somatic embryogenesis

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A request carried over from:

[ 1242580 ] TAIR process terms_july 2005

> 3. somatic embryogenesis ISA embryonic development (sensu Magnoliophyta) > GO:0009793 > Def: Initiation of embryos from previously differentiated somatic cells. > Ref: http://www.uwrf.edu/~dc01/somatlab.html

Jen

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/2749":https://sourceforge.net/p/geneontology/ontology-requests/2749

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I have written to several plant lists to get comments on this one.

Jen

Original comment by: jenclark

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Wrote to the development list with subject line:

'somatic embryogenesis'

Jen

Original comment by: jenclark

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Sorry it has taken me a while to comment on this, but it is way out of my expertise. Are the little plants that develop considered embryos? Or are they just little plants?

David

Original comment by: ukemi

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I wondered that as well actually. I'll ask one of the plant ontology experts. I have a feeling that calling them embryos might be going a bit far.

Jen

Original comment by: jenclark

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Jen,

The reason I ask is because in the def of an embryo we say that the timing of embryogenesis is a bit arbitrary and we say that in plants, it is up until the time of seed dormancy. These little plants never go through that stage.

David

Original comment by: ukemi

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Yes that's a good point. I really think it's unlikely that these would be considered to be embryos in that sense. I've written to Tody Kellogge to check. It may just be that they're using the phrase embryogenesis because a small plant results. It doesn't necessarily mean that there's been seed-style embryo structure with endosperm formation and dormancy though. We might need to think a bit creatively on this one. I'll wait for Tody's feedback.

I think this kind of problem is going come up a lot with plants because they don't get all their organ formation over and done with by the end of an embryo or larval stage. They can keep producing new organs right through the adult phase too. It may be tricky with our use of timing to categorise things.

Jen

Original comment by: jenclark

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Hi Jen - Sorry to be slow - was on holiday. I guess it depends on how you define embryo vs. small plant. Certainly the little things that appear in a grapefruit seed look like embryos to me. The definition of embryo in PO is "a young sporophyte contained within a seed", so I think a somatic embryo would be an instance of embryo. Toby

Original comment by: jenclark

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I need to talk to David about this because of conflicts in the def of the development term and the morphogenesis term.

Will do that tomorrow.

Jen

Original comment by: jenclark

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Hi Suparna,

Do you know if there is a difference between

plantlet formation on parent plant ; GO:0048624 def: The process whereby a new plantlet develops from a meristem on the plant body. As part 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.

and the somatic embryogenesis that you're asking for. I'm not sure of that.

Should the term about have included plantlets arising from previously differentiated cells? I'm starting to think it should.

Thanks,

Jen

Original comment by: jenclark

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Hi Suparna,

Reading around, it seems as if somatic embryogenesis can be induced by putting hormones on a fully differentiated cell and causing it to form an embryo.

Would you consider this the same as GO:0048624? Would you be happy if I just broaden the def and add a synonym?

Jen

Original comment by: jenclark

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Jen,

I am not so sure. I had included the reference I found for somatic embryogenesis and there is a paper at the end of the page which might have more info about the process of SE. I don't think it is the same as GO:0048624. Somatic embryogenesis refers to the initiation of embryos from previously differentiated somatic cells. Whereas the definition for GO:0048624 is "plantlet develops from a meristem" and meristem is undifferentiated.

Cheers, Suparna

Original comment by: smundodi

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Hi Supurna and Jen,

So, is somatic embryogenesis a normal process or is it only when you treat the plant in a special way?

David

Original comment by: ukemi

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Atleast the reviews I have read so far pretty much talks about the tissue culture media and somatic embryos. However, there are some plant enzymes that are known to induce somatic embryogenesis and if that is the case, it makes me believe that it could happen under normal plant growth conditions but I don't know.

Suparna

Original comment by: smundodi

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Hi,

Here is what one of the experts had to say about SE. According to her, it is a natural process in some plants(not all) and there are true embryos here as well.

Here is the reply from Eugenia Russinova(SE expert/TAIR user) "I am happy to help you. Yes, in general for most plant species (more than 300) somatic embryogenesis occurs in culture, in vitro. However natural somatic embryogenesis has been documented in plants such as orchid, Malaxis paludosa, the succulent plants of the family Crassulaceae (Kalanchoe) and Ranunculus scleratus. The process apomixis, asexual seed formation, can also be regarded as a case of natural somatic embryogenesis. Somatic embryogenesis follows a developmental pattern similar to zygotic embryogenesis meaning true embryos are formed. However there are differences. You can find more info in Mordhorst et al (1998) Somatic Embryogenesis in Arabidopsis thaliana is facilitated by Mutations in Genes Repressing Meristematic Cell Divisions. Genetics 149: 549563 or Mordhorst, A. P., M. A. J. Toonen and S. C. de Vries, 1997 Plant embryogenesis. Crit. Rev. Pl. Sci. 16: 535576."

