Micro dwarf x Indeterminate cross ideas.

[KaguyaCloud]

Update 2/10/25:
Very interesting development. It seems that nyctinasty might be an exclusive trait in micro-dwarfs.
Here's an image of a seedling not expressing nyctinasty(#7) and one that is(#8). The phenotype is quite distinct.


In addition, the segregation ratios are very strange. Dwarf(d) might not be the only gene responsible for causing the plant to express no nyctinasty. If we include the first F2 trials, only 4 out of 33 individuals so far exhibit no nyctinasty. This is much less than the number of actual plants that should have exhibited the dwarf(d) gene. There should have been around 8 plants that are at least dwarf, but it seems that around half of those individuals close their cotyledons at night instead of keeping them open.

This leads to the hypothesis that multiple genes may be triggering no nyctinasty, as well as causing a shorter seedling height. The dwarf gene may be one of the genes causing this, since all F2s so far in the previous generation are indeed dwarf.

This other gene or other sets of genes are definitely not recessive, as that would only give 2 out of 33 to exhibit that phenotype instead of 4. But if it were dominant, 24-25 out of 33 should have exhibited no nyctinasty.

So how do we solve this interesting problem? My hypothesis would likely be epistasis, or a gene that is dependent on the presence or absence of another gene for expression. So in this situation, let's say there are 2 genes: Dwarf and No-Nyctinasty.

Dwarf can be expressed regardless of nyctinasty. However, if we assume No-Nyctinasty can be expressed ONLY when the plant is homozygous recessive for the dwarf gene, then the ratios change.

What happens when no nyctinasty is recessive, but requires being homozygous for the dwarf gene?
Individuals: 32(an even number for convenience)
Percent chance dwarf: 25%
Percent chance homozygous for No-nyctinasty: 25%
Percent chance of being dwarf and has No-nyctinasty: 6.25% or 2 out of 32 individuals.

What happens when No-nyctinasty is dominant, but requires being homozygous for the dwarf gene?
Percent chance dwarf: 25%
Percent chance being heterozygous or homozygous for No-nyctinasty: 75%
Percent chance dwarf and expresses No-nyctinasty: 25% x 75% = 18.75% = 6 out of 32 individuals. This might be closer to the 4 in 33 possibility.

Therefore, I suspect that there is a micro-dwarf gene that is only expressed as a dominant trait when the plant is homozygous for the dwarf gene. Perhaps it's another mutation that causes another downstream hormone deficiency. I currently have seedling #16 germinating in the humidity chamber, and I suspect that it's possible it might be another no-nyctinasty individual. I am very curious to see what more F2 seedlings will yield.

[KaguyaCloud]

Update 2/11/25:


Seedling #16 has sprouted. I have cropped and size corrected the seedling as reference compared to the other seedlings. #16 also has the shortest root size out of the lot and the widest stem diameter, which makes me wonder if it has more micro genes. I have planted #16 in position 1. It has been around 2 days since I have planted the seedlings, and now none of the seedlings planted on February 9th display nyctinasty. It seems that this phenotype is quite short lived.

If my hypothesis is correct, following the phenotypes/behaviors at the cotyledon stage of the seedlings might be the key to early selection. Smaller root mass in my F3 trial might possibly indicate leaflet reduction, but that is speculation due to a sample size of 1 instance. Seedling #16 will help me determine if that is true.

Based off my logs, it seems that the 1-3-5 leaflet pattern is an incompletely dominant trait that can pop up in individuals that have a 3-5-5 leaflet pattern(An intermediate of the 3-5-7 and the 1-3-5 pattern). I wonder if this is related to Nyctinasty. Based off of this, I may need to grow out at least 64 total seedlings to be homozygous for dwarf, leaflet reduction, and early termination(likely a variation of self pruning/determinate). However, 3 out of the 64 will likely have an extremely compact size with partial leaflet reduction.

[bower]

It's hard to affirm these observations of no-nyctinasty as valid indications of genetics without a lot more data.
I know you are working small space and basically impossible to grow and observe the growth habit of all the seedlings. Maybe recruit some group of micro growers and micro breeders here to contribute observations of their seedlings as well.
I'm not growing any micros (well I don't plan it at this point) but I will certainly observe my seedlings closely for the signs of no-nyctinasty, and report back if I find any among non micros.

[KaguyaCloud]

It's hard to affirm these observations of no-nyctinasty as valid indications of genetics without a lot more data.

