pollination

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Here is the meeting summary from our (Leonore and my) consult with Sheila McCormick <http://www.pgec.usda.gov/McCormick/McCormick/mcla b.html>: (also as attachment)

Use the term 'pollination'.

pollination: Biological processes occurring in plants beginning when the pollen lands on the stigma up to, but not including, fertilization, as defined by sperm - central cell fusion.

Terms that should be part of pollination, at some level:

pollination ---<pollen germination ---<pollen hydration ---<pollen tube growth % tip growth ---<pollen recognition ---<synergid degeneration (def: an active process that occurs in the synergid after penetration by the pollen tube) ---<pollen tube adhesion ---<pollen tube guidance ---<pollen adhesion

comments on term definitions:

GO ontologies:

GO:0009856: currently 'interaction of male gametophyte and...."
comment: remove 'or pollen tube cell'. Better yet use definition above, restore term name name as 'pollination' as this is the term used in the community. The definition is the key.

GO:0009875:pollen-pistil interaction comment: modify definition to be "process by which pollen from the pollen donor and pistillate tissues of the egg donor are determined to be compatible or not."

GO:0009846: microspore germination comment: microspore germination != pollen germination!!!, microspore!= pollen grain, they are different developmental stages, microspores do not germinate very narrow definition, tip growth to make little tube through aperture = tip growth that extends the pollen tube. Should be microgametophyte germination.Sheila considered germination to be the whole shebang and impossible to distinguish from growth. I think this is like the seed germination issue- when we see that the pollen has germinated it's already growing. It's the resumption of development following a period of dormancy.A basic definition for germination.

GO:0009858: compatible pollen-pistil interaction comment: modify the word 'unimpeded', sounds like there is a barrier that needs to be crossed

GO:0009876: pollen adhesion comment: tomatoes don't have stigmatic papillae, papillae are crucifer specific, just say 'cells of the stigma'

GO:0009857: pollen recognition comment: replace "factors in the stigma" with "factors in the pistil"

GO:0009859: pollen hydration comment: '...water is taken up by the pollen.' should be sufficient

NOTE: In tomato, the second microspore mitosis occurs after pollination during the progamic phase. In Arabidopsis and maize, this second mitotic event is completed before pollination. We may need a sensu term which distinguishes pollen mitosis in Solanaceae from other plant families. Perhaps we should leave pollen development and similar processes (which are required for the process in question, here 'pollination') out of the pollination node until the relationship 'required for' is invoked- if at all.

Reported by: tberardini

Original Ticket: "geneontology/ontology-requests/1695":https://sourceforge.net/p/geneontology/ontology-requests/1695

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text summary file

Original comment by: tberardini

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This item covers a subset of issues begun in 'plant gametogenesis 2' SF item: 899726.

Original comment by: tberardini

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Original comment by: jenclark

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Hi

This brings us backto the time when we had the GO term "pollination". We obsoleted it based on the most commonly accepted definitions that the process of ponllination is not a biological process. In otherwords it starts when the pollen is dispersed/shed and ends with the landing on stigma.

Pollination: is a process of transferring the pollen from its place of production to the place where the egg cell is produced. This may be accomplished by the use of wind, water, insects, birds, bats, or other means.

Here are some more

Definition: The transfer of pollen from the male organ, where it is formed, to the receptive region of a female organ, e.g. from anther to stigma. http://www.hyperdictionary.com/dictionary/pollination

The transfer of pollen from the male part of flowers (the anthers) to the female part (a stigma). The transfer is accomplished by insects. homeorchard.ucdavis.edu/glossary.shtml

The transfer of pollen from an anther to a stigma. www.prairiefrontier.com/pages/glossary.html

The transfer of pollen from the anther to the stigma. www.an.psu.edu/jxm57/irp/glossary.html

Process of transferring the pollen from its place of production to the place where the egg cell is produced. This may be accomplished by the use of wind, water, insects, birds, bats, or other means. Pollination is usually followed by fertilization, in which sperm are released from the pollen grain to unite with the egg cell. www.ucmp.berkeley.edu/glossary/gloss8botany.html

