plant embryo and its children

[planteome-user]

Def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

-has no is_a parent, propose making it is_a whole plant?

Reported by: cooperl09

Original Ticket: obo/plant-ontology-po-term-requests/92

[planteome-user]

good with me.

I don't know if there is a terminological problem in that some people might consider the plant post-embryonic? I have no idea, just anticipating possible objections

Original comment by: cmungall

[planteome-user]

Need to work on definition, because there are embryos that occur outside seeds (in non-seed plants)!

Original comment by: rlwalls2008

[planteome-user]

is_a whole plant is_a collective plant structure

Also this is coming to a situation where you may want to introduce new relationship 'contained_in'

if that's the way to go you will have

develops_from zygote contained_in seed [which is true most of the time, with exception to non-seed plant]

Original comment by: jaiswalp

[planteome-user]

"contained_in seed [which is true most of the time, with exception to non-seed plant]"

Really!?!

Isn't the whole point of this exercise to be inclusive of non-seed plants?

Original comment by: rlwalls2008

[planteome-user]

I think its a intransitive aspect. So the embryo contained_in seed is intransitive., means not always true.

Original comment by: jaiswalp

[planteome-user]

There are also adventitious embryos and embryos that form in liquid cell cultures. They have identical development but are not directly from zygotes.

Original comment by: dws409

[planteome-user]

We have the term in cultured embryo to deal with in vitro embryos.

Cultured embryo PO:0000010: Definition: In vitro isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). [source: TAIR:ki] Child: cultured somatic embryo

Original comment by: rlwalls2008

[planteome-user]

Raven et al. define embryo as: a young sporophytic plant, before the start of a period of rapid growth (germination in seed plants).

We should try to find a physical form/state that demarkates the end of the embryo, instead of the vague "before ..rapid growth". In seed plants it could be germination. Can we define an equivalent state in non-seed plants?

Original comment by: rlwalls2008

[planteome-user]

In response to pj37's comment below:

1. I don't think that being transitive or intransitive has bearing on whether or not a relationship should apply to all instances of a class.

2. According to Smith et al. (2005 Genome Biology), contained_in should be applied as a relationship between a material structure and an immaterial structure (such as brain contained_in skull cavity). Since embryo and seed are both material structures, we should use part_of, rather than contained_in. However, I really don't think we should use this, since some embryos are not part of a seed.

Original comment by: rlwalls2008

[planteome-user]

POC Conf call: A young sporophyte before the period of rapid growth.

Parentage: is_a sporophyte (making it is_a whole plant) usually develops_from zygote

We should try to find a physical form/state that demarcates the end of the embryo, instead of the vague "before ..rapid growth". In seed plants it could be germination. Can we define an equivalent state in non-seed plants?

Original comment by: cooperl09

[planteome-user]

I am still not too happy with this definition- 'young' has the same issues as using 'mature'.

Proposed def'n: A sporophyte in the early stages of growth and differentiation, consisting of precursor tissues for the leaves, stem (see epicotyl/hypocotyl) and root (see radicle), as well as one or more cotyledons.

Original comment by: cooperl09

[planteome-user]

Proposed def'n: A sporophyte in the early stages of growth and differentiation, consisting of precursor tissues for the leaves, stem (see epicotyl/hypocotyl) and root (see radicle).

We could mention the cotyledons in a comment- specific to flowering plants

Original comment by: cooperl09

[planteome-user]

We may be able to use contained_in embryo contained in archegonium for all plants (although technically speaking, the archegonium is a material entity, and the embryo is contained in a chamber in the archegonium).

Original comment by: rlwalls2008

[planteome-user]

How does FMA define the relationship between the ovary/fallopian_tube/womb and the embryo. This may be a god precedence.

> Lol: A sporophyte in the early stages of growth.."

You need to define the boundaries of that stage start-stop. In my knowledge at least for flowering plants it starts from the formation of the formation of zygote to the germination. = embryonic stage.

Also add MAY consist of --------------^^^^^

> LOL: I am still not too happy with this definition- 'young' has the same issues as using 'mature'.

You can use 'juvenile'.

