Family tree of apple varieties with Gramps?

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Hi all,

I just installed Gramps 5.1.5 on Fedora 34, for an entirely different purpose than setting up a family tree of people. I am an absolute beginner regarding Gramps or even genealogy.

I would like to know whether it’s possible to use Gramps for setting up a family tree of fruit varieties, and to represent that tree graphically.

I do volunteer work in a Dutch pomological group of people who try to preserve old fruit varieties.
Recently, we acquired a data set with pedigree information of a few hundred apple varieties that grow in The Netherlands. Different varieties are made by cross-pollination and subsequently planting seeds that emerge from this cross pollination. Once the variety exists, it is further propagated vegetatively by grafting. This way varieties can become very old. The typical lifespan of a large apple tree is around 100 years, varieties can be very much older, some apple varieties from the late Roman Empire still exist today.

This means that once a variety exists, it virtually has an infinite life span. It also means that cross-pollination can be done over many generations. A 600-year old variety can be cross-bred with a variety that came into existence 10 years ago. This younger variety may very well be the great-great-grandchild of the 600-year old one.

The data set that we have contains information of a few hundred variety names, with the names of their parents. The year in which each variety was formed is known, or can be guessed from pomological literature.
Given the possibility of having multiple generations between different children from a single variety, and variety lifespans possibly covering multiple centuries (while hardly any of them die), it is clear that such a family tree can become very complex. Furthermore, apples do not really have sexes. Each flower is both male and female, although in a variety, the mother- and father variety can be distinguished. Because of the bisexuality of apple flowers, a parent can be either father or mother to a child variety.

Last week we had a discussion with the person who did the genetic (pedigree) analysis. He once made a small family tree for a few related varieties, and that already was a huge amount of work. So, we would like to automate this.

With apples having both sexes represented in a single child, and parents having the possibility to be either mother or father, and different offspring spanning multiple generations, would it be possible to construct such a complex family tree for apple varieties using Gramps, with only names of varieties and their parents, and years of “birth”?
If it would be technically possible, is more information on each variety needed, or are the already available data sufficient?

Looking forward to hearing from you,

Marcel

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I was thinking that apple tree varieties are mostly dioecious and so the pollen contributor would be the “father”.

Of course, it is more complex than that since it is so common to graft a scion to a rootstock rather than do seedlings.

I expect that you could use Gramps to keep records without much (if any) code modification, just using custom attributes. But it will probably require creating some 3rd party add-ons to get useful charts and reports.

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Technically, Gramps manages a directed acyclic graph. There is no reason why you couldn’t record your apple pedigree with it. However you must first think over how you adapt the principles to your use case.

Your varieties would be represented by a Person record. The notes allow to write down any description but you could “specialise” them for some specific data. Since the flowers are bisexual, you can as well assign “Unknown” sex to them, unless you want to record some subtlety which you seem to be able to distinguish.

A family would stand for cross-pollination. If you can make a difference between father-mother, that’s easier. But Gramps now has the possibility of recording same-sex marriage, which is consistent with “Unknown” sex if you choose so.

The child for this cross-pollination is the new variety. I assume that only a single variety can result from it (though DNA genes may be permuted randomly).

Along any path, you have an alternation person-family-person-…

So, using Gramps is possible but don’t run consistency checks on it as they will object against parenthood age or time differences between parents. You may have to review the preference settings.

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One of the interesting things that I read was that the kernels in an apple core could have different genetics… like puppies in a litter.

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Each apple can hold at most 10 seeds, each of them can stem from a different pollen donor. When the apple variety is triploid, it becomes even more complex. Puppies in a litter are most likely (although not necessarily) from the same father, with apples you can easily have seeds from different fathers inside a single apple.

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Thanks, from your answer I get the idea that it should be possible. Will try on a small subset later this week.
Another question: Can Gramps deal with multiple marriages (or even polygamy)?
Some apple varieties (Cox Orange Pippin is notorious for it) have been used as breeding stock for tens or even hundreds of different varieties, each cross-pollinated with a different variety, of the other way around, different varieties pollinated with such a popular apple variety.

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Any “person” may be part of several “families”. A “family” in Gramps is defined as an association between two partners. You give it a type, like marriage, extra marital relation, … It can even be a custom type (e.g. pollination). The temporal ordering of the “families” is not mandatory. It is implicit from the date of the associated events. Therefore, if you don’t enter events like banns, marriage, divorce, first dating, … you are only interested in the existence of such “families”. Transpose for your apples.

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I collect various comics dealing with genealogy. This one seems appropriate for this thread.

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Sorry, but we cannot really transpose human relations to apple tree (and varieties) into gramps!

Many (top) branches of one tree can have some minor genetic variations! So, one tree (like one apple tree) looks like rather like one family (trunk and roots) with multiple children… One variety and multiple variants, and this is for one subject…

I do not know apple sexuality… sorry, seeds and sexual reproduction, but I make some grafting (often old varieties from Rhine Valley). As far as I know varieties will never really be fixed with seeds… As one variety can have differents behaviors (type of rootstock, soil/biotop, pruning, localisation of the graft on the trunk, Bouche-Thomas hedge, etc.), to fill into gramps (or whatever), genealogy of an apple variety like done with individual, might lead to poor quality of data set!!!

