Micro dwarf x Indeterminate cross ideas.

[KaguyaCloud]

@bower @Doffer
Here is the progression of my Jochalos and Vilma micro dwarf tomatoes over the course of 4 weeks of time:
https://imgur.com/a/WmhFFec

[KaguyaCloud]

Since there isn't any research on the exact genes necessary related to Micro dwarf stature, specifically the Micro-Tom genotype, I have gone through the Micro Tom mutant database and through some research articles to determine which chromosomes may be linked to the shortest stature through process of elimination.

Here are the genes linked to chromosomes that don't seem to have a direct influence on size for Micro Tom:
Chromosome 1: High Pigment 2 https://www.esalq.usp.br/tomato/hp2.pdf High confidence
Chromosome 3: Yellow Flesh/RG1 https://sci-hub.ru/https://doi.org/10.1 ... 004.05.023 High confidence
Chromosome 5: Jasmonic acid insensitive1-1 https://www.esalq.usp.br/tomato/jai1.pdf High confidence
Chromosome 8: Lutescent https://www.esalq.usp.br/tomato/lutescent.pdf High confidence
Chromosome 9: Never ripe http://www.esalq.usp.br/tomato/Nr.pdf High confidence
Chromosome 10: Auborgine https://www.esalq.usp.br/tomato/Abg.pdf High confidence

Chromosomes with medium to low confidence on influencing size:
Chromosome 7 : lateral suppresser https://www.esalq.usp.br/tomato/ls.pdf Medium confidence
http://www.lcb.esalq.usp.br/publication ... 9-5703.pdf
Chromosome 11: Fasciated Flowers https://www.esalq.usp.br/tomato/fas.pdf Low Confidence
Chromosome 4: Unknown. Couldn't find images or info.
Chromosome 12: Unknown. Couldn't find images or info.

Chromosomes that do influence the short stature:
Chromosome 2: Dwarf https://www.esalq.usp.br/tomato/Dwarf.pdf
Chromosome 6: Self Pruning https://www.esalq.usp.br/tomato/Sp.pdf

I did this research due to common reoccurrences in the 1:27 ratio for obtaining the Micro Tom phenotype in a cross between Micro Tom and a Determinate. This would indicate 2 recessive genes plus 2 additional dominant genes responsible for the short stature of Micro Tom.

[AKgardener]

I cannot wait to see how it all turns out for you,saw your pictures I have those same blue planters

[bower]

Linkage is interesting because if you're not aware of it, it can really skew your ratios way off.
For example, the sp gene is very close to Beta orange locus. So if you're working with Beta orange and want to change the growth habit, it can be a lot more challenging than expected.
There's probably a lot more on tomato gene linkage out there if you look. Basically, any two genes that are really close to one another will strongly tend to segregate together instead of separately. So if you find a map of the chromosomes carrying your genes of interest, see what's near by, and there's a good chance they are sticking together.

[KaguyaCloud]

Genetics really are strange. I am trying to see if there is a definite linkage between size and certain chromosomes from the post above. If we know for certain which chromosomes don't influence size, then we can select for certain traits without worrying that those particular traits segregate with a desired sized gene. And you're right, if Beta carotene and sp are both in chromosome 6, then it's likely to be difficult to breed out the beta carotene gene through only homologous crossover alone.

Another example is the dwarf gene(dd) and potato leaf(cc), which are in chromosome 2. This would mean that crossing a dwarf normal leaf(ddCC) with a tall potato leaf(DDcc) will result in the F1 being tall normal leaf(DdCc). But the F2 generation will only show the phenotypes: tall normal(DDCC, DdCc), tall potato(DDcc), and dwarf normal(ddCC). It is very unlikely that dwarf potato(ddcc) can occur since the dwarf and normal leaf genes are linked together in one chromosome and the tall and potato leaf genes are linked in another chromosome.

In our case, however, we do know the positions of two of the main genes responsible for micro dwarf phenotype(sp and d). And they are in completely different chromosome locations. Not all tomatoes that have sp and d are micro dwarfs, such as the 4ft tall Rosella Crimson dwarf tomato(not to be confused with the Rosella Cherry indet. tomato developed by Gourmet Genetics) that grows to be a significantly larger size. The micro dwarf variety Vilma for example, exhibits the dwarf gene(d) and is determinate(sp) but still has shortened internodes compared to Rosella Purple. However, as you can see from the progression images, the size of the tomato leaves from Vilma seem to be regular sized(7 leaflets) compared to diminished 5 leaflet Jochalos. Despite that, they both are approximately the same height. So there also seems to be a gene responsible for reduced primary leaflets per tomato somewhere, which is desirable in my very limited space. If there is a pattern in my F2 generation, I should be able to detect some consistencies.