I agree, I do have more plans on growing out more F2 seedlings to see if there's a consistency in the trait with growth habit. As far as genetics are concerned, No-Nyctinasty seems to be a conserved trait in the micro parent as well as several other varieties. So much so that I found it highly irregular for cotyledons to close at night when I grew my first normal indeterminate tomatoes. This experiment is mainly a test to record down segregation and aggressively selecting the parental micro traits.

In terms of recruiting others to perform grow outs, I am very particular of the selection process, logging about 30 phenotypes per fully grown individual, and constantly observing for anything new to record down. That might be a bit too exhausting and unreasonable for any normal person to do. In addition, the flavors and sweetness of the F2 and F3s are not up to par.

However, I might be interested in releasing the backcrossed seeds if the flavor is drastically improved and if I find a way to refine the micro selection process. This way, we could truly test replicability as well as guaranteeing good flavor.

[bower]

Not sure if I missed something - is the non-closing at night pheno standard for all micros?
Is a short-lived period of closing at night then an indication of partial set of micro genes, only at the earliest stage.
Sorry, I'm a little brain dead from shoveling snow in the freezing cold. Maybe catch up on this later..

[KaguyaCloud]

Sorry about not being clear.

I can't say that non-closing at night is the absolute standard, just for all the varieties that I grew (Micro-Tina, Orange Hat, Jochalos, and Vilma).

1) No-nyctinasty: Do not close cotyledons at night at all.
2) Nyctinasty seedlings: Close their cotyledons for the first 2 days of growth, then cease to close their leaves at night after 2 days or when the first leaf is grown.

When I mean short lived, I was mainly talking about the seedlings that do display nyctinasty, as they only close their leaves at night for a set period of growth. This makes differentiating this phenotype quite time-sensitive.

[bower]

Closing at night is something I've seen in ordinary tomato seedlings well past the cotyledon stage iirc. Young seedlings.
I have noticed it when turning off the lights at night, that they had already 'gone to sleep'. Mine are in a window though so they had some daylight and then night, while lights continued on.
Are your lights on a timer? And, have you determined what length of 'day' the seedlings have before displaying the cot closing (or not). Just curious about the phenomenon generally, which I have seen but not paid attention to as a trait.

I appreciate the attention to detail which you're applying to find those early phenos of the micro.

[KaguyaCloud]

Closing at night is something I've seen in ordinary tomato seedlings well past the cotyledon stage iirc. Young seedlings.
I have noticed it when turning off the lights at night, that they had already 'gone to sleep'. Mine are in a window though so they had some daylight and then night, while lights continued on.
Are your lights on a timer? And, have you determined what length of 'day' the seedlings have before displaying the cot closing (or not). Just curious about the phenomenon generally, which I have seen but not paid attention to as a trait.

We can assume zero outdoor sunlight is in the equation. The lights are on a timer that is around 16 hours from 7:30am-9:30pm. So within the 2 days of being planted, they had a total of 32 hours of light that's around 40,000 lux in intensity.

Oh, that's rather intriguing. Based off my photo meta-data, the cotyledons begin closing at around 6:30pm and fully close at around 8:00pm, 1-2 hours before the lights even turn off.

I am germinating some Rosella Cherry seedlings to re-observe to see when the cotyledons stop closing at night.

[KaguyaCloud]

Update 2/15/25:


Seedling #4: Nyctinastic, Normal leaf, meristem terminated after 2 leaves.
Seedling #7: Non-nyctinastic, Rugose leaf, meristem terminated after 2 leaves.
Seedling #8: Nyctinastic, Normal leaf, meristem seems to be growing like normal.
Seedling #12: Non-nyctinastic, Rugose leaf, meristem terminated after 3 leaves. Axillary shoot seems to be growing between the last 2 leaves. Right cotyledon is bifurcated.
Seedling #13: Nyctinastic, Normal leaf, meristem terminated after 2 leaves. Right cotyledon is shortened.
Seedling #16: Nyctinastic, leaves and stem structure too early to tell.

Very strange phenotype arrangement yet again. It looks like the possible gene responsible for the termination of the vegetative cycle of the main stem is independent from Nyctinasty and the dwarf gene. The rate of occurrence seems too high for early meristem termination to be merely coincidence/blindness at this point.

Perhaps my next batch of seedlings should be grown out to at least 2 leaves to monitor a meristem termination gene. More seedlings need to be grown for reference purposes.

[KaguyaCloud]

Update 2/16/25:


Rosella Cherry seedlings have sprouted. Root length is considerably longer than the F2s except for seedling #3

[KaguyaCloud]

2/23/25 Update:


I have now isolated 3 of the original 16 seedlings from the F2 segregation experiment(#7, #12, #16). So far all the seedlings that have non-nyctinasty are 2-3 times shorter than their nyctinasty counterparts. It seems that nyctinasty may be linked to an extreme dwarfing gene in the seedling stage, regardless of the meristem terminating early. I've also noticed that internode distance between the first two leaves of the non-nyctinastic seedlings are almost zero.

