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#21

Tomatoes / Re: Montana Tomato Project

Last post by Carol Deppe - 2026-08-06, 10:43:43 AM

Tomato is the place where there is the most known. So this is a good example of what you can get out of that. Many people do fine breeding even tomatoes just from first principles. I pretty much operate just from first principles myself on corn, beans, squash, melons, and greens.

#22

Tomatoes / Re: Montana Tomato Project

Last post by Tim DH - 2026-08-06, 01:17:21 AM

Hi Carol,
       Thanks for sharing your methodology. I'm not particularly interested in colour genetics itself, but I am interested in the process.

Tim DH

#23

Tomatoes / Re: Montana Tomato Project

Last post by William Schlegel - 2026-08-05, 10:39:32 PM

For the OSU Jim Myers lab blue which is what I've been breeding for for my entire project I've found the blue color to be quite easy to breed for. It's more complicated than if it were a single trait but effectively with a large enough grow out it almost always re-emerges for me. I've gotten it stable now or mostly stable again in many lines. Lines 294, 303, 339, and 365 have good blue and are frequently used for new crosses as such. I plan to use 303 for sort of like back crosses perhaps part sibling crosses is the term if I ever get around to crossing this summer.

#24

Tomatoes / Re: Montana Tomato Project

Last post by Carol Deppe - 2026-08-05, 03:23:12 PM

Yes, it's true that not all phenotypes can be derived in stable (homozygous) forms from particular crosses. For example, if you have purebreeding red and white lines of an ornamental plant and the F1 flowers are pink and the F2 segregates as 1/4 red, 1/2 pink, and 1/4 white, that means in the contex of this cross, all the pinks are heterozygous and are not pure breeding, and can't be made to be pure breeding.
You may be able to get a pink some other way, though. Species that have had a lot of breeding work often have known color dilution genes.You might be able to get a pure breeding pink by crossing to something with a color dilution gene.

I have done tomato breeding, but not blue tomato breeding. So how complicated is the blue characteristic? If it involves multiple genes, you might find it hard to fix the trait, that is, make the trait pure breeding just for that reason. Tomato breeding has the advantage that it is much better known genetically than most vegetable crops. So just googling 'blue tomato genetics' produces the paper

https://horticulture.oregonstate.edu/oregon-vegetables/purple_tomato_faq

Which has a section

"What are the genes involved and where did they come from?

Aubergine (Abg), Anthocyanin fruit tomato (Aft) and atroviolaceae (atv) are genes introgressed from the wild species Solanum lycopersicoides, S. chilense, S. cheesemanii, respectively. The original introgression from wild species into cultivated tomato was done by other researchers. We discovered that when you combine these genes, you get an intensification of the pigment. The 'Purple Smudge' variety has a gene similar to Aft but it comes from a different wild species (S. peruvianum)."

So there are three genes involved, two dominant or codominant  and one recessive. (In tomatoes, the convention is mutations are named for the way they differ from standard red indeterminate tomatoes, I forget exactly which variety. And the gene's symbol is given a capital letter if it is dominant or codominant. The standard allele is symbolized by the symbol with a superscript '+'.)

Next I would like to know whether the two genes with capital letter symbols are dominant or codominant. And if there is any way I can recognize the genes by looking at the seedlings before transplanting. Or tell which genes I have by looking at tomatoes.

So I google 'tomato gene list university of californis davis' because I already know and am familiar with that list and know it is maintained by UC-davis. But I would be able to find it just googling 'tomato gene list'. That works for most crops. So I get:

https://tgrc.ucdavis.edu/monogenic

This gets you a lot of info. To get the most recent version I

download the 'mutant phenotypes' excel list. There is more info on specific genes in the much older pdf lists, but blue tomatoes are fairly recent.

So I find out:
arv has 'excess anthocyanin on leaves, stems, and fruits.' Cool. I might be able to tell if I had homozygosity for that gene on the transplants. And I would be able to identify when the gene was present as a homozygote even if one or both the other genes were present, not just by somewhat more purple fruit, something perhaps difficult to evaluate given affects of sun making fruit color variable, but also by also by color of the leaves and stems, which only atv affects.

Aug and Aft: Gene list doesn't say whether dominant vs codominant. Both genes expressed most when exposed to direct sun. But Aft makes purple on both green and ripe fruit. That would be obvious. And Aug presumeably does not affect fruits at green stage but affects shoulders more than the rest. My guess is I would be able to tell whether I had Aug_ alone, or Aft_ alone or both together, but possibly not in the presence of atv atv.

The blue trait is complicated enough genetically that it would not necessarily be easy to get it fixed. But not impossible.

This is a situation in which it is especially useful to grow one or more plants of the two parental varieties and the F1 along with F2s so you can better figure out what F2 plants are genetically. It is also a situation in which selfing a number of individual F2s and then selfing your favorite plant from each Favorite F2, etc to develop inbred lines is more likely to give you pure breeding lines than just making crosses among the most blue/purple plants in the entire project. If you aim to have a variety that is fairly genetically heterogeneous for genes that don't effect the primary traits, you can get that by combining inbred lines afterwards.

If you cross with something involving pink tomatoes it is easiest to identify the presence of homozygosity for pink by pulling a bit of skin off the tomato. It will have a clear instead of yellowish skin.

Some genes affecting tomato color also affect the color of the pollen.

Cheers,
Carol

#25

Tomatoes / Re: Montana Tomato Project

Last post by William Schlegel - 2026-08-04, 09:17:55 PM

Stupice is a well known good tomato here. I've underutilized it in my breeding so far. My mom really likes Black Krim. I think a lot of tomatoes that can be grown here including Amish Paste and Brandywine miss the optimal flavor window. I very much hope that I am breeding tomatoes that much more consistently hit that prime time.