So there are several genes that seem to be independent of each other:
sp, determinate gene(Example of segregation from other genes: Roma tomato)
d, dwarf gene(Example of sp and d segregation from other genes: Rosella Crimson Dwarf)
Gene A, causes extreme shortened internode length(Example of sp, d, and A: Vilma)
Gene B, causes diminished leaf size(Example of sp, d, A, and B: Micro Tom, Jochalos, Micro Tina)

It's possible that Gene A is responsible for the overall shortened phenotype of Micros with normal sized leaves and Gene B being responsible for smaller leaf size. If these genes are dominant, then it's possible that the recessive traits that give a taller stature and normal leaves will appear in future generations. I might just switch up the purpose of this project to exclusively study F2 generations.

[bower]

Your Gene A must be the one called brachytic (br).
It's on Chromosome 1, but IDK what other genes are close by. Says there are about 55 genes expected in the region where it is mapped, so maybe it has yet to be narrowed down some.
https://journals.ashs.org/jashs/view/jo ... e-p239.xml

Here's one: FPF1, yield related trait in the same region as br.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9352537/

[KaguyaCloud]

Update 1/9/24:
Jochalos are flowering profusely and Vilma is still doing well: https://imgur.com/a/WmhFFec

My Rosella cherry cutting has finally bloomed and grew large(13 inches) for being in a half-filled 4 inch pot, and at about the same height of the one growing in the 6 inch pot: https://imgur.com/a/WXCMthf

While it is quite large, the stem is relatively thin and flexible and the leaves are considerably smaller than the mother plant I took the cutting from. I may be able to tease it to grow horizontally in order to maximize the area of the grow light. Weirdly enough, the flowers in the cutting are about the same size of a standard Micro Dwarf flower and about half the size of it's mother plant growing in the 6 inch pot. I guess the process of growing the plant in a smaller pot miniaturizes the flower organs too.

This technique may be viable to grow my F1 Jochalos x Rosella Cherry cross in an indoor context. I also wonder what would happen if I cut the top of the main stem that's developing flower buds and then root it. Would it continue it's flowering and fruiting growth habit or would it reset back to being vegetative? If it does the former, I might be able to consistently maintain a line of F1 plants through just cuttings alone and skip the 3-4 week vegetative phase in indeterminates.

[bower]

A rooted cutting with buds will continue to flower and fruit, not reset to vegetative.
Not sure how the timeline for rooting would compare with your already super fast seedlings, but probably quicker as you say.
Definitely an excellent save for F1 plants, since the seeds are so expensive.

[SeanInVa]

Hey there! I am the lead on the Micro Tomato Diversity Project over at tomato-talk.com. Please feel free to drop by and review the project - we have a ton of seed, and would love a new participant that is active and approaching their grows from a scientific angle. Utilization of our current genetics is not required, and if you were open to collaboration of any kind, I would love to work with you. The project hasn't been real active due to lack of participation and some real life things on my side. But I'm looking to get back at it, as I'm also downsizing my home garden so I don't have so much going on at one time.

Right now, almost all of our crosses involve genetics from Red Robin as the micro ancestor, with a few exceptions.

I have not yet read through this entire thread, but am looking forward to doing so over the next few days. It looks like you've gathered a bunch of good information, and I will pitch in any input I have as I go through the thread.

[KaguyaCloud]

Not sure how the timeline for rooting would compare with your already super fast seedlings, but probably quicker as you say.

Rooting an axillary node actually took about the same time to flower as the Micro Tina I planted from seed, strangely enough. I have yet to root the fruiting meristem before, but it looks like it takes a week or so for the roots to develop and for the plant to grow.

Please feel free to drop by and review the project - we have a ton of seed, and would love a new participant that is active and approaching their grows from a scientific angle. Utilization of our current genetics is not required, and if you were open to collaboration of any kind, I would love to work with you.

