vivipary

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New term request for

term: vivipary process definition: A process promoting the germination of embryos while still attached to the mother plant.

REf: PMID: 7599651 Ref: PMID: 11244106 Ref: Annual Review of Ecology and Systematics November 2000, Vol. 31, pp. 107-138

Pankaj

Reported by: jaiswalp

Original Ticket: "geneontology/ontology-requests/1641":https://sourceforge.net/p/geneontology/ontology-requests/1641

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Hi,

Might need to sensu 'vivipary' or related forms of the word. I didn't actually find the form 'vivipary' in dictionary.com, but here's the definition for 'viviparous':

vi-vip-a-rous adj.

Zoology. Giving birth to living offspring that develop within the mother's body. Most mammals and some other animals are viviparous.

Botany. Germinating or producing seeds that germinate before becoming detached from the parent plant, as in the mangrove.
Producing bulbils or new plants rather than seed, as in the tiger lily.

http://dictionary.reference.com/search?q=viviparous

Thanks,

-Karen

Original comment by: krchristie

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I agree, vaviparous is the organism's feature/trait/characteristics, vivipary is the process. Sensu mechanism is required here.

In plants its known that Abscisic acid deficiency early in seed development, induces vivipary process. I don't know much about animals but seems that it related with providing thermoregulated environment for offspring development.

Pankaj

Original comment by: jaiswalp

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So what about:

seed germination ; GO:0009845 ---[i] vivipary (sensu Magnoliophyta)

definition: A process by which the germination of a plant embryo occurs while still attached to the mother plant.

Original comment by: jl242

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Original comment by: jenclark

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Would this modified def be okay?

seed germination ; GO:0009845 ---[i] vivipary (sensu Magnoliophyta)

def: Production of young plants upon various parts of the parent plant. This may occur through vegetative reproduction, or through the production of seeds or fruit that sprout before they fall from the parent plant.

I'll write to Tanya to get her views as well.

Thanks,

Jen

Original comment by: jenclark

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I think for parentage, it might be best to put this directly under reproduction since it has to include vegetative reproduction. I'm not sure how we'd related seed germination to it since seed germination is part of only the non-vegetative section of this process.

Thanks,

Jen

Original comment by: jenclark

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Maybe the term should have two children:

vegetative vivipary (sensu Magnoliophyta) non-vegetative vivipary (sensu Magnoliophyta)

or something like that, and the latter can have seed germination ; GO:0009845 as a parent...

Original comment by: jl242

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Yes that's a thought. non-vegetative vivipary (sensu Magnoliophyta) could have synonym viviparous sexual reproduction (sensu Magnoliophyta), or that could be the term name.

Jen

Original comment by: jenclark

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Yep - whichever you think works better.

Original comment by: jl242

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Is there really such a term as non-vegetative vivipary? I must admit, I've not heard of vegetative reproduction being referred to as vivipary but then, I haven't read extensively in this area. I tend to think of this as asexual propagation (like the strawberry plants in my garden).

How about we just instantiate the term that is necessary right now: vivipary (sensu M) as an instance of seed germination, with the definition as Jane suggested?

My two cents,

Tanya

Original comment by: tberardini

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Hi Tanya,

I was thinking of Bryophyllum: http://www.bryophyllum.com/b/articles/

It has little plantlets growing on the margins of its leaves. These are produced vegetatively from meristems and it seems to be considered to be vivipary.

Jen

Original comment by: jenclark

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Can thsi definition help to accomodate both the instances.

"A process promoting the germination of embryos from a seed or vegetatively propagated new plantlets while still attached to the mother plant. "

The literature I am finding is all saying that irrespective or whether it is in seed or on leaves or elsewhere on the mother plant, the phenomenon is always associated to "vegetative propagation". However in case of seeds it is a next generation plant (genetically), where as in case of bryophyllum like species it is more or less a clonal propagation. Atleast both the plantlet and the mother plant are genetically same..

Though I am not sure if the plant hormones associated with this process are the same as well.

