Handling seed propagations

[rjwhi...@gmail.com]

I am using Ghini to manage my private plant collection.

I have read your documentation on dealing with propagations, but I am still confused.

Say I have accessioned a batch of seeds into the database, then propagate some of those seeds, how do I record that? It seems that you can only make propagation records on plants, not accessions.

[Jaap Uilhoorn]

Hello

That is because, there is a diference between an accession and a plant. The plant is an actual plant or group of plants from the same species. at a specific location in your garden (or seeds in a drawer). The accession is the registration of this plant, or group of plants from the same species, in your collection database.

It is the actual plant, or group of plants from the same species, you are propagating. That's why you don't find a propagation editor in the accession editor screen.

So the accession is basically a registration number for an actual plant, (or group of....). Under this registration number you collect data about that plant. When you look carefully at the editor screens you will spot the differences in types of data registered.

Depending of the type of collection you have and the diferences between plant species there is some variation possible in how you register your plant or create the accession in your database.

In general you can say that an accessions consists of 1 species or taxon, comes from 1 source at the same time etcetera. A unique entry.

So the accession can represent a plant a single unique individual, but also a group of clones (for example cuttings) or genetically different (for example a batch of seeds), but always from the same species, source, etcetera. At this point you can choose what is appropriate and usefull way to accession it for your collection. One accession can this way represent several plants on several locations.

So if you receive a similar plant at another time or from a diferent source you have to create a new accession. In that case you have two accessions on the same species.

It is up to you if you create new accessions on new generations of your seeds. Or still consider them the same as the original seeds you once acquired and maintain them under the same accession.

I hope my explanation made it a bit clearer.

Jaap

Op vrijdag 24 augustus 2018 10:57:06 UTC+2 schreef rjwhi...@gmail.com:

[Mario Frasca]

Hi Jaap and thanks for your intervention.

it's nice to read it from a different source.

actually, I inadvertently answered in private, instead of to the group,
I'll forward what I wrote this morning ASAP.

On 08/24/2018 12:00 PM, Jaap Uilhoorn wrote:
> It is up to you if you create new accessions on new generations of
> your seeds. Or still consider them the same as the original seeds you
> once acquired and maintain them under the same accession.

well, it surely is up to you what you do with your data, but I would not
create a new accession on new generations from seeds.  what I guess you
ladies and guys do with a batch of seeds you germinate, you go to a
cabinet or to a shelf (a Location), grab a bag or a jar (a Plant),
collect some or all of the seeds (operation: Plant-Split), put them into
a germination pot (this is your newly created/split Plant), you possibly
do something special with it to favour or somehow influence germination
(write it down in some Note to the Plant), put it somewhere in your
greenhouse (a different Location than the original shelf or cabinet),
and start monitoring it (adding new Notes).

It's still the same material from the same source, acquired/accessioned
at the same time, so here I do not see the need and I would advise
against having a new accession.  imagine that someone comes to your
garden and helps you to refine the identification: you would want to
have the revised information apply to the whole accession.

I can imagine special cases, like you observe a variation you hadn't
expected.  but you would observe it on a set of germinated plants, not
on all of them, so you would create a new accession, but only after you
observe whether the plants indeed show some variation, and you would do
that only for those plants that show the variation.

well, this is the mathematician's point of view.  botanists may explain
it better.

:-)

Mario

[Mario Frasca]

hi RJ,

Say I have accessioned a batch of seeds into the database, then propagate some of those seeds, how do I record that?

let me first make sure we both understand ›propagate‹ in the same sense, I have the impression you're talking of ›germinate‹.

also, maybe since you're handling seeds in your database, you might be interested in our second batch of ›Contributed user recipes‹, ›using-ghini-for-a-seed-database‹.

It seems that you can only make propagation records on plants, not accessions.

well, yes, obviously… accessions are instances of an abstract concept, not physical objects.

seeds are, as far as ghini is concerned, a form of plant.  if you germinate them, you are altering their form, and you are very likely giving them a treatment, and moving them from one location to an other.  this is conceptually similar to sending seeds, described in the above recipes page.

if on the other hand you're really talking of ›propagate‹, then please add more information of what you do in practice, like describing the details of your handling and which are the physical objects involved, because I do not manage to imagine propagating anything else than a plant (if you're doing a cutting), or two plants (if you're pollinating a seed).  as stated in the docs:

In the case of a seed propagation trial, you have a pollen parent, and a
seed parent. You should always associate the Propagation trial to the seed
parent.

thanks for asking and for using ghini.

