#400 plant embryo stage (PO:0007631) and child terms

open-accepted
Laurel Cooper
5
2014-07-11
2011-11-17
Ramona Walls
No

At the POC meeting on 11-8-11, we decided to add a term for embryo stage, is_a sporophyte vegetative stage. Proposed definition is based on our definition of plant embryo (PO:0009009).

proposed def. of embryo stage (PO:0025369): A sporophyte vegetative stage that occurs during the interval between the first cell division and one of the following: germination in seed plants, formation of the first true leaf after the cotyledon(s) in pteridophytes, when the apical cell stops dividing and the sporangium begins to develop in bryophytes, or the beginning of the formation of organs (roots, shoot axes, or leaves) in cultured plant embryos.

Comment: Succeeds the zygote stage. The embryo stage generally starts 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 begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa.

Discussion

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  • Ramona Walls
    Ramona Walls
    2011-11-17

    Also see tracker for plant embryo (https://sourceforge.net/tracker/index.php?func=detail&aid=2982384&group_id=76834&atid=835555).

     
  • Ramona Walls
    Ramona Walls
    2011-11-17

    Actually, the PO already has a term for embryo stage: PO:0007631, embryo development stages.

    Def: Stages of development of the embryo. is_a seed development stage

    Subtypes: A zygotic stage, B proembryo stage, C globular stage, coleoptilar stage, D bilateral stage, E expanded cotyledon stage, F mature embryo stage, true leaf formation.

    I destroyed the new term I just created (PO:0025369) and moved PO:000763 to be is_a sporophyte vegetative stage, with the definition proposed above.

     
  • Ramona Walls
    Ramona Walls
    2011-12-14

    At the POC meetings on 11-22-11 and 12-13-11, we discussed whether is better to define stages in terms of structures or structures in terms of stages. We agreed that in general, it is better to define stages in terms of structures (the has_participant relation is preferred over the participates_in relation). This works well for terms like trichome development stage which have a trichome as a primary participant. However, in the case of embryo stage (and other whole plant growth stages), the primary participant is a whole plant that is undergoing certain processes, and the stage is a more fundamental term that defines what those processes are. It would be circular to define the embryo stage as a stage that has as participant an embryo, then define the embryo as a whole plant during a certain time. Better to define the embryo stage as a stage that has as participant a whole plant that is undergoing certain processes (in this case, everything between first cell division and the other events that mark the end of embryo stage).

     
  • Ramona Walls
    Ramona Walls
    2011-12-14

    At the POC meeting on 12-13-11, we agreed to the following definition:

    embryo stage (PO:0007631): A sporophyte vegetative stage that occurs during the interval between the first cell division and one of the following: germination in seed plants, formation of the first true leaf after the cotyledon(s) in pteridophytes, cessation of division of the apical cell and initiation of development of the sporangium in bryophytes, or the beginning of the formation of organs (roots, shoot axes, or leaves) in cultured plant embryos.

    Comment: An embryo stage generally starts 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 begins after the division of a single cell that is not a zygote. The end of an embryo stage varies among taxa.

    Barry suggested that it would be nice if we could have alternate definitions and comments for different taxa, so users would only have to see what they need. We can add that to our wishlist, since there is no way to do it in the current browser.

     
  • Ramona Walls
    Ramona Walls
    2011-12-14

    This should probably be called plant zygote stage.

     
  • Ramona Walls
    Ramona Walls
    2011-12-20

    Last comment should have said "plant embryo stage".

    Accepting and closing this item.

     
  • Laurel Cooper
    Laurel Cooper
    2012-03-19

    I propose the following modification of the definition of embryo stage (PO:0007631):
    "A sporophyte vegetative stage that occurs during the interval between the first cell division and one of the following: germination in seed plants, formation of the first true leaf in pteridophytes, cessation of division of the apical cell and initiation of development of the sporangium in bryophytes, or the beginning of the formation of organs (roots, shoot axes, or leaves) in cultured plant embryos."

    Note: I took out " after the cotyledon(s)", as pteridophytes do not have cotyledons.

     
  • Laurel Cooper
    Laurel Cooper
    2012-03-19

    After further reflection and revision of plant embryo (PO:0009009): I propose a new revised, annotated def'n:

    plant embryo stage (PO:0007631):
    A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the first cell division of the plant zygote (PO:0000423) and beginning of the next stage of growth, which varies among taxa. In seed plants, the plant embryo stage ends with seed germination stage (PO:0007057). In pteridophytes, the plant embryo stage ends with the formation of the first vascular leaf (PO:0009025).
    In bryophytes, the (plant) embryo stage ends when the (embryo) apical cell (PO:0025284) stops dividing and the sporangium (PO:0025094) begins to develop.

