plant embryo stage (PO:0007631) and child terms

planteome-user commented 13 years ago

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.

Reported by: rlwalls2008

Original Ticket: obo/plant-ontology-po-term-requests/400

planteome-user commented 13 years ago

Also see tracker for plant embryo (https://github.com/Planteome/plant-ontology/issues/92).

Original comment by: rlwalls2008

planteome-user commented 13 years ago

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.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

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).

Original comment by: rlwalls2008

planteome-user commented 12 years ago

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.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

This should probably be called plant zygote stage.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

Last comment should have said "plant embryo stage".

Accepting and closing this item.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

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.

Original comment by: cooperl09

planteome-user commented 12 years ago

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.

Original comment by: cooperl09

planteome-user commented 12 years ago

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.

Original comment by: cooperl09

planteome-user commented 12 years ago

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.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

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.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

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.

Original comment by: cooperl09

planteome-user commented 12 years ago

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

Original comment by: cooperl09

planteome-user commented 11 years ago

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.

Original comment by: cooperl09

planteome-user commented 10 years ago

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.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

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.

Original comment by: cooperl09

planteome-user commented 10 years ago

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".

Original comment by: rlwalls2008

planteome-user commented 10 years ago

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

Original comment by: cooperl09

planteome-user commented 10 years ago

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)).

Original comment by: cooperl09

planteome-user commented 10 years ago

-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.

Original comment by: cooperl09

planteome-user commented 10 years ago

Renamed: bilateral stage (PO:0004507): plant embryo bilateral stage was: Change from radial to bilateral symmetry takes place during this embryonic stage.

revised def'n: A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) develops bilateral symmetry.

Original comment by: cooperl09

planteome-user commented 10 years ago

renamed: coleoptilar stage (PO:0001094): plant embryo coleoptilar stage Was: The coleoptilar primordium, shoot apical meristem and radicle are formed in the embryo of grasses.

revised def'n: A plant embryo development stage (PO:0007631) during which a primordium (PO:0025127) of the plant embryo coleoptile (PO:0025286), a plant embryo shoot apical meristem (PO:0006362) and the plant embryo radicle (PO:0025296) are formed. Added comment: This stage occurs in grasses and other monocots.

Original comment by: cooperl09

planteome-user commented 10 years ago

Renamed of child terms, but still need to work on definitions: -expanded cotyledon stage (PO:0001078): plant embryo expanded cotyledon stage

mature embryo stage (PO:0001081): mature plant embryo stage
true leaf formation stage (PO:0001095); plant embryo true leaf formation stage

Original comment by: cooperl09

planteome-user commented 10 years ago

plant embryo expanded cotyledon stage (PO:0001078):

was: The stage during which embryo axis and cotyledons rapidly elongate as a result of cell division and cell expansion. Revised: A plant embryo development stage (PO:0007631) during which a plant embryo axis (PO:0019018) and embryo cotyledons (PO:0025470) rapidly elongate as a result of (GO:0051301) and cell expansion (GO:0016049).

Problem is that the label does not really fit the definition- it implies that teh cotyledons are already expanded.

Original comment by: cooperl09

planteome-user commented 10 years ago

mature plant embryo stage (PO:0001081) Was: Stage at which the embryo is fully developed. Revised: A plant embryo development stage (PO:0007631) at which the plant embryo (PO:0009009) is fully developed.

Problem is that this is more of a landmark than a stage.

Original comment by: cooperl09

planteome-user commented 10 years ago

plant embryo true leaf formation stage (PO:0001095):
Was: During this stage, the protrusion of the first leaf primordia takes place in succession.

Revised: A plant embryo development stage (PO:0007631) during which a vascular leaf primordium (PO:0000017) develops.

problem - The first leaf is the cotyledon, so we need to know if by "true leaf", it was meant the first leaf after the cotyledons. We do not have a term plant embryo true leaf- (it sounds more like a seedling stage). Also "In succession" makes no sense.

Again, the label does not fit the definition: is the "true" leaf forming, or just the primordium??
If the def'n is referring to the cotyledon primordium (PO:0000015), then this term is in the wrong place in the hierarchy.

Original comment by: cooperl09

planteome-user commented 10 years ago

I guess if we are going to start working on these definitions, we should go ahead an define them more precisely, so that is clear when one ends and one starts, similar to the flower development stages. I will put specific suggestions on each term.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

This one is good just as you propose.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

We need a way to distinguish the end of the proembryo and the beginning of this stage. I think the end can be distinguished by bilaterality. I will have to do some research to see if there are differences in when a proembryo stage ends across land plants.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

Not sure what happened when I posted this before, so it may show up twice.

According to Howell 1998, "Proembryo is the term given to describe the embryo up to the stage when the protoderm can be recognized, which is usually the globular stage."