Mario Frasca

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[Mario Frasca]

oops, I forgot to mention, Jaap's explanation is just perfectly correct,

thank you!

[rjwhi...@gmail.com]

Thank you Jaap and Mario for your explanations.

If I understand correctly, this is the process I need to follow:

1. When I receive a batch of seeds of the same species and from the same source, I create a new accession.
2. When I withdraw seeds from storage I create a new plant.
3. When I attempt to propagate plants from the seeds I withdrew I add a propagation record to the plant.
4. If the propagation was successful, I create a new accession and associate it with the propagation attempt.

Please correct me if I am wrong.

---

Robert White.

[Jaap Uilhoorn]

Hello Robert

Generally spoken, There are some minimum requirements in the administration and some variations depending on the type and purpose of the garden and or the collection. And depending on the plants and purpose of the plants you collect there maybe some variation.

A herbal garden with a more educational purpose has different data requirements than a more scientifically oriented garden or collection. The scientist of the second garden for example may put a lot of value on genetic purity of a wild collected plant or other valuable genetic material. Suppose the wild collected plant is an annual resown for 25 years in a row. Factors like hybridasation and/or selective adapting to garden conditions may affect the genetic makeup of your plant. For the herbal garden this is probably no issue. At this point you may want to choose about whether to create new accessions or not for your propagated material.

What I try to tell you is that it is very important to consider for your garden and collection what is important. As far as I can see Ghini can handle the data. But i suggest to make a copy of your database in which you can safely experiment without hurting the original data.

When I receive a batch of seeds of the same species and from the same source, I create a new accession.

Yes, Bassicaly the accession is unique, based on species, source, reception date, form (seed bulb cutting etc.) and so on. So it is possible and normal if through time you find more accessions of the same species in your collection.

When I withdraw seeds from storage I create a new plant.

yes, it is possible the accession is present as seed in your seedvault (a location) and as a plant in in a specific place in the garden (also a location). When you search such an accession in Ghini you can find several plants associated with it

It might look like this. one accession with 3 plants in 3 locations.

As Mario described you can split a plant. So register your seeds as a plant and do not forget to ad a (estimated) quantity as you cannot split a quantity of 1.

When I attempt to propagate plants from the seeds I withdrew I add a propagation record to the plant.

yes, because the database is also there to store information about what happened with your plants, what worked and what did not. what care did the plant receive. In general all sorts of event data can be described in the database. Therefore are the note fields. The propagation editor is a more specialised tool in this sense.

If the propagation was successful, I create a new accession and associate it with the propagation attempt.

Not necessarily, this depends on the type and purpose of garden, collection, species etc. as described above. That's for you to consider.

For the herbal garden for example we have a bed with pot marigold (Calendula officinalis). An Annual species. It is reproducing itself by seed year after year. We also store some seed for safety. We don't care about  genetic purity so we decided to maintain it under one and the same accession number. But we do register its lifecycle for future reference for the people maintaining the garden. Because you have to know these things while for example weeding or checking if the seeds in the soil survived the winter.

Jaap

Op zaterdag 25 augustus 2018 04:51:35 UTC+2 schreef rjwhi...@gmail.com:

[Mario Frasca]

Hi Robert and Jaap!

On 08/24/2018 09:51 PM, rjwhi...@gmail.com wrote:

Thank you Jaap and Mario for your explanations.

If I understand correctly, this is the process I need to follow:

• When I receive a batch of seeds of the same species and from the same source, I create a new accession.

yes, and a first new plant

• When I withdraw seeds from storage I create a new plant.

yes, by splitting the seeds plant

• When I attempt to propagate plants from the seeds I withdrew I add a propagation record to the plant.

this I'm not so sure.  you didn't comment on my question about ›propagate‹ and ›germinate‹.  if you're germinating the seeds in your accession, you are only altering the form in which plants are kept in the garden, and moving them from one location to an other. 

as Jaap is rightfully stressing, it depends on what's the purpose of your collection, if you're interested in keeping precise track of generations, for example if you're doing annuals.

I would use propagation records when collecting seeds from a plant, not when germinating seeds.

but if it serves you this way, you're welcome to use it this way.

• If the propagation was successful, I create a new accession and associate it with the propagation attempt.

this is indeed what a propagation record is meant for, yes.

Please correct me if I am wrong.