Fertilization of a flowering plant. The transfer of pollen from the anthers of one flower to the stigma of that or another flower. www.honey.com/pressrm/mkt/glossary.html

the transfer of pollen from the male part of a flower (stamen) to the female part of a flower (the style and stigma). www.growingedge.com/basics/glossary.html

the movement of pollen from a stamen to a pistil by pollinators (birds or insects). www.butler.edu/herbarium/treeid/treeglossary.html

the transfer of pollen to a receptive stigma. www.hosta.org/dictiona.htm

The transfer of pollen from the anther of a stamen to the stigma of a pistil. www.powen.freeserve.co.uk/Reference/Glossary/gloss-p.htm

The carrying of pollen from the male reproductive parts of the flower to the female reproductive parts. www.science.mcmaster.ca/Biology/4FF3/Archive/glossary.htm

The process by which pollen is transferred from an anther to the stigmatic surface of the pistil of a flower. www.seed.ab.ca/CIRC6/glossary.html

transfer of pollen from the stamens to the pistils of flowers westlake.k12.oh.us/bartos/plantglossary.htm

transfer of pollen from anther to stigma

www.users.zetnet.co.uk/computing/MainPage/SecDepts/Biology/biol_synopsis.htm

transfer of pollen from the anther to the stigma of a plant www.cogsci.princeton.edu/cgi-bin/webwn

Whereas the definition coming from the discussion suggests it starts after the pollen has landed on stigma. I am a little hesitant to use this.

Rest of the terms and definitions looks okay, but what about the pollen germination. Sometimes it occurs before pollen is shed.

So I have a suggestion here, can we have all these terms as children of microsporogenesis, because all these events are related to microspore (=pollen) development and growth, thus getting rid of the temporal hierarchy or events. The temporal phase info can be described in the definition.

Pankaj

Original comment by: jaiswalp

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Hi,

Actually, we didn't obsolete the term 'pollination'. We renamed it to be 'post-pollination', same GOid (GO:0009856).
The basis for reviving this argument, and seeking an expert outside opinion, is that 'post-pollination' is a completely artificial term that is NOT used in the scientific community. In practice, the term 'pollination' is taken to refer to exactly the processes described in Sheila's proposed definition:

pollination: Biological processes occurring in plants beginning when the pollen lands on the stigma up to, but not including, fertilization, as defined by sperm - central cell fusion.

Sheila was adamant in stating that 'pollination' should be the term to use for this purpose. This is why it is good to consult experts in the field and not rely strictly on textbook definitions.

From Pankaj's comments:

>Rest of the terms and definitions looks okay, but what about >the pollen germination. Sometimes it occurs before pollen is >shed.

Can you provide a concrete example of this? If this is true, I agree that the following modifications should be made: Make an appropriate sensu term that fits underneath here and have the parent term not be a child of pollination.

>So I have a suggestion here, can we have all these terms as >children of microsporogenesis, because all these events are >related to microspore (=pollen) development and growth, >thus getting rid of the temporal hierarchy or events. The >temporal phase info can be described in the definition.

From Sheila's comments above (see comment for GO:0009846), microspore != pollen. This is really not my area and I defer to her opinion in this matter. By transitivity, microsporogenesis != pollen development. In fact, we currently have 'pollen development' as a synonym for 'male gamete generation (sensu Magnoliophyta) ; GO:0048234.

As a side note, Leonore is on holiday for a week starting today and won't be able to contribute to the discussion till Friday next week (after she emerges from the pile of email that's sure to be awaiting her). Keep this in mind as we talk about these issues, as I know her opinion would be very valuable.

Tanya

Original comment by: tberardini

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>Rest of the terms and definitions looks okay, but what about >the pollen germination. Sometimes it occurs before pollen is >shed.

I am sorry . There is no such incidence. I mistook it for the II-mitotic division that may occur before pollination.

In -70% of plant families (e.g., Solanaceae and Liliaceae), the pollen grain is released from the anther when it consists of just these two cells; the second mitotic division of the generative cell, to give two sperm cells, occurs while the pollen tube grows through the female pistil. In other plant families (e.g., Cruciferae and Gramineae), this second mitotic division occurs before the pollen is shed from the plant.

ref: The Plant Cell, Vol. 5, 1265-1275, October 1993 ( This is one of Sheila's earliest review)

I will wait until Leonore returns.