-Pankaj

Original comment by: jaiswalp

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From Felipe Zapata fzqhd at umsl.edu

From APWeb's Glossary:

Viviparous: of seeds, germinating before being shed from the parent plant, often also including plants that produce plantlets in the inflorescence.

Vivparous seeds are common in Mangroves (Rhizophoraceae).

What do you mean by non-vegetative vivipary? and would be the instances of this term?

F

Original comment by: jenclark

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From Mary Polacco: PolaccoM at missouri.edu

Is there going to be consideration of the related process, dormancy?

Original comment by: jenclark

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Learned something new about vivipary! I'd rather not have the non-vegetative vivipary term since that appears not to be in use. Your suggestion of viviparous sexual reproduction might be ok but maybe someone from POC can suggest a better phrasing.

Tanya

Original comment by: tberardini

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Toby Kellogge wrote:

> What about putting it under germination - "on the parent plant" vs. > "independent of the parent", or something more or less equivalent? The > word "vivipary sensu plants" would then be a synonym, so if a corn > person searched on vivipary, the term would appear. The same thing > happens in mangroves; the seed never goes through the dessication > process - no increase in ABA, no accumulation of lea proteins, etc. > Development perfectly normal, but is continuous. And as Tom points out, > the process is reasonably well understood. > In vivipary as occurs in Bryophyllum and other piggy-back plants, a new > meristem is organized on the margin of the leaf, and a little plantlet > forms. It's mechanistically different from mangrove and cereal vivipary > so probably needs a different term. > Toby > >

Original comment by: jaiswalp

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Hi folks, In the small grains, this is called preharvest sprouting. It's well-understood, and as Mary suggests is the result of lack of seed dormancy and a wet harvest environment. Calling it vivipary won't improve understanding of the process. In both barley and wheat the genetics of dormancy and of preharvest sprouting is pretty well-understood.
Cheers, Tom Blake, barley breeder, Montana State University

Blake at Montana.edu

Original comment by: jenclark

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Note maize has a series of "Viviparous" mutants associated with abscisic acid synthesis and signal transduction, some orthologues have been identified in other spp. Pre-harvest sprouting is still a major quality problem for many wheat producers, and also affects other grains including rye, barley, rice, sorghum. PHS is conditional upon environmental triggers, but may be genetically related to vivipary....

John.Flintham at bbsrc.ac.uk

Original comment by: jenclark

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My reply:

Hi,

Thanks for all this information. It's really a huge help. :-)

From what you're saying I understand that the thing that we were talking about as 'non-vegetative vivipary' is properly called 'pre-harvest sprouting' amongst certain biologists. Perhaps that should be the name of the term? Do you have any more names for it? We can add as many names as you can give us just by putting them in a synonyms. The synonyms don't have to be exact. We can add absolutely any names that will help domain biologists to find the term that they're interested in.

Do you have special names for the kind of vivipary that happens in Bryophyllum?

Thanks,

Jen

Original comment by: jenclark

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REF: PMID: 10759503 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list\_uids=10759503&dopt=Abstract

vivipary is a instance of seed_hgermination (on parent plant)

A correct balance of Gibberellic acid (GA) and Abscisic

acid(ABA) is required in maturing seed (dormant stage) that prevents vivipary.

GAs stimulate a developmental program leading to vivipary

in the absence of normal amounts of ABA, and that a reduction of GA content re-establishes an ABA/GA ratio appropriate for suppression of germination and induction of maturation. In contrast, the induction of a GA deficiency did not suppress vivipary.