Nice to meet you. Rest assured I think I've read quite a few posts in the tomato-talk forum during my time trying to find publicly available processes of crossing micro dwarfs. I'm willing to join and collaborate data, but I think I prefer to see for myself on attempts to stabilize a cross. And I do have some thoughts on the project:

• Breeding micros is quite a complex thing as I have seen, have you and your group decided on what exactly defines to be a "micro" variety compared to others such as "compact", "basket", and "dwarf"? It seems really difficult to be able to define completely as varieties that are labelled as "micro dwarf" exhibit an extremely wide range of phenotypes and growth habits. In all the scientific articles I've read, the main way of selecting a micro/dwarf trait is through hypocotyl length. However that only helps to a certain extent. Once I grow out my F1 cross, I plan on selecting towards rugose foliage, 5 leaflet pattern growth(1,3,3,5,5...), shortened internodes, and compact leaves.
  
  Do you have statistical percentages on traits arising in the F2 population? I think I've seen quite a lot of selections from carrot leaf, to multiflora, to variegation. But if we were to judge based on size alone, the likelihood of obtaining a "micro-tom"-like phenotype from a Micro-Tom and an indeterminate parent is a 1 in 108 chance(https://sci-hub.ru/https://www.scienced ... via%3Dihub).
  Many seeds from multiple fruits have to be sown to get even one single desirable plant for just size.
  
  How many different lines are there so far in the projects and do you have a publicly available spreadsheet of every breeding line? I can't possibly imagine how difficult it is to keep track of everything.

[SeanInVa]

Nice to meet you. Rest assured I think I've read quite a few posts in the tomato-talk forum during my time trying to find publicly available processes of crossing micro dwarfs. I'm willing to join and collaborate data, but I think I prefer to see for myself on attempts to stabilize a cross.

Sounds good! I am really interested in the data sharing side for sure.

And I do have some thoughts on the project:
Breeding micros is quite a complex thing as I have seen, have you and your group decided on what exactly defines to be a "micro" variety compared to others such as "compact", "basket", and "dwarf"? It seems really difficult to be able to define completely as varieties that are labelled as "micro dwarf" exhibit an extremely wide range of phenotypes and growth habits. In all the scientific articles I've read, the main way of selecting a micro/dwarf trait is through hypocotyl length. However that only helps to a certain extent. Once I grow out my F1 cross, I plan on selecting towards rugose foliage, 5 leaflet pattern growth(1,3,3,5,5...), shortened internodes, and compact leaves.

As of now, we do not have any firm definition. In fact, there is thread over there essentially asking the same general question: https://www.tomato-talk.com/forum/the-l ... warf-begin.
I don't think we ever tried to answer that question from a scientific perspective. In our minds, we're thinking of plants that, generally speaking, can be grown easily in a 1 gallon planter such that they reach around 12" in height or less, perhaps up to 18" if the structure allows or perhaps in a small container on a patio. That is to say, we're not trying to define or limit micros to tiny 6" plants. I suppose there is room here for multiple classifications.

Do you have statistical percentages on traits arising in the F2 population?

Unfortunately no. When we started, the goal was simply to grow out as many crosses as we could and find plants that were promising for one reason or another. Dan tried to scope down with his two initial projects - multi-flora and "BLT worthy".

I think I've seen quite a lot of selections from carrot leaf, to multiflora, to variegation. But if we were to judge based on size alone, the likelihood of obtaining a "micro-tom"-like phenotype from a Micro-Tom and an indeterminate parent is a 1 in 108 chance(https://sci-hub.ru/https://www.scienced ... via%3Dihub).
Many seeds from multiple fruits have to be sown to get even one single desirable plant for just size.

Carrot leaf is definitely a prominent trait in many of the crosses. Dan did most of the initial work of "fixing" the short stature in the crosses that he carried past F2. His normal method around this stage was to sow several hundreds of seeds in a large flat, and go through a few rounds of terminating any seedlings of noticeable height. After a couple rounds, he was left with those that were pretty much guaranteed to be "micros" - or at least very short in stature.

How many different lines are there so far in the projects and do you have a publicly available spreadsheet of every breeding line? I can't possibly imagine how difficult it is to keep track of everything.