Original comment by: jaiswalp

[planteome-user]

The term juvenile is sometimes used (at least in flowering plants) for post-embryonic plants that are pre-reproductive - during the period of vegetative growth before flowering and sometimes marked by a morphological shift such as a change in leaf form.

Original comment by: rlwalls2008

[planteome-user]

There are several issues with this definition. 1- I disagree with Ramona "that may be able to use contained_in embryo contained in archegonium for all plants (although technically speaking, the archegonium is a material entity, and the embryo is contained in a chamber in the archegonium). I am against this since origin and development of the archegonium and the seed (for seed plants) are completely different. 2- The term "embryo" implies the hypocotyl-root axis bearing the root apical meristem and the shoot apical meristem and the cotyledon/s, sometimes other structures as well. Depending on the taxon, the embryo can be few cells (orchids) or a complete "mini-plant". The problem here is "when" we consider an embryo to be an embryo. It starts when it is initiated by the division of the zygote? (embryo development). Independently of the origin and development, all embryos become differentiated at maturity into three main parts (root tip, stem tip and cotyledon/s) See Pankaj comment from yesterday. Remember that after syngamy the zygote sometimes undergoes a period of rest as well. So we have define "proembryo" for the structure that is formed from the first division of the zygote until it reaches the full embryo stage. 3- we need to also include notes or comments on abnormal embryos such as those that originate from cells of the embryo sac and not from the egg and embryos arising from cells outside the embryo sac. 4- We need to consider to add also the term Polyembryony

Original comment by: magandolfo

[planteome-user]

Polyembryony will have at least three states: simple polyembryony and cleavage polyembryony and probably apomixtic polyembryony

Original comment by: dws409

[planteome-user]

Before tissue differentiation.

This should also work for adventitious (apomictic) embryos and cultured embryos, and for all plant groups.

Original comment by: dws409

[planteome-user]

I am not sure what the definition is now.

"A young sporophyte contained within a seed."

The one above only works for seed plants.

We need to broaden in for the rest of the land plants.

A young sporophyte contained within the female reproductive tissue.

Original comment by: dws409

[planteome-user]

A whole plant in the post zygotic, sporophytic phase, consisting of undifferentiated tissues.

This is a working definition- comments

Original comment by: cooperl09

[planteome-user]

'....consisting of undifferentiated tissues.' may not work. Sometimes, it has differentiated tissue portions, cell types and may have differentiated organs in early or juvenile phases. Majority have an apical meristem.

A post zygotic, multicellular plant structure prior to its development into early stages of a self sustainable whole plant.

Original comment by: jaiswalp

[planteome-user]

Better to say that it consists of not yet fully differentiated tissues, rather than say undifferentiated.

Potential problem with saying "prior to its development into early stages of a self sustainable whole plant" is that many embryos (in non-vascular plants) never develop into self-sustaining plants -- they are always dependent on gametophyte.

Original comment by: rlwalls2008

[planteome-user]

Here are two things that might resolve this. Incorporate something "on prior to meiosis" which takes care of the bryophytes and charophytes and "prior to cotyledon expansion", which takes care of all of the vascular plants.

Original comment by: dws409

[planteome-user]

prior to meiosis in non vascular plants and prior to germination in vascular plants.

Original comment by: jaiswalp

[planteome-user]

yes to Pankaj's formulation. Also "to is a whole plant"

Original comment by: dws409

[planteome-user]

I don't understand how prior to meiosis describes the embryo in bryophytes. Seems like this would include most of the sporophytic phase.

I prefer prior to cotyledon expansion in vascular plants, because prior to germination only works for seed plants.

Original comment by: rlwalls2008

[planteome-user]

Some bryophytes have a very short sporophytic phase of mainly archesporial cells followed by meisois. Basically a very short period of delayed zygotic meiosis that produces a few extra meiospores. So there is an undifferentiated sphere of cells that become and archesporial and then all except the surface ones become meiotic. So if we do not want to use premeiotic (=archesporial) then we need to use prearchesporial.

Original comment by: dws409

[planteome-user]

Proposed definition from POC meeting on 7-21-10: A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.

Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are <i>in vitro</i> plant structures. Embryos occur prior to germination in vascular plants.

is_a whole plant

Original comment by: rlwalls2008

[planteome-user]

This definition was accepted at the POC meeting on 11-5-2010. There is ongoing discussion about how embryo and embryonic phase will fit into the PO if we restructure the PGDSO, but since the request made in this tracker has been dealt with, I am closing this item.

Accepted definition: A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues. Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures. Embryos occur prior to germination in vascular plants. is_a whole plant

Original comment by: rlwalls2008

[planteome-user]

Somatic and adventitous embryos do have a bipolar axis with a hypotase at he distal end. So perhaps they are not true embryos?

Original comment by: nobody

[planteome-user]

Nobody Comment was me. I had forgotten to Log-in.

Original comment by: dws409

[planteome-user]

Now that we are doing land plants, the definition above needs to be modified. How about:

A young sporophyte contained within a gametophyte or in Angiosperms, a seed.

Original comment by: dws409

[planteome-user]

The definition above is not the final definition. See my comment from: Date: 2010-11-11 15:35:50 EST

At least someone out there thinks it is "super" and "great".

Original comment by: rlwalls2008

[planteome-user]

What about "contained in an archegonium or a seed"?

I'm a bit dubious about saying it "does not yet consist of fully differentiated tissues," because we have terms like embryonic epidermis and embryonic cortex.

Original comment by: rlwalls2008

[planteome-user]

Proposed definition: A whole plant in the sporophytic phase that is contained in an archegonium or a seed.

Comment: The embryo is a whole plant after fertilization (post-zygotic) and before emergence from the archegonium (for bryophytes and pteridophytes) or seed germination (for seed plants). Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures.

Logically, an embryo could be treated like a sporophyte or gametophyte, that is, as a cross-product of whole plant and the appropriate life cycle phase. However, since we don't have embryonic phase yet, and since so much research is done on embryos, it may be appropriate to keep the class embryo, and pre-compose the cross-product once we have embryonic phase.

Original comment by: rlwalls2008

[planteome-user]

New proposed definition: A whole plant in the early part of a sporophytic phase after the first cell division.

Comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. In seed plants, the embryonic phase ends with germination. In non-seed plants and cultured embryos of seed plants, the end of the embryonic phase is less clearly defined and varies among taxa.

We could add more details about the end of the embryonic phase if we want.

Original comment by: rlwalls2008

[planteome-user]

New proposed comment: An embryo is generally formed 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 is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop.

Original comment by: rlwalls2008

[planteome-user]

I suggest rewording slightly to ".....after the first zygotic cell division."

Original comment by: nobody

[planteome-user]

The last comment was from me. I forgot to log in.

Original comment by: dws409

[planteome-user]

We intentionally avoided saying ".....after the first ZYGOTIC cell division," because the definition needs to include embryos that do not arise from zygotes. The comment goes on to clarify that it is usually from the division of a zygote.

Original comment by: rlwalls2008

[planteome-user]

At the 4-26-11 POC meeting we agreed on the proposed new def'n: "A whole plant in the early part of a sporophytic phase after the first cell division."

With the revised comment: An embryo is generally formed 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 is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryonic phase ends when organs (roots, shoot axes, or leaves) begin to form.

Original comment by: cooperl09

[planteome-user]

Based on the 4-26-11 POC meeting, I added the following new terms as children of plant embryo:

*zygotic plant embryo (PO:0025303):def'n: A plant embryo that forms as a result of the fusion of gametes. is_a plant embryo

*cultured zygote-derived plant embryo (PO:0025304): def'n: A zygotic plant embryo that is grown or maintained in culture. exact synonym: cultured zygotic embryo, is_a zygotic plant embryo, and is_a cultured plant embryo

*microspore-derived cultured plant embryo (PO:0025305):def'n: A cultured plant embryo that develops from isolated microspores.

is_a cultured somatic plant embryo, exact synonym: microspore-derived haploid embryo

*somatic plant embryo (PO: 0025302): A plant embryo that arises from previously differentiated somatic cells, rather than from fused haploid gametes, i.e., the zygote.