When comparing to my first F2 trials, the pattern seems to be the same. The seedlings of the non-nyctinastic individuals are always half to a third of the height of the other seedlings and always produce rugose leaves.

Seedling #7: Non-nyctinasty, rugose leaves, terminated after 2 leaves, began growing axillary shoots. Growth habit very similar to my first F2 batch.

Seedling #12: Non-nyctinasty, rugose leaves, did not terminate meristem early. Has a strange 1,3,3,3,5 leaflet pattern.

Seedling #16: Nyctinasty, normal leaves, seemingly has the leaflet reduction gene where the pattern is 1,3,3,5. This might hint that shorter roots are linked to leaflet reduction and may be independent from the dwarf gene. However, I would need to grow out the progeny of #16 to see if this short-root trait is heritable. If it is a recessive gene, then it should be stabilized.

Overall, I feel that more work is about to happen in my immediate future, as I have worried. I don't think I have the heart to cull these 3 individuals without growing them out fully first. But they did give me more insight on what to look for during micro-dwarf selections.

[KaguyaCloud]

2/23/25 Update:


I have now isolated 3 of the original 16 seedlings from the F2 segregation experiment(#7, #12, #16). So far all the seedlings that have non-nyctinasty are 2-3 times shorter than their nyctinasty counterparts. It seems that nyctinasty may be linked to an extreme dwarfing gene in the seedling stage, regardless of the meristem terminating early. I've also noticed that internode distance between the first two leaves of the non-nyctinastic seedlings are almost zero.

When comparing to my first F2 trials, the pattern seems to be the same. The seedlings of the non-nyctinastic individuals are always half to a third of the height of the other seedlings and always produce rugose leaves.

Seedling #7: Non-nyctinasty, rugose leaves, terminated after 2 leaves, began growing axillary shoots. Growth habit very similar to my first F2 batch.

Seedling #12: Non-nyctinasty, rugose leaves, did not terminate meristem early. Has a strange 1,3,3,3,5 leaflet pattern.

Seedling #16: Nyctinasty, normal leaves, seemingly has the leaflet reduction gene where the pattern is 1,3,3,5. This might hint that shorter roots are linked to leaflet reduction and may be independent from the dwarf gene. However, I would need to grow out the progeny of #16 to see if this short-root trait is heritable. If it is a recessive gene, then it should be stabilized.

Overall, I feel that more work is about to happen in my immediate future, as I have worried. I don't think I have the heart to cull these 3 individuals without growing them out fully first. But they did give me more insight on what to look for during micro-dwarf selections. Having an individual with leaflet reduction but not dwarf is going to be quite interesting.

[bower]

That looks like a solid finding, @KaguyaCloud !

I hope you don't have to cull those interesting seedlings.

[KaguyaCloud]

Update 3/6/25
Big update.


Seedling 16: Non-rugose, nyctinastic. Flower truss after 7 leaves have grown. Unsure if it is determinate or indeterminate. 1 main long leader with 1 axillary branch growing to the side. This is quite strange, as typically tomato plants usually would grow 1 main leader followed by much smaller axillary branches, but it seems that apical dominance is somewhat suppressed for this individual. Enlargement of the base above the cotyledons are very similar to the twin branched individuals of my breeding project. If it is similar, then there should be side shoots sprouting at random areas from this enlarged region of the stem after the plant has matured.

Seedling 7: Rugose, non-nyctinastic. Flower truss after 7 leaves in every axillary shoot growing from the terminated stem. Growing 3 equally sized stems from the base of the plant. Likely indeterminate based off of the flowering pattern.

Seedling 12: Rugose, non-nyctinastic. Flower truss after 8 leaves have grown. Only 1 main stem followed by 2 shorter axillary stems that grew from the base of the cotyledons.

It's rather unfortunate that the early termination gene didn't seem to appear in this group. Out of the 4 non-nyctinastic seedlings, only 1 seems to have early termination. Considering the 1/4 ratio in non-nyctinastic seedlings, it's possible that early termination is a recessive trait that might not be linked to the other dwarf traits. I must have been quite lucky during my first round of F2s.

Another update on my backcrossing project.