This might match for tests or an “industrial” production with one hydrid (or a new variety). But this will not be a long (or “middle”) time/term value/solution.

For me, one tree is rather a family/patronymic (or set of genetic data changes/grows and modifications). Varieties are just the human transcription for a pseudo-classification… Both third-parties of the same “variety/name”, may be completly different after eating/testing/looking them…

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I beg to differ.

New apple varieties are created by cross-pollination of older varieties, resulting in hundreds of different new seedlings from a single pair of parents. From these new seedlings, only the very best in terms of taste, pest resistance, growth characteristics, transport and storage tolerance etc., are selected and may make it into a new named variety, which is subsequently propagated asexually by grafting scions onto rootstocks. There may be phenotypical differences between individuals of this variety because of different rootstocks being used, or different soil/climate/elevation where the tree is growing, but genotypically, they will be exactly the same. Bud sports may emerge sometimes, afaik especially in triploid varieties, but again, these will have no or hardly any genetic difference with the original tree.

I am interested only in named varieties, so the seedlings that made it into the fruit market after thorough selection. These mostly have been well described in pomological literature. From the ones in my database the pedigree is (mostly) known and asserted by DNA analysis.

Right now I am ploughing through pomological literature to find the years of “birth” of each of the apple varieties. Takes a lot longer than anticipated…

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Just think of it as documenting relationships. Yes, it might be easier to create a relational database unique to their purpose.

But as we always remind ourselves… “There is no one way to utilize Gramps.”

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You may want to explore Custom Attributes and even perhaps collaborate with someone who has written reports for Gramps.

I do not know of any example report writing analysis reports on Custom Attributes. But that seems like the target. (Although Gary Griffin did a fork of Nick Hall’s DNA segment map Gramplet comparing CSV data in Association notes.

It seems like parts of that might be adapted.

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There may be phenotypical differences between individuals of this variety because of different rootstocks being used, or different soil/climate/elevation where the tree is growing, but genotypically, they will be exactly the same.

What about transposable element? Is it what you mean by phenotypical issues? Such “mutations” could be common on the top of an “old” oak.
Why this cannot occur on “old” apple tree? (or “old branches” do not exist
on your apple tree?)

Sorry, but how do you fix (normalize) a variety?
statement or rules for the classification.

these will have no or hardly any genetic difference with the original tree.

Sure, grafting does not make genetic variations, but the size, taste, etc. might be different. So, should we use the same name of variety for differents results? Do not misunderstand me, I just prefer to use a name of a variety as a direction, because it is just a word like many standards (human). In the real world and natural environment (inbreeding, mutations, etc.) such classification might lead to end of life of the variety…

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Just by looking at a possible translation (from french) for “bud mutation” (?), found a representation with pears:

386×669 96.3 KB

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Thanks, had a quick peek. Actually, I have most of these data available for the apple varieties I’m looking at. For now at least, this approach looks fairly complex to me. Remember that I’m a novice regarding Gramps …

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Those are phenotypic differences. Not all features of the genetic makeup (genotype) are expressed in the same way in every tree, resulting in different phenotypes. And yes, we should use the same name for these phenotypically different varieties. The name follows the name of the variety of the graft. Whether it’s grafted onto a dwarfs-size tree (typically M9 rootstock, yielding large fruits in 2-3 years) or a high standard tree (typically grafted onto a seedling rootstock with an intermediate graft as trunk, yielding smaller fruit, after 5-8 years), it will still bear the same name. The reason is simple: genetically, it’s still the same variety.

The apple genome of ~800Mb has approximately 300Mb of TE’s. Within one variety, when the plant or parts of it are stressed, spontaneous mutations in these TE’s may occur, occasionally leading to bud sports. Probably, many of these sports go unnoticed when the fruit is picked.
In any case, only when these sports are propagated vegetatively, they may lead to a new variety. Typical examples are the red-coloured sports of e.g., Jonagold: Jonagored, Red Jonagold, Red Jonaprince, etc. I’m not sure if these sports are the result of TE’s. Not sure either if there has been extensive genetic research on the specific differences between these varieties. Anyway, current DNA fingerprinting methods (SSR, SNP) do not detect differences in the DNA of these different sports of the same variety. The differences, however, are not differences in phenotype. These bud sports consistently exhibit their typical differences with the original variety under varying conditions, on a variety of rootstocks.
As for old varieties: The oldest varieties in my family tree-to-be are from the 12th and 13th century. The oldest known varieties of Malus domestica in existence today stem from the late Roman empire, 4th century.

We strayed a bit far off the topic of using Gramps for apple family trees. Even though I like the discussion, I’m not sure if it should be conducted on this forum, in this thread. Maybe something for the moderators to decide.

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