Dan has made north of 180 crosses, some of which were scrapped early on. Many of these are crosses of prior crosses. There is no publicly available spreadsheet, but I have tried to provide some basic documentation on the various crosses here based on a private spreadsheet Dan has provided to me: https://www.tomato-talk.com/forum/the-m ... es/crosses

It is extremely difficult, and I've gone through a few different methods. At this time, I've scoped down to a few crosses per project and I'm still focused primarily on just growing out and not being scientific about it. I just sowed some seed and will be attempting to track more information per generation on these.

[KaguyaCloud]

Your Gene A must be the one called brachytic (br).
It's on Chromosome 1, but IDK what other genes are close by. Says there are about 55 genes expected in the region where it is mapped, so maybe it has yet to be narrowed down some.
https://journals.ashs.org/jashs/view/jo ... e-p239.xml

Here's one: FPF1, yield related trait in the same region as br.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9352537/

Hmm, that's rather interesting. They did try breeding the br gene into Micro Tom. What's strange is that Micro Tom ended up growing slightly shorter: https://www.esalq.usp.br/tomato/br.pdf

If the br gene is responsible for the short stature, then it might be difficult to get a white/pink fruiting micro dwarf. The colorless fruit epidermis gene that is responsible is also located in chromosome 1. But I've heard that Rosy finch has a clear epidermis.

[Doffer]

So the original MT does not include the br gene?
I already suspected that this gene could cause extra dwarf.

Is br linked to the colorless fruit epidermis gene?
The fact that they are both on chromosome 1 does not mean that there is a linkage. In addition, a linkage can be broken by crossover.

[bower]

IDK about a linkage between epidermis color and br, but the point about linkage is that it works both ways.
Taking Beta and sp as an example, you can find OP's that are Beta determinates and you can find Beta indeterminates. Issues are expected if you want to use an indeterminate Beta parent for an sp project outcome, in terms of numbers you would have to grow.
But as Doffer said, these linkages are not absolute. If you grew thousands you would find a breakage, and that's why we have OP parent stocks with a firm link between Beta and both determinate or alternatively indeterminate condition.

There are ways to increase the chance of separating linked traits. Crossing unstable generations is said to help. It depends on your goals and expectations, whether you prefer to keep stirring the pot with crosses, or whether you'd be better off choosing appropriate parents in the first place, to get ratios that are workable for a direct route to stabilize the intended result.

[wykvlvr]

Another example is the dwarf gene(dd) and potato leaf(cc), which are in chromosome 2. This would mean that crossing a dwarf normal leaf(ddCC) with a tall potato leaf(DDcc) will result in the F1 being tall normal leaf(DdCc). But the F2 generation will only show the phenotypes: tall normal(DDCC, DdCc), tall potato(DDcc), and dwarf normal(ddCC). It is very unlikely that dwarf potato(ddcc) can occur since the dwarf and normal leaf genes are linked together in one chromosome and the tall and potato leaf genes are linked in another chromosome.

I found this interesting. There are a fair number of potato leaf dwarf varieties and there are those who claim that Micro Tom is a type of potato leaf. Something to think about/be aware of is that being on the same chromosome is only part of the story when talking linkages. Distance between the physical location of the genes on that chromosome affects how often they get separated. The closer they are to each other the less likely that they will be separated, but conversely if one is at each end of the chromosome the chances of being separated are much higher.

If the br gene is responsible for the short stature, then it might be difficult to get a white/pink fruiting micro dwarf. The colorless fruit epidermis gene that is responsible is also located in chromosome 1. But I've heard that Rosy finch has a clear epidermis.

Rosy Finch grew only 12 inches tall in a 3 gallon pot and it does indeed produce tomatoes with a clear epidermis. Groovy Tunes also has a clear epidermis as it is a purple not brown tomato. So it is possible to produce them but I think starting with a micro dwarf that already has a clear epidermis would be the best approach for developing more purple, pink or white varieties. Which luckily is the approach I had already picked for other reasons...

Waves hi to @SeanInVa Grin among some of the first things the OP was told was to check out Tomato Talk and I posted a link to a thread there I thought he would find interesting.

[KaguyaCloud]

So the original MT does not include the br gene?
I already suspected that this gene could cause extra dwarf.

Well in this case, we do not know for sure. The difference in size is not that significant based off the image of Micro Tom-br. However, other experiments that inserted other genes into Micro tom in chromosome 1 did not change size at all. We do know that introducing other hormone disrupting genes such as dumpy(https://www.esalq.usp.br/tomato/dumpy.pdf) and curl3(https://www.esalq.usp.br/tomato/curl3.pdf) causes very extreme cumulative effects in size and morphology.