I hope this helps.

Suparna

Original comment by: smundodi

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Hi Jen and others,

Sorry I am jumping in little late. Yes, term 'somatic embryogenesis' is needed in GO, at TAIR, we are using GO terms to describe phenotypes and I am curently annotating LEC2, which is directly involved in induction of somatic embryogenesis in Arabidopsis, so this term would be very useful.

To answer to David's question, yes, it does occur naturaly in some plants, like in citruses, where somatic (nucelar) polyembryony is indeed a case of somatic embryogensis in vivo, or in orchids, as Suparna mentioned (there are others, I just don't remember them right now).

And last, but not least, in PO, we have terms 'somatic embryo', with current definition:" An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote. ". However, we are planing to modify this definition and include cases where somatic embryos occur in vivo.

Best,

Katica

Original comment by: katica

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Hi David,

Please let me know if you have any more comments on this issue. If not, I will add this term this week. Thanx

Suparna

Original comment by: smundodi

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Hi David,

Please let me know if you have any more comments on this issue. If not, I will add this term this week. Thanx

Suparna

Original comment by: smundodi

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Original comment by: jenclark

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Hi Suparna,

I see you have put the term in according to your initial submission, but we have to work on this a bit more as there is now a true path violation as explained David in his comment of 2005-08-05 13:03. We need to at least reconsider the def of embryo development (sensu Magnoliophyta)

The comments from your expert Eugenia Russinova are very helpful. Can you ask her more questions please?

We have this term:

plantlet formation on parent plant ; GO:0048624 def: The process whereby a new plantlet develops from a meristem on the plant body. As part 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.

This was intended to cover the kind of vivipary that is seen when small plantlets develop on the edge of kalanchoe leaves. Can you ask her the following:

1) Should the def of the term above say 'The process whereby a new plantlet develops from a previously differentiated somatic cell on the plant body.'

2) Would it be appropriate to give this term the exact synonym 'somatic embryogenesis'

3) Is somatic embryogenesis a broader concept than the process by which small plants arise on the leaves of kalanchoe?

4) If it is a broader concept then how do they relate to one another?

The two options that I can see are

plantlet formation on parent plant exact synonym: somatic embryogenesis exact synonym: apomixis

(with def modified to have 'previously differentiated somatic cell' instead of 'meristem'.

or

[i]somatic embryogenesis ; GO:new ---[i]plantlet formation on parent plant ---[i]apomixis

Do you have access to copies of the papers that you mentioned? I do not so I'd have to order them specially. It seems to me that for this kind of think it might be better to get the info from an expert who has an overview of the subject anyway.

Thanks for your help in this.

Jennifer

P.S. I have moved this item to low priority as the term you need is now in the ontology and we just need to get things tidied up to get the right parentage and to eliminate true path violations.

Original comment by: jenclark

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Original comment by: jenclark

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Hi Suparna,

No, I just wanted to be sure we had considered all the options.

David

Original comment by: ukemi

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Hi Jen,

Have sent out an email message to Eugenia(SE expert) with your questions. Will post the answers from her as soon as I get one.

Suparna

Original comment by: smundodi

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Hi Suparna,

Did you get an answer to that yet?

Thanks,

Jen

Original comment by: jenclark

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Jen,

Yes, i did. Sorry for the delay. Here is the transcript of my conversation with Eugenia.

>> [plantlet formation on parent plant ; GO:0048624 >> def: The process whereby a new plantlet develops >> from a meristem on the plant body. As part 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. >> Jenny: In general somatic embryos can be distinguished from adventitious shoots, because they are bipolar, having both a shoot and root pole, and they do not have any vascular connections with the underlying parental tissue. You have to distinguish between adventitious shoot formation and embryogenesis. In case of Kalanchoe bipolar embryo is develop but it remains connected to the parental tissue for some time.