Original comment by: jaiswalp

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Hi All I clearly have a case of pollination tourettes. In the back of my mind is the vague recollection that at a long ago GO meeting the issue of commonly used scientific verbiage and the 'classical' definition. At that time it was clear that if we were to serve the interests of the research community - there are terms which are in use and their meanings understood even if they are different than a classical definition.

Sheila was pretty emphatic that -"no one but ONE person " used 'post- pollination' that pretty much everyone in the field equates pollination with sex. Now if we were ecologists- that might be a different story.

So we could add something to the definition which says "classically/ acurately defined as blah blah birds and bees. In the context of the GO refers to..blah blah blah." and thus admit we are using a more colloquial (sp?) definition.

Based on some feedback from colleagues here- one of the big problems people have with GO/controlled vocabs is that the language is obtuse. Take for example, Male gamete formation (sensu Magnoliophyta) which=pollen development and frankly no one I can think of would ever 1) write in a paper that a gene is involved in male gamete formation (sensu Magnoliophyta) 2)think of searching for that term. 3) display it in a figure in a paper (e.g. microarray cluster).

Are there any other types of male gametes formed in flowering plants other than pollen??

OK back to pollination- maybe for a second opinion talk to Hugh Dickenson at Oxford (for the euro point of view). While cruising the web found this paper for Germ Online http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi? cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14681481

so he might have a vested interest in helping out more with this ontology.

Im looking at a paper by Daphne Pruess in which she has a figure describing pollination in arabidopsis. (http://www.plantcell.org/cgi/rapidpdf/tpc.015800v1) May not be the avowed expert in this- but it sort of argues for common usage of the term to represent 'post-pollination' events.

With respect to the second mitotic division in microgametogenesis. If this is a part of pollen development (and it always is) regardless of when it occurs it will be true. I dont see the reason for having pollen mitosisII represented in any pollination node. Pollination (post pollination- whatever) requires pollen development and ovule/embryo sac development- but they are not necessarily a part of. Frankly- Id not put this node in anywhere other than pollen development and Id only associate pollen development when a different relationship type (requires) is allowed. Its like metabolism. Many biochemical pathways depend on products of other pathways- but I thought it was agreed to not represent this interdependance in go (its not a pathway database)...so why do it for developmental pathways. So I totally agree with the last bit tanya wrote ( in the note).

Pollen germination- I dont think the definition says anything about when it occurs, only that it occurs and is a resumption of growth following a period of dormancy (a generic germination definition).

Well sorry for the rambling... Leonore

Original comment by: lreiser

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Hi,

This seems very sensible to me. Shall we try to rework this stuff along these lines then?

Jen

Original comment by: jenclark

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Yes. please do.

Original comment by: syrhee

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Shall I, first of all, rename the term that was post-pollination to pollination?

Jen

Original comment by: jenclark

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Yes.

Original comment by: syrhee

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Would it be okay if I change the def of 'pollination' from

Interactions between the female tissues (stigma, style and ovary) and the male gametophyte or the pollen tube cell, which contains the sperm cells. These processes begin with pollination and end with fertilization.

to:

Interactions between the female tissues (stigma, style and ovary) and the male gametophyte or the pollen tube cell, which contains the sperm cells. These processes begin with the deposition of pollen on the stigma and end with fertilization.

Jen

Original comment by: jenclark

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Sounds good to me Jen.

Original comment by: syrhee

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I've changed the term name to pollination with the def below. I'll have a look at the additional child terms and defs suggested above now.

Jen

Original comment by: jenclark

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I have looked at the rest of Sheila's comments. They seem to suggest the following actions. Would people agree that I should implement these?

1) Shall I change the pollination def from:

Interactions between the female tissues (stigma, style and ovary) and the male gametophyte or the pollen tube cell, which contains the sperm cells. These processes begin with the deposition of pollen on the stigma and end with fertilization.

to:

pollination: Biological processes occurring in plants beginning when the pollen lands on the stigma and continuing up to, but not including, fertilization, as defined by sperm - central cell fusion.

2) Shall I add/redefine these child terms:

pollination ---<pollen hydration ---<pollen recognition ---<synergid degeneration ---<pollen adhesion

3)Defs:

a) synergid degeneration def: Degeneration of one of the synergid cells is an active process that occurs in the cynergid after penetration by the pollen tube. PMID: 12028577

b) GO:0009875:pollen-pistil interaction currently: def: The interaction between a pollen grain and pistil. suggested by Sheila: def: process by which pollen from the pollen donor and pistillate tissues of the egg donor are determined to be compatible or not."