    In cultured plant embryos (PO:0000010), the (plant) embryo stage ends when a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or leaf (PO:0025034) begins to form.

     
  • Laurel Cooper
    Laurel Cooper
    2012-03-20

    Revision to the def'n:
    "In bryophytes, the plant embryo stage ends when the seta meristematic apical cell (PO:0030016) stops dividing and the sporangium (PO:0025094) begins to develop."

    I think the plant embryo stage in bryophytes would end when the seta starts to elongate- maybe we need something like a "seta elongation sporophyte vegetative stage". Raven et al calls it the "young sporophyte".

    Sporangium formation should mark the beginning of the sporophyte reproductive stage PO:0007130.

     
  • Ramona Walls
    Ramona Walls
    2012-03-21

    For pteridophytes:

    The cotyledon is defined as "A (vascular) leaf formed at the first node of a sporophyte." so it is appropriate to refer to the cotyledon of a fern. However, the term is not used frequently for ferns, and the few papers I could find on fern embryology refer to the "first leaf". They are the same thing, just with different names. One solution is to add "first vascular leaf" and "first leaf" as synonyms to cotyledon. An alternative is to put a taxonomic restriction on cotyledon, so it is only used for seed plants and then say "first vascular leaf" for ferns.

    For bryophytes:

    It will not work to say that the embryo stage ends when the seta apical cell stops dividing, because many bryophytes lack a seta. In fact, there are also some that lack an apical cell, and just have a globular embryo. It would be better to simply say that the embryo stage ends when formation of the sporangium begins. This means that the embryo stage is concordant with the sporophyte vegetative stage in bryophytes, but that is okay and is consistent with the treatment in the literature.

    Based on this, the seta apical cell should in fact be a type of embryonic apical cell. There is nothing wrong with leaving it as a sporophyte apical cell, but it would be more specific to say it occurs during the embryo stage.

    Re. seta elongation: The seta generally continues to elongate after the sporangium has started to develop, so much of seta elongation occurs during the sporophyte reproductive stage. This can happen both by expansion cells that arose during the embryo stage and by growth from an intercallary meristem in the seta. If we are going to have a stage to describe the elongation of the seta, I think it would be better to create a plant organ development stage subtype for seta development stage, and have seta elongation stage be a subtype of that, than to try to add seta elongation stage into the whole plant development stage. I would suggest waiting until someone needs the term before we add it, so that we can add it in a way that is consistent with how it is used, once someone actually starts using it.

    Sporophyte reproductive stage (PO:0007130) is already defined as beginning with the initiation of a sporangium.

     
  • Ramona Walls
    Ramona Walls
    2012-03-21

    I suggest we go back to a slightly modified version of the accepted definition, which specifically references other PO terms, as Lol suggested:

    plant embryo stage (PO:0025369): A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and one of the following: the beginning of a seed germination stage (PO:0007057) in seed plants, formation of the first true vascular leaf (PO:0009025) after the first leaf/cotyledon (PO:0020030) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes*, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in cultured plant embryos.

    comment: Succeeds a plant zygote stage (PO:0001097). The plant embryo stage generally starts after the first division of a zygote, but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa.

    *We could say that sporangium development in bryophytes begins with the development of the ampithecium (PO:0030084), but I think that might make the definition too complicated. Maybe better to just add sporangium development stages at some point.

     
  • Laurel Cooper
    Laurel Cooper
    2012-03-21

    On the 3-21-12 conf call, we agreed to the following definition:
    plant embryo stage (PO:0025369): A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and one of the following: the beginning of a seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).

    comment: Succeeds a plant zygote stage (PO:0001097). The plant embryo stage generally starts after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa.

    Accepted and closing this tracker.