Original comment by: rlwalls2008

planteome-user commented 10 years ago

Of course, the problem with this is that we define the protoderm as arising from an apical meristem, and that is not the case in the embryo. Seems like some authors refer to it as an epidermis and some as a protoderm at this stage. I am not an expert in this, but I think I feel more comfortable with calling it a protoderm rather than a fully developed epidermis. In that case, I suggest modifying the definition of protoderm, which I will post on isssue 125.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

New proposed definition: plant embryo globular stage (PO:0001185): A plant embryo development stage (PO:0007631) that occurs during the interval between when a protoderm (PO:0006210) is first recognizable in a plant embryo (PO:0009009) and the onset of a plant embryo bilateral stage (PO:0004507).

New comment: During the plant embryo globular stage, a plant embryo proper (PO:0000001) increases in diameter through cell division but retains radial symmetry, and differentiation of the three main tissue systems (vascular system (PO:0000034), epidermis (PO:0005679), and the portion of ground tissue (PO:0025059)) begins. During a plant embryo bilateral stage, the embryo begins to develop bilateral symmetry. Preceded by a plant proembryo stage (PO:0001180).

Original comment by: rlwalls2008

planteome-user commented 10 years ago

New proposed definition:

plant embryo bilateral stage (PO:0004507): A plant embryo development stage (PO:0007631) that occurs during the interval between the transition from radial to bilateral symmetry in a plant embryo proper (PO:0000001) and the onset of a plant embryo expanding cotyledon stage (PO:0001078).

new comment: During a plant embryo expanding cotyledon stage, the embryo axis (PO:0019018) and embryo cotyledons (PO:0025470) begin to elongate. A plant embryo bilateral stage contains the stage commonly known as the heart stage. Preceded by a plant embryo globular stage (PO:0001185).

Ref: PMID:24784759

Original comment by: rlwalls2008

planteome-user commented 10 years ago

The problem here is that the name/definition combination is ambiguous and we don't know the original intentions of the creators. I agree that the definition Lol proposed is perfectly valid interpretation, but I also think it could be interpreted in other ways.

In interpreting, my main concern is with how the term has been used to date. Looking at the annotations on this term, all of them come from Schmid et al.'s gene expression map. Looking at their supplementary table 1, I can see that the tissue source was cotyledon, with no indication of whether it was expanding or fully formed. However, because these annotations were created by TAIR, and because they placed many annotations from the same study on mature embryo stage, I assume that they read the definitions for both and had a reason to choose expanded cotyledon stage over mature embryo stage. The mature embryo stage is defined as when the embryo is fully formed, which implies that the cotyledons are fully formed, which implies that they are not fully formed in this stage, which implies (yes, I realize this is a triple chain of weak inference) that TAIR chose this stage because the cotyledons were still developing. Therefore, I suggest that we interpret this term to mean the one during which the cotyledons and hypocotyl are developing, and that it ends once they stop developing.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

new proposed name and definition: plant embryo expanding cotyledon stage (PO:0001078): A plant embryo development stage (PO:0007631) that occurs during the interval between the beginning of rapid elongation of the plant embryo axis (PO:0019018) and embryo cotyledons (PO:0025470) and the onset of a plant embryo true leaf formation stage (PO:0001095), when present, or a mature plant embryo stage (PO:0001081).

comment: During this stage, the plant embryo (PO:0009009) continues to undergo a process of developmental growth involved in morphogenesis (GO:0060560), which ends with the beginning of a mature plant embryo stage. For species that develop true leaves, that is, the vascular leaves that develop after the cotyledon(s), developmental growth involved in morphogenesis may continue in the plant embryo true leaf formation stage. For species in which true leaves do not develop in the embryo, the plant transitions directly from a plant embryo expanding cotyledon stage to a mature embryo stage. Preceded by a plant embryo bilateral stage.

Ref: PMID:24784759

Original comment by: rlwalls2008

planteome-user commented 10 years ago

We added a term for plant embryo dormant stage (see issue http://sourceforge.net/p/obo/plant-ontology-po-term-requests/426/). I think, based on "normal" plant embryo development, the plant embryo undergoes dormancy after it has matured. We can either make these two stages successional - mature embryo >> dormant embryo - or make plant embryo dormant stage a subclass of mature plant embryo stage.

Right now I vote for making it a subclass, because to me it makes more sense to define the mature stage as spanning from when the embryo is fully developed until germination. However, I could easily be convinced that the other way is better, because I don't have access to any books on embryo development today and I am not an expert on this.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

This approach is consistent with the current annotations on plant embryo dormant stage from Footitt et al.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

New proposed definition, based on plant embryo dormant stage being a subclass of mature plant embryo stage:

mature plant embryo stage (PO:0001081): A plant embryo development stage (PO:0007631) during the interval between when a plant embryo (PO:0009009) has stopped developmental growth involved in morphogenesis (GO:0060560) and and one of the following: the beginning of the 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: In some seed plants, this occurs some time after the fruit ripening stage (PO:0025502) and after the dispersal of the seed. This stage may be very short in plants that do not enter a plant embryo dormant stagem (PO:0025377).