I'm not sure that this is really saying the same thing. It maybe that this is what the author of the term was getting at when the def was written but the implications were pretty subtle. If we want to make this change I'd be inclined to obsolete the term and make a new one with the new def. Having said that, this is not a field that I'm massively familiar with so maybe people who would wish to annoatate to this term would have realised what it meant.

c) GO:0009858: compatible pollen-pistil interaction comment: modify the word 'unimpeded', sounds like there is a barrier that needs to be crossed

This term has been made obsolete because it represented a phenotype. Does this mean that GO:0009875:pollen-pistil interaction, above also represents a phenotype?

d) GO:0009876: pollen adhesion

currently: The process by which pollen deposited on the stigma adheres to cells of the stigmatic papillae.

Sheila's comment: tomatoes don't have stigmatic papillae, papillae are crucifer specific, just say 'cells of the stigma'

suggested: The process by which pollen deposited on the stigma adheres to cells of the stigma.

e) GO:0009857: pollen recognition currently: The recognition by factors in the stigma, of molecules present in or produced by pollen. Sheila's comment: replace "factors in the stigma" with "factors in the pistil" suggested def: The recognition by factors in the pistil, of molecules present in or produced by pollen.

f) GO:0009859: pollen hydration currently: The process by which water is taken up by pollen which may involve induction of water release from (dry) stigmas. comment: '...water is taken up by the pollen.' should be sufficient suggested def: The process by which water is taken up by pollen.

g) pollen tube adhesion currently undefined. suggested (by me): The process by which the pollen tube adheres to cells of the stigma and style. PMID: 12602877

h)I haven't done pollen germination here.

Jen

Original comment by: jenclark

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Jen-

1. great pollination defintion 2.yes
2. Defs.

b) pollen-pistil interaction I might have been the one to add that as a way of saying a gene product was involved in pollen-pistil recognition in self incompatability but since SI is a 'trait' its not appropriate and I agree with Sheila that its not necessarily all about compatability or incompatability. And its hard to say what is involved in this interaction because its largly a biological unknown (involves some kinases- but mecahnistically not well understood). Maybe something like processes of intracellular communication between the paternal pollen and the is maternal tissues.

One could I suppose consider pollen hydration a pollen- pistil interaction since the pollen is getting the water from the stigmatic tissue.

Rest seem good to me.

Original comment by: lreiser

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I have implemented the changes that I suggest below except for the stuff on pollen-pistil interaction. I don't quite get what Leonore was saying about that below. Leonore: can you explain a bit more strightforwardly what you mean me to do about those terms? Thank you :-)

I also implemented the parentage:

pollination ---<pollen germination ---<pollen hydration ---<pollen tube growth % tip growth ---<pollen recognition ---<synergid degeneration (GO:new = GO:0048470) ---<pollen tube adhesion ---<pollen tube guidance ---<pollen adhesion

Are the any modifications to this parentage that people would like?

Jen

Original comment by: jenclark

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Jen

Im advocating NOT taking out pollen-pistil interaction but rather leave it in. Your 'pollen recognition' term would be an instance of a pollen-pistil interaction. Based on what Sheila said- there could be a similar 'pistil recognition' function (e.g. processes within the pollen grain that are involved in recognition of self/non-self pistillate tissues.) Im sure there are pollen pistil interactions that are more than just those involved in self (in)compatability- but that is the most studied.

Original comment by: lreiser

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Great. Now that that's all done shall I get back to trying to figure out the plant gametogenesis terms? This discussion started because I had made some new terms to cover plant gametogenesis and Tanya and I were trying to figure out which ones should go under post-pollination and which should go under the sexual reproduction term under the development node.

I had made a first stab at doing the terms and was looking for feedback to help get them properly logical and user-friendly.

Jen

Original comment by: jenclark

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Jen Thanks so much for taking this on. Seems like a good idea to go for the gametogenesis part now. Leonore

Original comment by: lreiser

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Excellent. :-) I'll close this one since it's done now, but add a note to the plant gametogenesis one that this is here. Thanks for all the help. :-)

Jen

Original comment by: jenclark

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• milestone: --> TermGenie
• status: open --> closed-accepted

Original comment by: jenclark