:-)

also, as Jaap suggests: make experiments with your data.  you can also write a script describing the events in a couple of years in your garden, run it and see if you get into excessive trouble with limited advantage.

this is a screenshot from a presentation by an employee at the mobot, held a couple of years ago at the regional conference 'building botanical bridges':

they are using a `-` instead of a `.` as a separator, that's the only difference.

accession 2016.0100 arrives in seeds, and you germinate them (bit by bit).  when you germinate a seeds-plant, you get a living-plant, and it stays in the same accession, but it should be a different plant.

accession 2016.0038 arrives in plant form, and you place it at different locations in the garden.

ciao, regards,

Mario

[Mario Frasca]

Hallo Robert and Jaap

On 08/24/2018 09:51 PM, rjwhi...@gmail.com wrote:

• When I receive a batch of seeds of the same species and from the same source, I create a new accession.

let me describe a more complex scenario and please help me correct and complete it (scenario and/or description).

imagine you are authorized to collect plant material in a wild area within your country…

actually, you might need to keep track of your authorizations, too, and the software at the moment does not help.  feel free to open an issue describing the case.  we've never dealt with this part.

the material you collect is in dried form, in practice: vouchers and seeds, but you leave (most of) the (living) plant in place.  (consider the role of the multiplier 'quantity' to a Plant object.)

if you do this, I would add to the database an accession describing the parent plant, and I think I also would keep the parent plant in the database, indicating its (approximate) location.  vouchers, they may be plant parts, or whole plants.  if they are whole plants, that's easy: add them to the database as plants with pictures and notes.  if you keep them yourself in your herbarium, that would be your location.  if it's plant parts I would not know.  consider your practice, check it against the software, and come with hints.

collected seeds, in this case, would be propagation trials of the parent wild plant.  you may also be able to collect seeds from the same plant in different occasions.  if successful, these would become separate accessions, and their association to the parent wild plant makes it possible to relate them to each other.

maybe too complex for a simple herbal garden, maybe needing further refinement for a scientifically oriented garden?

regards, and interested in comments.

Mario

[Mario Frasca]

Hi Jaap!

I'm commenting to the screenshot you shared.  you're actually missing
the authorship for your Achillea millefolium.  is it a big deal, not
mentioning ›L.‹?  maybe not, or maybe a deadly sin according to others.

the ghini species editor lets you retrieve this information from 'the
plant list', while you review the rest of the fields, just click on the
green button next to the epithet text field, and ghini will start an
internet interaction with 'the plant list' online service.

https://ghini.readthedocs.io/en/ghini-1.0-dev/use_cases.html#taxonomy

in particular

Adding a new species — the plant list.

it helps with authorship, synonyms, but also to avoid errors like:

 Apeiba membranacea
 Bactris bronniarti
 Cupania cineria
 Inga cilindrica
 Miconia dolychorrincha
 Perebea xantochima
 Protium glabrecens
 Vismia callenensis

right, some are typical Latin-American mistakes (ll/y; sce/ce), some are
typical neolatin (y/i; h/∅), but there are epithets that really
challenge us, and our memory, in my opinion.

if the mistake is too early in the epithet, if your guess contains too
many errors, like in dolychorrincha (three mistakes, first mistake in
fourth position), the plant list might not find any match.  for these
cases you may try the Tools→Taxonomy Check.  admittedly, more complex in
use, but more powerful, and you can run it on an already imported database.

regards,

Mario

[Jaap Uilhoorn]

Hey Mario

No it's not a big deal mentioning the author, but it appears something strange is going on. I actually use the green button. I did a few species manually. Two more screenshots one of the list with species and one of the accessions.

See the difference, the authors are not passed on. I checked on my laptop and it shows the same. Authors are also missing on labels I made a few days ago.

Issue for Github? Not now, it's getting late for me

Jaap

Op zaterdag 25 augustus 2018 17:05:36 UTC+2 schreef Mario Frasca:

[Mario Frasca]

buongiorno Jaap

I see, I had forgotten this behaviour, and I would not know what is the best thing to do.  as my scientific taxonomic advisor said: "providing a binomial without authorship is a mistake".

so we have the author, and we're not reporting it in accession nor plant.

meaning that, if you have a result list with plants or accessions, you will not know if the authorship is missing, since ghini anyway doesn't report it.

it's a very small correction, and if you want to report it, please do so.

Mario

[Jaap Uilhoorn]

Good morning Mario

I will open an issue on Github. I hope it's not to complicated to solve this problem.

Jaap

Op zondag 26 augustus 2018 13:36:19 UTC+2 schreef Mario Frasca:

[piet paardebloem]

I will come back to you on this one. I haven't used the voucher editor yet, for example. I suppose an institute  can also have a herbarium beside of the garden. Or work together with a herbarium.