note 1: I did not add preceded by plant embryo expanding cotyledon stage, because it is not in all taxa.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

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

Original comment by: rlwalls2008

planteome-user commented 10 years ago

I am pretty sure that what is meant here is the first leaf after the cotyledon. That is how the term is commonly used. See e.g., http://www.plantphysiol.org/content/165/2/670.long. I don't think we need to have a term for true leaf in order to use the phrase true leaf in the name of this term, as long as we define it clearly.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

new proposed definition:

plant embryo true leaf formation stage (PO:0001095): A plant embryo development stage (PO:0007631) during the interval between the beginning of the formation of the first vascular leaf primordium (PO:0000017) after the cotyledons and the onset of a mature plant embryo stage (PO:0001081).

comment: A true leaf is vascular leaf that forms after the cotyledon(s). Not all species form true leaves in the embryo. Preceded by a plant embryo expanded cotyledon stage (PO:0001078).

note: I am not sure if any grasses develop true leaves in the embryo, in which case this could also be proceded by a coleoptilar stage.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

This should be reworded as an interval, but I am not sure exactly when it starts and ends. In the dev brower, coleoptilar stages is a subclass of bilateral stage. That makes sense because the development of the coleoptile primordium, SAM, and embryo radicle begin during the bilateral stage. However I wonder if this stage isn't meant to describe the embryo stage when a coleoptile is forming, in which case it would follow the bilateral stage.

The annotations to this stage come from Sekhon et al. 2011, but when I look at the table Mary used to map their stages to PO stages, I don't even see embryo coleoptilar stage uses. I may not have the most current version of that table, though.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

We have annotations to true leaf development stage for maize, so I guess they do.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

See proposed definition of plant embryo dormant stage at https://sourceforge.net/p/obo/plant-ontology-po-term-requests/426/#b75d/e79b.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

Note that some of the preceded by relations that I have proposed are different from the ones currently in the dev browser.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

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

Original comment by: cooperl09

planteome-user commented 10 years ago

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

Original comment by: cooperl09

planteome-user commented 10 years ago

I think referring to the development of the protoderm is fine, but we should retain the reference to the globular shape (radial symmetry) as many curators will most likely just have an image, not microscopic detail of the developing embryo.

From the classic paper: Goldberg et al, 1994 Science: "Two critical events must occur after the embryo proper forms: (i) regions along the longitudinal apical-basal axis must differentiate from each other and generate embryonic organ systems, and (ii) the three primordial tissue layers of the embryo need to be specified. Both of these events take place during the globular-heart transition phase (Fig. 2 and Table 1). The embryo proper has a spherical shape during the proembryo and globular stages (Fig. 2). The first visible cell differentiation events occur at the 16-cell stage when the protoderm, or outer cell layer of the embryo proper, is produced and the hypophysis forms at the top of the suspensor (Fig. 2). Subsequent cell differentiation events within the embryo proper result in the production of an inner procambium tissue layer and a middle layer of ground meristem cells (Fig. 2)."

Propose re-revised def'n: plant embryo globular stage (PO:0001185): A plant embryo development stage (PO:0007631) that occurs during the interval between when a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry,(with the concomitant formation of a protoderm (PO:0006210)), and the onset of a plant embryo bilateral stage (PO:0004507).

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.

I would avoid describing the plant embryo bilateral stage here as it is confusing to the user. Could also mention the development of the embryo hypophysis (PO:0020109).

Original comment by: cooperl09

planteome-user commented 10 years ago

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

Original comment by: cooperl09

planteome-user commented 9 years ago

Propose revised name: plant embryo cotyledonary stage (PO:0001078): This parallels the plant embryo coleoptilar stage (PO:0001094) and encompasses the confusion as to whether or not the cotyledons have already expanded or are in the process of expanding. Basically, they are present.

Propose revised definition: plant embryo cotyledonary stage (PO:0001078): A plant embryo development stage (PO:0007631) that occurs during the interval between the beginning of rapid elongation of the plant embryo axis (PO:0019018) and plant embryo cotyledons (PO:0025470), and the onset of a plant embryo true leaf formation stage (PO:0001095), when present, or a mature plant embryo stage (PO:0001081).

Basically as you had it

Slightly revised comment: During this stage, the plant embryo (PO:0009009) continues to undergo a process of developmental growth (as a result of both cell division (GO:0051301) and cell expansion (GO:0016049), which ends with the onset of a mature plant embryo stage (PO:0001081). For species that develop true leaves in the plant embryo, (vascular leaves (PO:0009025) that develop after the cotyledons (PO:0020030) or coleoptile (PO:0020033)), growth may continue in the plant embryo true leaf formation stage (PO:0001095). For other species, the plant embryo transitions directly from a plant embryo cotyledonary stage (PO:0001078) to a mature plant embryo stage (PO:0001081).

Original comment by: cooperl09

Planteome / plant-ontology

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