It seems like my backcrossing worked this time. I have developed a better method of collecting pollen from Rosella Cherry, as it has an extremely low amount of pollen shedding. This time, I had to carefully take off the anther cone, open it up, and then scrape out the pollen from the anther cone with the tip of a needle. This should yield a bunch of pollen about the size of a grain of sand that can be pressed onto the stigma of a de-masculated micro flower. I have also backcrossed more flowers on Joro F3-2.

I will dry out the seeds for approximately a week, freeze them for one day, and then begin germination in the chamber. Hopefully I will have some nyctinastic seedlings as proof of the cross. If not, well, there's always another month of waiting and more F2s to grow out.

Overall, I think I am getting closer to my goal. It seems that early dwarf micro selection is possible at the cotyledon stage and then early termination can be selected at 20-26 days. I would need to at least obtain 4 non-nyctinastic seedlings, which means growing out at least 32 seedlings.

[bower]

Still very valuable for early selection at 1/4. When you have so many stacked traits in the growth habit, every reduction in numbers you need to grow is really a huge plus.

[KaguyaCloud]

For sure. I'm quite grateful that there is possibly a way to select for 2 of the 3 micro traits required early on. It seems that I can cull seedlings with extremely long roots during the germination stage, but I will need to perform another 2-3 rounds of F2 grow outs to see if the pattern is consistent.

[Doffer]

Selection at seedling stage is very powefull te reduce the amound of plants to grow.

[KaguyaCloud]

Update 3/12/25


I have confirmed that the growth habit is indeterminate in all 3 seedlings, and no signs of the early termination gene. Axillary shoots behave very similarly to the main stems with the same number of leaves to flower truss. I will prune down seedling 7 to 2 stems in order to keep a more compact size. Seedling 16(largest plant), was very interesting. At end of one of the stems, it has grown an axillary shoot that is even thickness with the main stem. I noticed that this happens to Rosella Cherry once it's grown at least several flower trusses, where it decides to grow a very thick axillary shoot close to the tip of the main stem.

I see why many micro-breeders might have mistaken certain lines to be "micro" despite the fact that they have an indeterminate growth habit. Once flowers are setting, the growth of the main stem slows quite a bit. This does lead to an overall compact habit at flowering, but eventually will cause the plant to grow much larger once the fruit begins to set.

Another update on the backcrossing. The seeds are dried and I have placed them in the freezer for about 18 hours before I start my germination trial. I had the opportunity to taste Rosella Cherry to compared the flavor of my F3s and F2. The difference is very staggering, the tomatoes of my breeding project taste abysmal in comparison to the original parent. I am glad that I am performing a backcross, as 50% the genetics of the tasty parent plant isn't enough to establish good flavor. Hopefully Joro F3 BC1 will fair better, with 75% genetics of the tasty parent.

Worst case scenario, I will likely breed out certain micro traits after a second round of backcrossing.

[bower]

The axillary shoot at the plant growing tip is a trait very typical of determinates, and the shoot will have a determinate flowering pattern from sp gene, likely also putting on a new axillary shoot at its tip and continuing to repeat if resources allow.

Technically, these are not indeterminate plants unless they follow the standard pattern of 3 leaves between clusters. They do have sp gene, making them determinate in spite of the other (likely unnamed) growth habit genes that cause them to continue.
I guess you could call them 'repeating determinates' for the axillary shoot.
This is the growth habit rabbithole which I found in crosses of indeterminates and determinates. Not only cluster patterns vary within the determinate group, but indeterminate genes seem to keep the plant growing taller by one means or another.

It's a shame about the taste but the backcross should help with that.
Hoping to see your early tells in action for the backcross, and I hope none of the unnamed indeterminate growth habit genes make a mess of it.
I would definitely choose your most micro Joro parent for backcrossing, to avoid doubling any of those growth habit pushing genes.

[KaguyaCloud]

The axillary shoot at the plant growing tip is a trait very typical of determinates, and the shoot will have a determinate flowering pattern from sp gene, likely also putting on a new axillary shoot at its tip and continuing to repeat if resources allow.

Technically, these are not indeterminate plants unless they follow the standard pattern of 3 leaves between clusters. They do have sp gene, making them determinate in spite of the other (likely unnamed) growth habit genes that cause them to continue.

That's good to know. The micros I have grown this far typically exhibit this behavior, but only once the stem terminates or is close to terminating.

These plants are following the 3 leaves between flower cluster patterns in their main stems for at least 2 flower clusters so far, which I think would make them indeterminate. I will continue to grow out the main stem to see if it is consistent. Based off my previous F2 grow-outs, the Joro F2-Red was indeterminate based off the flowering pattern and continuous growth.

If the backcross expresses nyctinasty, then it should be a good sign that the cross is successful. I will begin germinating them this afternoon.