Op 15:49 ZA 25 Aug 2018 schreef Mario Frasca <ma...@anche.no>:

--

[Mario Frasca]

Hi Robert!

did Jaap and I help you answer your question?

regards, Mario

[Mario Frasca]

just opened an issue, if you want to have a look?

https://github.com/Ghini/ghini.desktop/issues/415

[rjwhi...@gmail.com]

Hi Mario and Jaap!

Sorry for my late reply, I've been quite busy.

you didn't comment on my question about ›propagate‹ and ›germinate‹

I use 'propagate' to mean produce a new plant from a parent plant and 'germinate' to mean sprout seeds or spores.

this is a screenshot from a presentation by an employee at the mobot, held a couple of years ago at the regional conference 'building botanical bridges'

That screenshot was very helpful. Do you happen to have the full presentation?

did Jaap and I help you answer your question?

Yes, thanks for your help. As you suggested, I am going to create a new database to experiment in.

Once again, thank you both for your assistance.

---

Robert White

[Mario Frasca]

hi everybody,

On 08/31/2018 04:25 PM, rjwhi...@gmail.com wrote:

Hi Mario and Jaap!

Sorry for my late reply, I've been quite busy.

you didn't comment on my question about ›propagate‹ and ›germinate‹

I use 'propagate' to mean produce a new plant from a parent plant and 'germinate' to mean sprout seeds or spores.

sounds ok, but you didn't completely remove all of my doubt.
if you 'germinate' seeds from a parent plant, you also call that 'propagate' (the parent plant), right?

oh, by the way, some time ago I found a very good paper from an Irish garden, which allowed me edit the 'accession' article on the wikipedia.

https://en.wikipedia.org/wiki/Accession_number_(library_science)
http://www.botanicgardens.ie/educ/accnosho.pdf

this is a screenshot from a presentation by an employee at the mobot, held a couple of years ago at the regional conference 'building botanical bridges'

That screenshot was very helpful. Do you happen to have the full presentation?

eh, what to say, how silly it may sound, I hinted the author at distributing their paper under a Creative Commons license, and I was explicitly instructed not to spread the document any further, except a couple of screenshots as the one I just posted here.  and here comes the one that makes a couple, so don't ask for more ;-)



it is titled "best practices in living collection management".  if you couple these words with 'botany' and ask duckduckgo, you get more than a few usable hints.

according to me, if you explore ghini, experiment with it, and take advantage of what it offers, it will be the software itself, hinting you towards similarly good practice.  only thing really missing in ghini and mentioned in the presentation is that we do nothing to keep your phytosanitary permissions in order.  not yet.  if anybody asks, and they tell me what it is that they need, we do that.

one more thing, not often mentioned in best practices, missing in ghini (and I don't know who's ever financing that part) is the old "issue-9", now https://github.com/Ghini/ghini.desktop/issues/92.

we have workarounds, check the contributed recipes.

ciao, enjoy,
Mario

[Mario Frasca]

these considerations also apply (I checked some automatic translations,
and they are quite correct.)

»In principe moeten alle zaden die via seksuele reproductie in de tuin
gevormd zijn, een nieuw
accessienummer krijgen, omdat het genetische materiaal ‘vervuild’ kan
zijn met andere planten in
de tuin. Dit zou bij met name eenjarige perk- en landschapsplanten weer
niet per sé hoeven,
omdat ieder jaar weer een nieuwe generatie oplevert, en er dus vanaf het
eerste jaar dat een
accessie in de tuin staat ieder jaar er één bij geteld kan worden. Zeker
wanneer planten in het wild
verzameld zijn en voor wetenschappelijk onderzoek gebruikt kunnen gaan
worden, moeten deze
zaken nauwkeurig bijgehouden worden. Als er ieder jaar bij dezelfde
kweker dezelfde éénjarigen
opnieuw besteld worden, kan het accessienummer om praktische redenen
gelijk blijven. In zo’n
geval zou het jaar in het accessienummer in theorie ook ‘0000’ of
‘-----’ kunnen zijn.«

from a quite lengthy document (298 pages), that can be downloaded from
www.botanischetuinen.nl.

M

[Jaap Uilhoorn]

Hello Everybody

Mario, in reaction to: sounds ok, but you didn't completely remove all of my doubt.

if you 'germinate' seeds from a parent plant, you also call that 'propagate' (the parent plant), right?

Germinate is about the proces of the embryo in the seed is developing into a seedling. And propagate is about the act of reproducing. Creating more plants or a new generation so to speak. Propagation can be done by means of seeds, cuttings etcetera.