Comment: Somatic plant embryos may arise where embryos normally would not arise, i.e. on the edges of leaves on Kalanchoe or ferns,

*cultured somatic plant embryo (PO:0000011) def'n: A somatic plant embryo grown or maintain in vitro. is_a somatic plant embryo and also a cultured plant embryo

Original comment by: cooperl09

[planteome-user]

At the POC conf call 4-28-11, we accepted the new terms and definitions with a few slight revisions: Closing this tracker

- added zygotic embryo as exact synonym of zygotic plant embryo (PO:0025303) -cultured zygote-derived plant embryo (PO:0025304): def'n: A zygotic plant embryo that is grown or maintained in vitro- made consistent

-*microspore-derived cultured plant embryo (PO:0025305): def'n: A cultured somatic plant embryo that develops from isolated microspores.

*somatic plant embryo (PO: 0025302): A plant embryo that arises from previously differentiated somatic cells, rather than from fused gametes, i.e. the zygote.

Comment: Somatic plant embryos may arise where embryos normally would not, as a product of apomixis. They may occur on the edges of leaves on some species of Kalanchoe or some ferns.

added: 'apomictic plant embryo' as an exact synonym

cultured somatic plant embryo (PO:0000011)

revised comment: Cultured somatic plant embryos are commonly induced after the formation of callus from an explant and treatment with plant growth regulators.

*nucellar plant embryo(PO:0004537): revised def'n: A somatic plant embryo derived directly from nucellus cells.

revised comment: Common in Citrus. synonyms broad; adventitious embryo subset citrus

Original comment by: cooperl09

[planteome-user]

Now that we have a term for embryo stage, I suggest that we redefine plant embryo in terms of that.

current definition of plant embryo (PO:0009009): A whole plant in the early part of a sporophytic phase after the first cell division. comment: An embryo is generally formed 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 is formed after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. In seed plants, the embryo stage ends with germination. In pteridophytes, the embryo stage ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryo stage ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryo stage ends when organs (roots, shoot axes, or leaves) begin to form.

new proposed definition of plant embryo: A whole plant that participates in the embryo stage (PO:0025369). -keep existing comment -change from participates_in sporophyte development stage to participates_in embryo stage

Also see tracker for embryo stage: https://sourceforge.net/tracker/?func=detail&aid=3439459&group\_id=76834&atid=835555

Original comment by: rlwalls2008

[planteome-user]

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

plant embryo (PO:0009009): A whole plant that participates in the embryo stage.

comment (basically the same as existing comment): An embryo is generally formed 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 is formed after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. In seed plants, the embryo stage ends with germination. In pteridophytes, the embryo stage ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryo stage ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryo stage ends when organs (roots, shoot axes, or leaves) begin to form.

Will change from participates_in sporophyte development stage to participates_in embryo stage

Original comment by: rlwalls2008

[planteome-user]

Current definition of a plant embryo (PO:0009009): A whole plant (PO:0000003) that participates in the (plant) embryo stage (PO:0007631).

I propose adding the words and PO ids, in brackets.

I also propose the following modification of the comment of plant embryo:

"A (plant) embryo is generally formed after the first division of a (plant) zygote (PO:0000423), but in the case of an adventitious embryo (nucellar plant embryo (PO:0004537)) , somatic embryo (PO:0025302), other embryos that arise through apogamy, or microspore-derived cultured plant embryo (PO:0025305), it is formed after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. In seed plants, the (plant) embryo stage (PO:0007631) ends with germination. 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."

Note: I took out " after the cotyledon(s)", as pteridophytes do not have cotyledons and added "plant" where appropriate, and added the PO ids, in brackets.

Original comment by: cooperl09

[planteome-user]

At the POC conf call 3-21-12, we accepted the following def'n and comment: plant embryo (PO:0009009): def'n: A whole plant (PO:0000003) that participates in the (plant) embryo stage (PO:0007631).

Comment: A plant embryo is generally formed 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; 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).

Accepted and closing

Original comment by: cooperl09

[planteome-user]

Removed the relation "plant embryo participates_in plant embryo stage", because it causes a conflict with the intersection_of relation "plant embryo stage has_participant plant embryo". It would be nice to be able to have both of these relations, but the browser can't handle it at this point.

Original comment by: rlwalls2008