Therefore here is a suggestion:

In the suggestion, I have considered to use VIVIPARY exclusive to the use of plants. Perhaps this may require sensu Mangnoliophyta term if users consider that they need a term to represent the similar phenomenon from metazoans. Looks like pregnancy is analogous to vivipary. Since this is seed specific term you may want to use the words "germination of the embryo from a seed" in the definition, thus excluding the so called vivipary (vegetative propagation) as seen in bryophyllum.

seed germination GO:0009845 -[i]-negative regulation of seed germination GO:0010187 --[i]-vivipary GO:new

seed dormancy GO:0010162 -[i]-regulation of seed dormancy GO:new --[i]-positive regulation of seed dormancy GO:new --[i]-negative regulation of seed dormancy GO:new ----[i]-vivipary GO:new

maintenance of dormancy GO:0010231 This term exists as a child of (seed dormancy GO:0010162) and looks like it needs obsoletion, if the above tree under seed dormancy is adopted. Basically maintenance of dormancy = positive regulation of dormancy.

response to hormone stimulus GO:0009725 -[i]-response to gibberellic acid and abscisic acid GO:new ----[i]--vivipary GO:new -[i]--response to abscisic acid stimulus GO:0009737 ----[i]--response to gibberellic acid and abscisic acid GO:new -------[i]--vivipary GO:new -[i]--response to gibberellic acid stimulus GO:0009739 ----[i]--response to gibberellic acid and abscisic acid GO:new -------[i]--vivipary GO:new

I did not use the XX-acid mediated signalling terms as parent terms because the literature does not use the word signalling. Perhaps it is but I am not sure.

Original comment by: jaiswalp

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Hi,

I know this is almost exactly the same comment I made on this discussion earlier, but we cannot use plain 'vivipary' in a way that restricts it plants. The word has a broader meaning and is applied to animals as well as plants. Here's the dictionary.com definition for 'viviparous':

vi-vip-a-rous adj.

Zoology. Giving birth to living offspring that develop within the mother's body. Most mammals and some other animals are viviparous.

Botany. Germinating or producing seeds that germinate before becoming detached from the parent plant, as in the mangrove.
Producing bulbils or new plants rather than seed, as in the tiger lily.

http://dictionary.reference.com/search?q=viviparous

Thanks,

-Karen

Original comment by: krchristie

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I see your point. Going by your suggestions, can we have

organismal physiological process GO:0050874 -[i]-vivipary ---[i]-vivipary sensu metazoa -----[i]-pregnancy GO:0007565 ---[i]-vivipary sensu magnoliophyta -[i]-seed germination GO:0009845 ---[i]-vivipary sensu magnoliophyta

It looks kind of odd but it may work. In my previous suggestion all the terms AKA "vivipary" can be replaced with 'vivipary sensu magnoliophyta"

For Jen: I suggest excluding the bryophyllum type of vivipary from this . It should be considerd as a vegetative propagation (is_a asexual reproduction).

-Pankaj

Original comment by: jaiswalp

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from Nicholas Tinker:

But, If an ontology defines "vivipary" as a "type of" preharvest sprouting (or vice-versa) then won't it help the corn people do comparative genomics with the barley people?

TINKERNA at AGR.GC.CA

Then from David Marshall:

preharvest sprouting is of particular interest. There are a number of
advances at the molecular level. It is interesting to place preharvest sprouting in the context of related processes i.e. grain development, "normal germination", dormance and in the case of barley- malting.

David.Marshall at scri.ac.uk

Original comment by: jenclark

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Have sent this proposal to the list:

[i]germination ---[i]germination on parent plant

[i]asexual reproduction ---[i]vegetative vivipary (sensu Magnoliophyta)

Term:germination on parent plant synonym: non-vegetative vivipary (sensu Magnoliophyta)

Term: vegetative vivipary (sensu Magnoliophyta) synonym: pre-harvest sprouting

Original comment by: jenclark

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Hi Jen,

This is more confusion. germination on parent plant is the same as vivipary (your vegetative vivipary or pre-harvest sprouting).

At this time we just need the structure I suggested. In my suggestion, term " vivipary sensu magnoliophyta" can have the synonym "pre-harvest sprouting". This will make a a perfect sense to the people.

-Pankaj

Original comment by: jaiswalp

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Hi Pankaj,

We can't just ignore the vegetative vivpary as it occurs in Bryophyllum. Toby has confirmed that this exists and I don't think there's any harm in having two terms to cover the two concepts. We certainly can't just have a single term 'vivipary (sensu Magnoliophyta)' and ignore the vegetative component entirely.

