ntr: children of pollination

[gocentral]

Can we have two new children of pollination, "self-pollination" and "pollination by other organism" (not sure if this has another name or not - cross-pollination, maybe?).

In that area of the ontology, could 'synergid degeneration' be given a better def? ATM, all that can be derived from the def is when the process happens. That doesn't really tell you what the process actually is.

The term 'recognition or rejection of self pollen' is rather dodgy, too. Could this not be split into two terms, one for recognising the pollen (because presumably the plant can detect both self and nonself pollen), and the second for the rejection of self pollen? What's the equivalent term for accepting nonself pollen? Is it 'pollen germination'?

Cheers!

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/2986":https://sourceforge.net/p/geneontology/ontology-requests/2986

[gocentral]

Logged In: YES user_id=579762

HI,

I'm not sure what genes one would annotate to 'self-pollination' or 'pollination by other organisms'. Did you have some particular examples in mind? The term 'recognition or rejection of self pollen' actually addresses this issue. There are gene products that are involved in self pollen recognition/rejection - if selfing is allowed by that plant, the pollen is recognized and can germinate, whereas is selfing is not allowed by the plant, the pollen is rejected and cannot germinate. Similarly, if the plant is only an outcrossing species, non-self pollen is recognized and can germinate while self pollen is rejected and cannot. 'Pollen germination' is a separate process that is enabled by pollen recognition.

As for 'synergid degeneration', I think this term could probably be merged with GO:0010198 'synergid death'. A little bit of tweaking with the parentage needs doing as the parentage of both terms does not overlap and I'm not positive that 'synergid death' should be a child of 'female gametophyte development'. The def for GO:0010198 is more descriptive and appropriate than that of 'synergid differentiation'

My 2 cents,

Tanya

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=614564

'pollination by other organism'- do you mean the pollinating agent or transfer of pollen between flowers from different plants. If it is the latter, then it is the same as cross pollination.

I am a little confused about the term 'recognition/rejection'. If a gene involved in recognition, then it is not involved in rejection and vice versa. This term doesn't allow us to make this distinction at a gene level. So, as Amelia suggested, we need to have 2 separate terms: one for recognition and the other for rejection.

I agree with Tanya in that, synergid death and synergid degeneration could be merged and have 2 parents: pollination and cell death.

Suparna

Original comment by: smundodi

[gocentral]

Logged In: YES user_id=473796

The reason I ask about the pollination terms is that Jane and I are trying to find all the processes which involve another organism (yes, it's almost as much fun as it sounds!). Obviously cross pollination would involve another organism and self pollination wouldn't. What's the deal in self-pollinating plants - do they lack the mechanism that checks whether the pollen is from another organism or not? And what stops pollen from other species from successfully germinating? Is that the same recognition mechanism as that which rejects self pollen in non-selfing plants?

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=473796

Also, the term 'pollen-pistil interaction' - would there ever be pollen-pistil interactions outside the process of pollination? This term is currently under 'cell communication' but maybe it needs to be moved/given additional parentage elsewhere.

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=561361

> The term 'recognition or rejection of self pollen' is rather dodgy,

This term was added after consultations with the expert June Nsarallah. So I don't think this should be modified.

---

Can you give some examples where the terms "self-pollination" and "pollination by other organism" are required for annotation. So far I do not see the reason to have them. I am not sure of the motive, but presume, this is another way to bring in the terms for 'compatible' and 'incompatible' pollination or pollen pistil interaction, that we decided are phenotype terms.

---

I see that children of pollen-pistil interaction (GO:0009875) must have the parent pollination (GO:0009856) individually. Ideally the term pollen-pistil interaction (GO:0009875) must be assigned additional part_of parent pollination (GO:0009856) this all its children get a grand parent pollination (GO:0009856).

---

Following relationship is correct. The interaction requires a signal transduction pathway to establish the interaction.

----cell communication (GO:0007154) -----[i]--- pollen-pistil interaction (GO:0009875)

-Pankaj

Original comment by: jaiswalp

[gocentral]

Logged In: YES user_id=473796

The concept behind recognition or rejection of self-pollen is fine, I just think that it should be represented slightly differently, eg:

pollination [p] recognition of self pollen [p] rejection of self pollen

Is the mechanism here one where the self pollen is recognised and rejected, or is it that nonself pollen is recognised and pollination allowed to proceed? What happens if it's pollen from a different species? Are the same mechanisms used?

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=561361

It is basically the same process. As you said if compatible it proceeds, if not no further action. The process is carried out via different individual mechanisms in different species. These pathways are subject of some very competitive research now as it deals with teh speciation aspects as well. Though it is yet to come up with some concrete results.

At least in Brassica it is an allele specific protein-protein interaction, with one protein from pollen and another from stigma and involves signal transduction.

Therefore, I would leave it as it is.

-Pankaj

Original comment by: jaiswalp

[gocentral]

Logged In: YES user_id=614564

The term 'recognition/rejection of pollen' is similar to what happens when an organism encounters a pathogen/microbe. It is the same locus that is involved in recognition and rejection. Depending on which 2 organisms come in contact, it results in either a disease or a defense response. All these are simply put in 'response to xxx' terms in host-pathogen world. So, we can try to be consistent here. Eventhough, I must admit that 'response to self pollen' sounds a little weird.

Suparna

Original comment by: smundodi

[gocentral]

Logged In: YES user_id=473796

Is everyone agreed on merging 'synergid degeneration ; GO:0048470' into 'synergid death ; GO:0010198', with the resulting term having the parentage is- a 'cell death' and part-of 'pollination', and removing the parentage under 'female gametophyte development'?