>> This was intended to cover the kind of vivipary >> that is seen when small plantlets develop on the >> edge of kalanchoe leaves. Can you ask her the >> following: >> >> 1) Should the def of the term above say 'The >> process whereby a new plantlet develops from a >> previously differentiated somatic cell on the >> plant body.' >>

Jenny: Yes, you can say that

>> 2) Would it be appropriate to give this term the >> exact synonym 'somatic embryogenesis'

Jenny: Yes, that would be appropriate

>> >> 3) Is somatic embryogenesis a broader concept than >> the process by which small plants arise on the >> leaves of kalanchoe? >>

Jenny: Yes, SE is broader concept

>> 4) If it is a broader concept then how do they >> relate to one another? >>

Jenny: Formation of plantlets in Kalanchoe is an example of SE but this process also occurs in vitro in cultures.

>> The two options that I can see are >> >> plantlet formation on parent plant >> exact synonym: somatic embryogenesis >> exact synonym: apomixis >> >> (with def modified to have 'previously >> differentiated somatic cell' instead of 'meristem'. >>

Jenny: There are lots of debates if the cells that give rise to SE are meristematic or differentiated. From what I know SE may arise for meristematic kind of cells (for example direct SE, SE in Kalanchoe) but also from differentiated cells that have to first undergo process of dedifferentiation for example SE that arise for callus (indirect SE).

>> or >> >> [i]somatic embryogenesis ; GO:new >> ---[i]plantlet formation on parent plant >> ---[i]apomixis >>

Jenny: The last classification will be better

Let me know if you need anything else.

Suparna

Original comment by: smundodi

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Hi Suparna,

Thanks for asking all those questions. That was really a huge help.

Strangely, though I gave a choice of two conflicting options, your expert has said 'yes' to both. However, it does give us something to work on. :-)

I have also dug up a text book with a nice straightforward explanation that may help.

The book says:

somatic embryogenesis is the production of embryos from vegetative tissue. The embryos closely resemble zygotic embryos and pass through the same developmental stages, except that they don't have a suspensor cell. (Instant Notes Developmental Biology, ISBN 1859961533, p409)

Going by this and what your expert says I think I can come up with a graph to accommodate all the issues.

I had to do a bit of juggling of terms to get the structure right. The only way I could see was to give the improved ontology file and the before and after pictures of graphviz. I have put these in my public directory as a zip file. I hope it's okay.

http://www.ebi.ac.uk/~jclark/stored/content/ somatic_embryogenesis/somatic_embryogenesis.zip

There is a change to the def of embryonic development (sensu magnoliophyta).

It is now:

The process whose specific outcome is the progression of the embryo over time from the initial to the mature state. In the case of the zygotic embryo this would be from zygote formation to the end of seed dormancy. In the case of the vegetative embryo this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. As in, but not restricted to, the flowering plants (Magnoliophyta, ncbi_taxonomy_id:3398).

We will also need to change the def of embryonic development but I have not done that yet.

Thanks,

Jen

Original comment by: jenclark

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(David: read on as this involved a proposal to modify the definition of 'embryonic development.' #6 below)

Hi Jen,

I've finally had time to sort through this email thread and have a look at the new structure that you propose. You're right. This is a brain-twister. I like 'zygotic embryo development (sensu Magnoliophyta)' and its relationships look good.

A few questions:

1. From reading Jenny's comments, it sounds like we can modify the definition of SE to be something like "Initiation and development of a somatic embryo, an embryo arising from previously differentiated somatic cells or from a meristem, rather than from fused haploid gametes."

2. Are we modifying the definition of 'plantlet formation on parent plant" to be: "The process whereby a new plantlet develops from a previously differentiated somatic cell on the plant body..."?
   The older definition ("The process whereby a new plantlet develops from a meristem on the plant body....") is still in your gzip file. From the SE def and the structure, plantlet = embryo, right?

3. The part_of relationship between 'somatic embryogenesis', and 'vegetative embryo development (s. M.) confuses me. Is this because the latter term refers to the 'development' vs. 'initiation and development of ...'? In practice, what would I annotate to SE vs. VED (s.M.)? Should we also then have a term for the 'initiation of ...'?

4. Where will the synonym 'apomixis' go?

5. Is the convention to capitalize the word that comes after sensu or not? If yes, please capitalize Magnoliophyta when the terms go live.

6. Still need to modify the definition of 'embryonic development.' Currently:

"The process whose specific outcome is the progression of an embryo from zygote formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific and may be somewhat arbitrary. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants."

I propose this change:

"The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific and may be somewhat arbitrary. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant."

I hope this gets the ball rolling towards the goal.

Thanks,

Tanya

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Original comment by: jenclark