Jen

Original comment by: jenclark

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I agree that Toby has conbfirmed it. My argument is that this term may not be required at this moment for curational purposes. I am not even sure if some is working on that phenomenon.

Incase we do want to have this process, then previously I suggested on Date: 2005-07-01 14:00

For Jen: I suggest excluding the bryophyllum type of vivipary from this . It should be considerd as a vegetative propagation (is_a asexual reproduction).

Though I suggested for exclusion, you may like to add this term under asexual reproduction.

-Pankaj

Original comment by: jaiswalp

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Hi Pankaj,

I agree that Toby has conbfirmed it. My argument is that this term may not be required at this moment for curational purposes. I am not even sure if some is working on that phenomenon.

* We may not need the term now but if we are going to use the word 'vivipary' in the ontology then we need to define it as it is defined in the literature. If it really means two things in the literature then it would be safest to represent both of them rather than pretend that the word only means one thing.

* I know at least one group that is working on this over at the plant science department at Oxford University.

Incase we do want to have this process, then previously I suggested on Date: 2005-07-01 14:00

For Jen: I suggest excluding the bryophyllum type of vivipary from this . It should be considerd as a vegetative propagation (is_a asexual reproduction).

Though I suggested for exclusion, you may like to add this term under asexual reproduction.

*Righto. Thanks.

Jen

Original comment by: jenclark

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Hi Jen,

From an earlier comment of yours:

"From what you're saying I understand that the thing that we were talking about as 'non-vegetative vivipary' is properly called 'pre-harvest sprouting' amongst certain biologists."

But then in the proposal:

Term: vegetative vivipary (sensu Magnoliophyta) synonym: pre-harvest sprouting

Shouldn't this really be:

term:pre-harvest sprouting synonym: germination on parent plant synonym: non-vegetative vivipary (sensu Magnoliophyta)

The proposal would then be:

[i]germination ---[i]pre-harvest sprouting

[i]asexual reproduction ---[i]vegetative vivipary (sensu Magnoliophyta)

Term:pre-harvest sprouting synonym: germination on parent plant synonym: non-vegetative vivipary (sensu Magnoliophyta)

Term: vegetative vivipary (sensu Magnoliophyta) synonym: vegetative reproduction (maybe even switch these as term name and synonym)

How does that sound?

Tanya

Original comment by: tberardini

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Hi Tanya,

Sorry I've put pre-harvest sprouting with the wrong term. I mean it to be the synonym of the non-vegetative vivipary. Jane reckons we shouldn't have pre-harvest sprouting as the term name since it's specific to agricultural crops, and might not be a term that's in use for example with a model organism. Would you agree with that? Nobody seems to have come up with a term that describes this concept exactly and that would work with species that don't have a harvest.

Jen

Original comment by: jenclark

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Hi Jen,

Jane has a good point. This arrangement sounds good to me:

Term: germination on parent plant synonym:pre-harvest sprouting synonym: non-vegetative vivipary (sensu Magnoliophyta)

Tanya

Original comment by: tberardini

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How about "seed germination on parent plant"?

or "seed germination on ex-plant" = non-vegetative vivipary. This gives rise to a seedling, i.e plant formed from a seed.

and

"plantlet formation on ex-plant" = vegetative vivipary. This gives rise to a plantlet and NOT seedling.

-Pankaj

Original comment by: jaiswalp

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Hi Pankaj,

I only get two hits on "ex-plant" in pubmed so we'd better not use that. I'd be happy to use this though: "seed germination on parent plant".

Thanks,

Jen

Original comment by: jenclark

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Shall I just add this then? Tanya, do you have views on Pankaj's suggested name?

Jen

Original comment by: jenclark

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I prefer:

seed germination on parent plant

and

plantlet formation on parent plant

Tanya

Original comment by: tberardini

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Yes that seems good. Pankaj, would you be happy with that?

