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coleoptile and coleorhiza emergence stages #370

Closed planteome-user closed 9 years ago

planteome-user commented 13 years ago

It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be: Emergence of coleoptile from the seed (rather than above ground) . This could compare well to the radicle definition: The stage at which the radicle or root emerges from seed. PO:0007015 radicle emergence.

Reported by: mlschaeffer

Original Ticket: obo/plant-ontology-po-term-requests/370

planteome-user commented 13 years ago

PO:0007045 cotyledon emergence is_a shoot emergence, and shoot emergence (PO:0007030) is defined as "Shoot or leaf breaks through soil surface." All of the sibling terms to cotyledon emergence (coleoptile, epidcotyl, and hypocotyl emergence) are also defined as when they break through the soil surface. If we were to change the definition to emergence from the seed, we would have to obsolete this term and create a new one.

Perhaps a better solution would be to create a new set of terms for the stages when structures emerge from a seed. PO:0007030 could be renamed "shoot emergence from the soil" and we could create a new term "shoot emergence from the seed" with children like "coleoptile emergence from the seed".

Also, all of these terms should be renamed as stages or phases rather than developmental processes - so it should be called coleoptile emergence stage, rather than coleoptile emergence - and the definitions modified accordingly.

Original comment by: rlwalls2008

planteome-user commented 13 years ago

No need to make it obsolete. Breaking through soil is not approriate (avoid non-plant variables). We need to stay focused on the plant structure itself. So as Mary says, breaking through the seed/seed coat is fine with me. A slight change in definition is not changing the concept drastically. Its just an improvement.

Pankaj

Original comment by: jaiswalp

planteome-user commented 13 years ago

At the POC meeting on 9-11-11, we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages and reference emergence from the growth medium (rather than soil), and to add new terms for emergence from seed coat.

Need to copy over list of existing synonyms to new emergence terms and make sure they are appropriate.

Proposed definitions are below. If these stages begin with emergence from the seed coat or growth medium, we need to figure out when they should end. Stages are generally not a single point in time (don't know if they even are allowed to be).

current: shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

proposed: shoot emergence from growth medium development stage (PO:0007030): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the growth medium and ???. Comment: This terms is used only for seed plants.

proposed: shoot emergence from seed coat development stage (new number): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the seed coat and ???. Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.

current: coleoptile emergence (PO:0007045): Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]

proposed: coleoptile emergence from growth medium development stage (PO:0007045): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the growth medium and ??? Comment: This terms is used only for seed plants.

proposed: coleoptile emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the seed coat and ??? Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.

Similar treatments will be used for cotyledon emergence (PO:0007049), epicotyl emergence (PO:0007054), and hypocotyl emergence (PO:0007043).

Original comment by: rlwalls2008

planteome-user commented 13 years ago

Emergence of coleoptile from the seed. This is much better. Otherwise it can not be used for those grown in petri dishes etc.

Original comment by: dws409

planteome-user commented 12 years ago

At the POC conf call 3-21-12, we agreed on the revised definitions and comments: coleoptile emergence stage (PO:0007045): A sporophyte vegetative stage (PO:0007134) during which the coleoptile (PO:0020033) emerges from the seed coat (PO:0009088). part_of seed germination stage, Revised comment: Occurs in Poaceae and some other monocotyledons. May occur simultaneously with coleoptile emergence from the growth medium. This terms is used only for seed plants. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium.

coleorhiza emergence stage (PO:0025475): A root development stage (PO:0007520) during which a coleorhiza (PO:0020034) emerges from the seed coat (PO:0009088). part_of the seed germination stage (PO:0007057) revised comment: The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium.

Original comment by: cooperl09

planteome-user commented 12 years ago

Mary raised the issue that in many grains, the "seed" is actually a fruit with a thin, dry pericarp, and therefore, when the seed germinates, parts of it actually emerge form the pericarp, rather than from the seed coat.

I think that we should keep these terms defined as they are (as emerging from the seed coat), because it is more general. In order for a coleoptile or coleorhiza to emerge from the pericarp in a caryopsis, it still has to emerge (simultaneously) from the seed coat. Coleoptile and coleorhiza only occur in some other monocots, and I don't know if any of them have fleshy pericarps. In fruits that have fleshy pericarp, it may also be the case that the pericarp is retained and seedling germination is not visible until structures emerge from the pericarp. However, I think it is much easier to standarize across taxa if we use emergence from the seed coat.

We can add something to the comment for these terms, as well as the other emergence stage terms.

Revised proposed comment: Occurs in Poaceae and some other monocotyledons. May occur simultaneously with coleoptile emergence from the growth medium. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium. In fruits with a persistent pericarp, emergence from the seed coat may not be observed. If the fruit is a caryopsis, the dry pericarp is fused with the seed coat, and emergence from the pericarp is simultaneous with emergence from the seed coat. This term is used only for seed plants.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

This is not limited to grasses. Any angiosperm with an indehiscient fruit will have to do the same, that is cotyledons emerge through the fruit.

Original comment by: dws409

planteome-user commented 12 years ago

coleoptile emergence stages- and coleorhiza emergence stages: Modified comment: Occurs in Poaceae and some other monocotyledons. May occur simultaneously with coleoptile emergence from the growth medium. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed (PO:0009010) is underneath a growth medium. In a fruit (PO:0009001) with a persistent pericarp (PO:0009084), emergence from the seed coat may not be observed. If the fruit is a caryopsis, the dry pericarp is fused with the seed coat, and emergence from the pericarp is simultaneous with emergence from the seed coat. This terms is used only for seed plants.

Original comment by: cooperl09