     
  • Laurel Cooper
    Laurel Cooper
    2012-04-16

    I propose a slight modification to the definition, based on a discussion between BS and LC (by email). Change "a" to "the", since there is only one seed germination stage.

    revised def'n: A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and one of the following: the beginning of THE seed germination stage (PO:0007057) in seed plants,....etc

     
  • Laurel Cooper
    Laurel Cooper
    2013-10-21

    Slight revisions were made to the children of plant embryo stages:

    B proembryo stage (PO:0001180)
    C globular stage (PO:0001185)
    D bilateral stage (PO:0004507)
    E expanded cotyledon stage (PO:0001078)
    F mature embryo stage (PO:0001081)
    true leaf formation stage (PO:0001095)

    Removed the letters in the names and added preceded_by to order the stages.

     
  • Ramona Walls
    Ramona Walls
    2013-12-17

    I suggest the following name changes, just for clarity:

    globular stage (PO:0001185) >> globular embyro stage
    bilateral stage (PO:0004507) >> bilateral embryo stage
    expanded cotyledon stage (PO:0001078) >> expanded cotyledon embryo stage
    true leaf formation stage (PO:0001095) >> true leaf formation embryo stage

    If you think it is better to add "development" before stage in each name, that would be okay too, but I think I prefer it without, just to keep the names slightly shorter.

     
  • Laurel Cooper
    Laurel Cooper
    2013-12-17

    I think we can avoid putting "development" before stage in each of these names, but I suggest it should be added to the parent term:

    plant embryo stage (PO:0007631)- propose revised name: 'plant embryo development stage',

    Also, I think the child terms should be renamed as 'plant embryo ...', rather than 'embryo' to avoid confusion, and correspond with the PAE term:

    • proembryo stage (PO:0001180)- >> plant embryo proembryo stage (although its a bit repetitive, should include for completeness)- or maybe 'plant proembryo stage'?

    • globular stage (PO:0001185) >> plant embryo globular stage

    The following are very dicot-specific (Arabidopsis-) and do not work for the grasses and presumably other monocots:
    - bilateral stage (PO:0004507) >> plant embryo bilateral stage
    - expanded cotyledon stage (PO:0001078) >> plant embryo expanded cotyledon stage

    Here is an image from Itoh et al, 2005 showing rice embryo development: http://pcp.oxfordjournals.org/content/46/1/23/F2.expansion.html

    • true leaf formation stage (PO:0001095) >> plant embryo leaf primordium formation stage
      This proposed name will work for the grasses as well. Corresponds to the 5 DAP rice embryo (Itoh fig. 2; Panel F).

    All the definitions need to be revised as well.

     
  • Ramona Walls
    Ramona Walls
    2013-12-18

    I think using names like "plant embryo bilateral stage" is a good idea. For proembryo stage, I prefer "plant proembryo stage" to "plant embryo proembryo stage".

     
  • Laurel Cooper
    Laurel Cooper
    2014-07-09

    Renamed plant embryo stage (PO:0007631): plant embryo development stage (PO:0007631)
    No change in the definition

     
    • Ramona Walls
      Ramona Walls
      2014-07-11

      I suggest adding the following to the comment:
      "No single species undergoes all of the sub-stages of plant embryo development stage listed here."

       
      • Laurel Cooper
        Laurel Cooper
        2014-07-14

        Agreed, with a slight modification:
        Added comment: No plant species undergoes all of the sub-stages listed here.

         
        Last edit: Laurel Cooper 2014-07-14
        • Laurel Cooper
          Laurel Cooper
          2014-07-14

          Added relation: plant embryo development stage (PO:0007631) preceded_by plant zygote stage (PO:0001097).

           
          • Laurel Cooper
            Laurel Cooper
            2014-07-17

            Moved the preceded_by relation from: plant embryo development stage preceded_by plant zygote stage to sporophyte vegetative stage preceded_by plant zygote stage.

             
  • Laurel Cooper
    Laurel Cooper
    2014-07-09

    Renamed proembryo stage (PO:0001180): plant proembryo stage
    was: Early embryo development from two cell stage to a multicellular globular stage before three main tissue systems are differentiated.

    revised def'n: A plant embryo development stage (PO:0007631) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and the onset of the plant globular embryo stage (PO:0001185).

    Add comment: The plant proembryo stage occurs prior to the differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)).

     
    • Ramona Walls
      Ramona Walls
      2014-07-10

      This one is good just as you propose.

       
  • Laurel Cooper
    Laurel Cooper
    2014-07-09

    -Renamed:
    globular stage (PO:0001185): plant embryo globular stage
    was: During this stage the embryo proper retains radial symmetry (increasing in diameter), and three main tissue systems are established.

    revised def'n: A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry.
    Add comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.

     
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