There are a fair number of potato leaf dwarf varieties and there are those who claim that Micro Tom is a type of potato leaf.

Distance between the physical location of the genes on that chromosome affects how often they get separated. The closer they are to each other the less likely that they will be separated, but conversely if one is at each end of the chromosome the chances of being separated are much higher.

After closer inspection of growing the limited micro dwarf stock that I have(Jochalos, Orange Hat, and Micro Tina), I think it is very easy to confuse the Micro-Tom growth habit to the potato leaf gene due to the similar initial smooth 5 leaflet leaf pattern. However, once those specific Micro Dwarfs grow their 5th-8th leaf, secondary leaflets begin to form, which is attributed to the regular leaf gene. Whatever gene that causes the smallest growth pattern seems to influence how smooth the outer leaves are and decreases the number of primary leaflets.

For sure, there linkage isn't always a guarantee thanks to chromosomal crossover. However, I was under the impression that genes are completely unlinked if they are in separate chromosomes and that genes in the same chromosome are linked at varying degrees. Do we know what the frequency of chromosome crossover might be in tomato plants? If the chances are not comparatively high, I think it's best to assume that crossover of the specific genes desired is possible but not likely.

[Doffer]

In the case of MT, the best known mutant alleles already present in this cultivar are: dwarf (d), a brassinosteroid (BR)-related mutation responsible for the small plant size, and self-pruning (sp), responsible for its determinate growth habit.

https://www.esalq.usp.br/tomato/

I don't know now if they mean BR or br gene in Micro Tom? (probably my english is not good enough)

[KaguyaCloud]

I don't know now if they mean BR or br gene in Micro Tom? (probably my english is not good enough)

BR in that line stands for the Brassinosteroid Related and not the brachytic gene(br). They both share a similar abbreviation. What it is trying to say in that line is that the dwarf gene d alters the pathway to produce a brassinosteroid related hormone(BR for short).

[bower]

I have not read nor fully understood the linkage questions discussed in the full text here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060673/
I remember seeing a reference to a distance in centimorgans between linked genes, so I just googled some search terms until I found a reference to the distance in centimorgans for linkage on the same chromosome in tomato, and found this in the abstract at the top of the page:
"A genome-wide survey indicated that linkage disequilibrium (LD) decays over 6–8 cM when all cultivated tomatoes, including vintage and contemporary, were considered together. Within contemporary processing varieties, LD decayed over 6–14 cM, and decay was over 3–16 cM within fresh market varieties."
It also goes on to reference linkage between different chromosomes in the sub-populations of tomatoes.
Worth a read if linkage is on your mind.

[KaguyaCloud]

Update 1/17/24: Jochalos, Micro Tina, and Vilma are still doing well as we speak. However I have found a very strange observation when closely looking at my micro dwarf and my rooted indeterminate Rosella Cherry sucker.
https://imgur.com/a/PXrZkWi

It almost looks like indeterminate growth. Upon closer observation I have found that the suckers on Jochalos and Micro Tina still do terminate despite the fact that a set of flowers grew in the middle. The suckers on these micro dwarf tomatoes have a chance of growing a set of flowers, followed by leaves, then followed by 1-2 terminating flowering buds. Another sucker from the terminal flowering end has a chance of growing out and continuing, leading to a vine-like continuous growth pattern. The suckers can be ID'd by seeing if the leaves are reduced and/or smaller than the last leaf before the flowering truss on the main stem.

When I rooted my indeterminate Rosella sucker, something interesting also happened. The regular growth pattern of the Rosella is 8 true leaves followed by a set of flowers. Then 3 leaves grow and another set of flowers grow and the pattern continues. However, for the sucker, it grew 8 leaves, produced a set of flowers, then again grew another 8 sets of leaves, produced flowers, and finally grew 3 of leaves and another set of flowers.

I wonder if suckers are somewhat programmed to grow differently from the mother plants. My initial idea of determinate plants was that all ends must terminate with a flower truss. However I suppose that genetics and regulation of the sp gene are more complicated than I thought. I guess it is safer to assume how the main stem grows vs the suckers that sprout from determinates. But these growth patterns might be reasons why certain varieties grow horizontally more than vertically.