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=579762

Is everyone agreed on merging 'synergid degeneration ; GO:0048470' into 'synergid death ; GO:0010198', with the resulting term having the parentage is- a 'cell death' and part-of 'pollination', and removing the parentage under 'female gametophyte development'?

I agree. But then, again, I was the one who proposed this. 8-). In any case, I still think this is correct.

Tanya

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=473796

re: "recognition or rejection of self pollen"

Is it right to say that if a compatible pollen grain comes along, there is an interaction between the pollen and the pistil, which might eventually lead to fertilization; however, if it's an incompatible pollen grain, nothing happens - there's no interaction?

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=579762

Hi,

Here's a link to a site that explains the processes of gametophytic and sporophytic self-incompatibility.'

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SelfIncompatibilty.html

In short, there are interactions that occur between both incompatible and compatible pollen and the pistil. They are different types of interactions with differing results.

Tanya

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=473796

Thanks for the link Tanya!

I think that we should have terms for the processes involved in incompatibility interactions; having read PMID:14659710 (on sporophytic self-incompatibility) and PMID:14659709 (on gametophytic SI), there are at least three distinct mechanisms for SI which could be represented in GO. Before embarking any further on this, is there any reason why we shouldn't put these processes into the ontology? The structure would probably be something like this:

self-pollination [p] regulation of self-pollination ---[i] neg. reg. of self-pollination ------[i] prevention of self-pollination ; syn: self-incompatibility ; syn: self- pollination, incompatible interaction ---------[i] gametophyte-mediated prevention of self-pollination ; syn: gametophytic self-incompatibility ; syn: GSI ------------[i] S-RNase mediated prevention of self-pollination ------------[i] S-ligand-signaling mediated prevention of self-pollination ---------[i] sporophyte-mediated prevention of self-pollination ; syn: sporophytic self-incompatibility ; syn: SSI ------------[i] receptor-ligand mediated prevention of self-pollination <-- need a better name for this!

The names are a bit clunky but 'incompatibility' isn't a process, so we can't really use that in the term string. If anyone has better suggestions, let me know... 'termination of self-pollination' or perhaps 'termination of self pollen germination' or 'termination of pollination by self pollen'...?

I would also like to be able to capture info about whether a plant can self-fertilize, and whether it can create a hybrid with another species (since that was the original reason for this proposal!). To that end, we could have terms something like this:

pollination [i] self-pollination [i] cross pollination, intraspecies [i] cross pollination, interspecies

Using the soon-to-be-announced-and-clarified dual taxon annotation system, you would be able to specify which species the hybrid was between. Imagine how useful that would be!

I look forward to the gasps of horror at these suggestions! ;)

Cheers, Amelia.

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=579762

Hi Amelia,

I'd just like to draw your attention to some terms that TAIR added a long time ago and that are currently obsolete. The definitions might be useful. You may even want to rehydrate the terms.

GO:0009874 sporophytic self-incompatibility GO:0009872 gametophytic self-incompatibility

http://www.godatabase.org/cgi-bin/amigo/go.cgi?view=details&show\_associations=list&search\_constraint=terms&depth=0&query=GO:0009872 http://www.godatabase.org/cgi-bin/amigo/go.cgi?view=details&show\_associations=list&search\_constraint=terms&depth=0&query=GO:0009874

I see no harm in adding the other terms you suggested in the first DAG below. The GSI ones could potentially be used by Gramene and the SSI ones could be used by us and we'll be covering the terms needed by any other plant annotation effort that will come along.

As for the parentage, why do you have 'prevention of self-pollination' as a child of 'neg. reg. of self-pollination' instead of as a synonym? Seems like you don't need the extra layer. Or was there another child you were thinking of for 'neg. reg.' that would be a sibling of 'prevention'?

Finally, trying to capture whether a plant can self-fertilize or not in GO process seems like not the thing to do. The process of self- or non-self-pollination is described by the terms we've been discussing above - there's no need for additional terms - they would not describe a different process.

Tanya

Tanya

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=473796

Hi Tanya,

Thank you for the comments! We may well be able to reuse those GSI and SSI terms, but the names would probably have to change so that they didn't sound like phenotypes. I'm not really sure why they were obsoleted in the first place, since they represent processes, and it's just the name which could be considered dodgy.

Re: the regulation structure: the reason for having a separate neg. reg. term is that you could have processes that slowed pollination down without stopping it completely (downregulation), or processes that keep pollination turned off once it has been terminated (inhibition of activation of pollination).

Re: self-fertilization, cross-fertilization and hybridization: I realize that the process of successful pollination and fertilization is probably going to be very similar regardless of the source of the pollen. Unfortunately there isn't a good way of representing that a gp in involved in a certain subprocess and that subprocess is the same whether the plant is undergoing self, intraspecies or interspecies pollination without creating a whole bunch of terms. It's the same with any subprocess that can occur during a number of other processes - e.g. "MAPKKK cascade during osmolarity sensing" and "MAPKKK cascade during cell wall biogenesis". Hopefully in the future we can create combinatorial terms which would allow us to generate specific terms on the fly without having to add them all into the ontology, but that is a way off at the moment. To be able to say that a process can involve one organism, two organisms or two species is important, especially when the processes differ depending upon the organisms involved - consider self vs intraspp pollination in a plant which employs GSI - some of the process will be the same, but other parts will be different.

Cheers! Amelia.

Original comment by: girlwithglasses

[gocentral]

• assigned_to: nobody --> jenclark

Original comment by: mah11

[gocentral]

• status: open --> closed-out-of-date

Original comment by: jenclark