-embryonic stage'.

Revised def'n: shoot-borne root (PO:0000042): A root (PO:0009005) that develops from shoot axis (PO:0025029) tissue.

-Removed in the post-embryonic phase- Are there roots that form from shoot axis tissue in the embryonic phase? Check with dws

is_a shoot-borne root

Revised name and def'n: shoot-borne nodal root (PO:0003005): A shoot-borne root (PO:0000042) that forms at a shoot axis node (PO:0005004).

Created new term:

Revisions to the SA meristem layers terms:

- Are these specific to the shoot system? Otherwise, we should use the more general term:

  • meristem L1 (PO:0009020): The outermost layer of a shoot apical meristem that gives rise to a shoot epidermis. [source: GR:Pankaj_Jaiswal, PMID:12221985] Comment: None
    • shoot system epidermis (PO:0006035): A portion of epidermis that is part of a shoot system. Comment: Often interrupted by stomata and other structures. The shoot epidermis is different from the root epidermis in its origin, function and structure.
  • meristem L2 (PO:0009021)]: A cell layer directly beneath a meristem L1 layer in a shoot apical meristem which gives rise to subepidermal tissue. Comment: None
  • meristem L3 (PO:0009022): A multicellular layer beneath a meristem L2 layer in a shoot apical meristem which gives rise to internal tissues of leaf and stem. Comment: None

Revised names and def'ns:

  • meristem L1 layer (PO:0009020): A portion of meristem tissue (PO:0009013) that is the outermost layer of a shoot apical meristem (PO:0020148) and gives rise to a shoot system epidermis (PO:0006035). comment: The cells of the meristem L1 layer divide in a strictly anticlinical fashion.

Add synonym: 'tunica'

Comment: Often interrupted by stomatal complexes (PO:0002000) and other structures. The shoot system epidermis is different from the root epidermis (PO:0006036) in its origin, function and structure.

Need to revise 'root epidermis (PO:0006036)' to match this

  • meristem L2 layer (PO:0009021): A portion of meristem tissue (PO:0009013) directly beneath a meristem L1 (PO:0009020) layer in a shoot apical meristem (PO:0020148) which gives rise to ground tissue (PO:0025059). Comment: Cells in the first subepidermal layer, the L2, divide in a largely anticlinal fashion, forming a completely separate population of cells from the other cell layers. Within developing organs, the meristem L2 layer divides anticlinally and periclinally.

Note: "Cells in the first subepidermal layer, the L2, also divide in a largely anticlinal fashion, forming a completely separate population of cells from the other cell layers. Within developing organs, the L2 divides anticlinally and PERICLINALLY. (Clark 2001).

  • meristem L3 layer (PO:0009022): A portion of meristem tissue (PO:0009013) beneath a meristem L2 layer (PO:0009021) in a shoot apical meristem (PO:0020148) which gives rise to internal tissues of leaf and stem. Comment: The meristem L3 layer cells frequently divide in various orientations. (from Clark 2001)

Note: The L3 layer is different, in that whereas the apical edge of the cell layer — the boundary between the L2 and L3 layers — is clearly defined, L3 cells frequently divide in various orientations. The net flow of cells is from the centre and the apex to the flanks and the basal regions of the shoot meristem (Clark 2001).

Cell signalling at the shoot meristem Steven E. Clark


ground meristem

Interestingly, we have no term "ground meristem" but it is mentioned in the comment on portion of ground tissue:

  • portion of ground tissue (PO:0025059): Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015). Comment: Develops from the ground meristem (eg, meristem L2 and meristem L3).

This definition is problematic because now portion of plant tissue (PO:0009007) has many other children that are not part of the ground tissue, such as bark (PO:0004518), chalaza (PO:0020056) seed coat (PO:0009088), and many other examples. PoPT has more than 50 is_a children.

This definition does not work if the L1, L2 and L3 are specific to the SAM.

  • Revised: portion of ground tissue (PO:0025059): Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015). Comment: Develops from the ground meristem.

-Added comment: The L2 and L3 layer of the meristem are part of the shoot system ground meristem (PO:0025595).

Upcoming meetings and Presentations 2013-2014:

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

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

Systems Biology and Ontologies Workshop

Link to: Googledoc

Confirmed speakers:

  • Trey Ideker, UC San Diego
  • Barbara Ambrose, NYBG
  • Stefan Rensing, Marlburg Germany
  • Sushma Naithani
  • Jim Beynon, Warwick, UK
  • Laurel Cooper

Next meeting scheduled for Tuesday, Nov 18th, 2013 at 10:30am Pacific/1:30pm Eastern

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