Jen

Original comment by: jenclark

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fine with me. -Pankaj

Original comment by: jaiswalp

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Hi,

I've added these two terms:

id: GO:0048623 name: seed germination on parent plant namespace: biological_process def: "The process by which a seed germinates before being shed from the parent plant." [GO :curators] exact_synonym: "non-vegetative vivipary (sensu Magnoliophyta)" [] exact_synonym: "pre-harvest sprouting" [] broad_synonym: "vivipary (sensu Magnoliophyta)" [] is_a: GO:0009845 ! seed germination

[Term] id: GO:0048624 name: plantlet formation on parent plant namespace: biological_process def: "The process whereby a new plantlet develops from a meristem on the plant body. As pa rt of this process\, when the plantlet is large enough to live independently\, the physical connection between the new plantlet and the main plant is severed." [GO:curators] exact_synonym: "vegetative vivipary (sensu Magnoliophyta)" [] broad_synonym: "vivipary (sensu Magnoliophyta)" [] is_a: GO:0019954 ! asexual reproduction is_a: GO:0048507 ! meristem development

Pankaj made some good points in his comment of Date: 2005-07-01 17:17

which we haven't discussed yet.

What do you think about having parentage under response to hormone terms? Also we currently have maintenance of dormancy and Pankaj was wondering about changing it to positive and negative regulation terms. I'd be interested to know what the domain biologists think about that. I guess they have particular language that they use to discuss these things. I understood that maintenance of dormancy was a particular type of positive regulation of dormancy and that there would be a place for both terms, and a value in keeping both.

Thanks,

Jen

Original comment by: jenclark

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I have written to the po-dev list to ask if anyone knows which hormones cause these processes to occur.

Jen

Original comment by: jenclark

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Toby Kellogge says:

Seed germination on the parent plant is caused by reduction in or insensitivity to abscisic acid levels.

It sounds to me as if normal maintenance of seed dormancy on the plant could be a child of response to abscisic acid and that 'seed germination on parent plant' should not be connected to a hormone term since the hormone is not acting in this case.

What do you think?

Jen

Original comment by: jenclark

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• priority: 5 --> 3

Original comment by: jenclark

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Hi,

I've been thinking a lot about this and reading PMID:15752999 Dormancy release, ABA and pre-harvest sprouting.

I think it's reasonably clear that ABA is involved in maintaining dormancy so we could make this relationship:

[i]response to hormone stimulus ---[i]response to abscisic acid stimulus ; GO:0009737 ------[p]maintenance of dormancy ; GO:0010231

However, they don't seem to have figured out how the hormones are involved in pre-harvest sprouting so I'm not keen to make a statement about that in the ontologies.

However, I think it would be nice to make a connection between 'maintenance of seed dormancy' and 'preharvest sprouting' (which is really just the premature release of seeds from dormancy.

What would you think about the following relationships being made:

[i]reproductive organismal physiological process ; GO:0048609 ---[i]seed dormancy ; GO:0010162 ------[p]maintenance of dormancy ; GO:0010231 ------[p]release of seed from dormancy ; GO:new ---------[i]seed germination on parent plant ; GO:0048623

Thanks,

Jen

Original comment by: jenclark

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I have added:

[i]seed germination on parent plant ; GO:0048623 ---[p]release of seed from dormancy ; GO:new

[i]seed dormancy ; GO:0010162 ---[p]maintenance of dormancy ; GO:0010231 ---[p]release of seed from dormancy ; GO:new

id: GO:0048838 name: release of seed from dormancy namespace: biological_process def: "The processes by which the dormant state comes to an end in a seed." [GOC:jic] relationship: part_of GO:0010162 ! seed dormancy relationship: part_of GO:0048623 ! seed germination on parent plant

and

[i]response to hormone stimulus ---[i]response to abscisic acid stimulus ; GO:0009737 ------[p]maintenance of dormancy ; GO:0010231

Jen

Original comment by: jenclark

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• milestone: 224410 --> Plant Ontology
• priority: 3 --> 5
• status: open --> closed-accepted

Original comment by: jenclark