With this in mind I looked at the propagtion editor and the discussion above. The propagation editor is about recording data about propagation attempts. Which is usefull, so we don't have to invent things twice. But I think there is no link with creating new accessions or linking generations off accessions. Is this what you were hinting at?

I have been pondering about these generations of annuals also. Creating new accessions on a yearly base is a lot of work. I prefer to keep it as simple as possible, but if a garden wants to be aware of these generations I thought of this

I noticed (in my test database) that the format of the accession number could be changed manualy . So I invented Perpetual Reproduction Cycle. I thought that with a similar numerical value and a simple code one keeps al the important data together, And in case info is needed in the context of the reproduction cycle one can do the math himself. Of course my question, am I violating any data integrity?

The accession number, in my example, without the PRC code I used for the seed in storage.

Jaap

Op zaterdag 1 september 2018 02:15:34 UTC+2 schreef Mario Frasca:

[Mario Frasca]

hi everybody from me too again,

On 09/12/2018 01:26 AM, Jaap Uilhoorn wrote:

[…] The propagation editor is about recording data about propagation attempts. Which is usefull, so we don't have to invent things twice. But I think there is no link with creating new accessions or linking generations off accessions.

well, actually it does, I mean there is a link between Propagations - generations and new Accessions.  when you create a new Accession, you may switch to the second pane, called 'Source'.

among the Contacts there is a hard coded value, reading 'Garden Propagation'.

you choose that, and you get the chance to relate your new Accession to a successful plant Propagation.  only those Propagations will show which are successful, and have not yet been accessioned in full.

I think I have a video about this, or you can experiment yourself.

https://www.youtube.com/user/mrgsfs/videos?shelf_id=0&sort=dd&view=0

no, looks like I only have how to "follow propagations", not how to create them.

Is this what you were hinting at?

my concern is that if you have an Accession where the Plant material is still in seeds form, and you are changing the form by germinating the seeds, these plants are absolutely still in the same Accession as the seeds, same genetic material, same source, same time (entering the collection), so same Accession.  you are really not adding anything to your collection, only changing form.

a different thing if you collected seeds from your own Plant, are germinating them, and you are still keeping all the action within a propagation attempt, that is, still within the parent Plant.  then, at the moment you decide the attempt was successful, you would create a new Accession and you go through the steps I described above.

I also suppose that, if you do annuals and you don't precisely care about the genetic traceability of generations, you would not go through the whole nuisance of propagations etc, and you would simply sow your seeds in your garden, and possibly renew the plant count estimate when you think so.

I have been pondering about these generations of annuals also. Creating new accessions on a yearly base is a lot of work.

your idea, of having annuals inside the same accession, is something I have seen in other sources too.  your Popular Republic of China TLA is a bit funny.  the hint I had seen was about removing the year altogether, and have these accessions as ----.####.  from ghini's point of view, this is easier, for it does not conflict with ghini counting for you.  you can have two accession templates in your ID format, like this:

and you would be able to let ghini count for you, which would be the next available accession code.  …  actually, you better have also this one: »%{Y-1}.####«, helping you add (in January) stuff still related to the previous year.  the trailing PRC in your idea stands in the way of ghini automatic counting.  (btw: you really need to press <enter> after you edit a template format.)

you are not exactly breaking anything special, just this help mechanism, and it easily fixed if you insist, but I would expect more practical difficulties at several points downstream, for example reserving space on your labels, and possibly with the print and scan resolution needed to produce QR codes, possibly with bad written code we may have, where I rely on the four(dot)four(dot)any structure.  these are practical things, not database related, but I would keep them in consideration.

I noticed (in my test database) that the format of the accession number could be changed manualy . So I invented Perpetual Reproduction Cycle. I thought that with a similar numerical value and a simple code one keeps al the important data together, And in case info is needed in the context of the reproduction cycle one can do the math himself. Of course my question, am I violating any data integrity?

again, not really violating, but you are defining logical links that you can follow, but which the software and much less the database knows anything about.  it's risky, I think.

The accession number, in my example, without the PRC code I used for the seed in storage.

I'm not sure I follow this part, and I'm wondering.  you do so, only to keep track of the year when the seeds were collected, or any other reason?  if it is only so that you know when to germinate them, I'm afraid I would do this with a note to the plant (in seeds form).  something like deciding that every jar or bag of seeds has a note with category collection-season, or germinate-by, or whatever fits you, that help you choose it (the jar) when you decide you want to germinate stuff in your annuals.  the code of such a plant might be `----.0032.13`.  this is what I would do, or what I suppose I would do.

again too many words, I hope that some were useful,

best,

Mario