I'm sure that uniform gene is mixed into my work because it's so ubiquitous. I'm also sure a lot of my lines don't have it because they don't ripen uniformly on the shoulders.

The line I've been chasing for flavor the longest has become a fusion of my and Joseph's work. Line 339 a blue bicolor potato leaf dwarf but every year it seems like they don't all have the best flavor. It's a mystery and I hope it ripens some fruit this year of the proper flavor so stabilization can continue. Though maybe it is possible that not everything can exist in a stable form?

#26

Tomatoes / Re: Montana Tomato Project

Last post by Adrian - 2026-08-04, 08:36:39 AM

One aspect of flavor has to do with the u gene. For uniform shoulders. One reason why most university and big seed company bred tomatoes are so tasteless is because they all have been chasing the fad of wanting uniform shoulders, that is, for example, a red tomato that is uniform red with no greenish shoulders. Uniform shoulders requires uu. When the plant is uu the chlorophyll in the green tomato is less, and when the chlorophyll lessens a bit during ripening there is too little chlorophyll to give the shoulders an off color. Apparently the chlorophyll in the tomato skin is needed for best flavor.

You may have noticed that all the heirlooms with the greatest flavor have distinctively off color shoulders.



I suspect all my favorite varieties are relatively resistent to cold effects on growth, production, or flavor. For my early crop I use Stupice. It's a small red tomato up to about 2" across. The earliest tomato I know that has full flavor.  For my pink tomato I use Pruden's Purple. About 1 lb. It has flavor just as good as Brandywine but is considerably earlier. Brandywine doesn't always ripen here. For my main crop red tomato I like Amish paste. It has great flavor raw even though a paste. My favorite tomato of all and favorite black is Black Krim. See photo below. All these are indeterminate. Stupice is determinate but smaller than most determinates. I plant it at 2' apart in the row, the rest at 4'.

https://www.flickr.com/photos/caroldeppe/15602875910/

The most part of black varietys are the mosts tasty but they give back a lot of water. If the weather is bad they can be rot before their maturity.

Black krim has a low vigor is the weather is too hot and the fruits caught easily the apical necrosis.


Thoses varietys can be improved for me. The better varietys for me was the black and pink descendants of a red variety x green giant.

#27

Tomatoes / Re: Montana Tomato Project

Last post by Carol Deppe - 2026-08-04, 07:35:31 AM

One aspect of flavor has to do with the u gene. For uniform shoulders. One reason why most university and big seed company bred tomatoes are so tasteless is because they all have been chasing the fad of wanting uniform shoulders, that is, for example, a red tomato that is uniform red with no greenish shoulders. Uniform shoulders requires uu. When the plant is uu the chlorophyll in the green tomato is less, and when the chlorophyll lessens a bit during ripening there is too little chlorophyll to give the shoulders an off color. Apparently the chlorophyll in the tomato skin is needed for best flavor.

You may have noticed that all the heirlooms with the greatest flavor have distinctively off color shoulders.

A prof at one of the Florida universities studied the u gene and showed it causes a dramatic drop in sugar content as well as various "aromatics." And the u gene is cause, not mere correlation. When he used genetic engineering to knock out just theu gene, the sugar and aromatics dropped dramatically.

I suspect all my favorite varieties are relatively resistent to cold effects on growth, production, or flavor. For my early crop I use Stupice. It's a small red tomato up to about 2" across. The earliest tomato I know that has full flavor.  For my pink tomato I use Pruden's Purple. About 1 lb. It has flavor just as good as Brandywine but is considerably earlier. Brandywine doesn't always ripen here. For my main crop red tomato I like Amish paste. It has great flavor raw even though a paste. My favorite tomato of all and favorite black is Black Krim. See photo below. All these are indeterminate. Stupice is determinate but smaller than most determinates. I plant it at 2' apart in the row, the rest at 4'.

https://www.flickr.com/photos/caroldeppe/15602875910/

#28

Tomatoes / Re: Montana Tomato Project

Last post by William Schlegel - 2026-08-03, 09:04:31 PM

Carol,

I have learned that July and August are the best flavor months here. Sometimes in September and October the frost spares us now. However the cold doesn't let the same level of flavor develop. So I feel like a bad tomato grower this year.

The exception I've noticed is Black Cherry. I really want to make some crosses with it because it seems to have good flavor when cold. I bought a plant or two this year for that purpose. Though if I had two only one of them is still uneaten by deer!

#29

Tomatoes / Re: Montana Tomato Project

Last post by William Schlegel - 2026-08-03, 07:31:58 PM

It really doesn't seem to be getting easier, does it?

Generally it is. Though have a lot of new F1s this year. Though almost regardless of adaptation this is just a challenging tomato year so far.

#30

Tomatoes / Re: Mid-Ohio Valley Tomatoes

Last post by Carol Deppe - 2026-08-03, 05:01:26 PM

Commercial F1 hybrids are usually crosses between two inbred very uniform lines. So you don't need many plants to start a dehybridization project or to cross to something else. One plant might do fine for hybrid tomatoes. I usually have at least three plants with bee-pollinated crops because bees can fail to find a single isolated plant.

If you cross two relatively uniform lines one cross involving just one plant of each parent is fine if the cross works. I am more likely to grow at least three plants of each parent and cross them in all possible combinations.

How many F2s you "need" is a matter of what you are trying to do. If the cross involves four genes segregating in a diploid plant like tomatoes, and you want all the recessives in one variety, with each recessive having  a 1/4 probability, the probability of getting all four simultaneously, assuming independence, is one in 256. And you would probably want more than just one. So if you had unlimited land and labor, probably more like a thousand.

As far as I am concerned, I don't ever "need" 1000 F2s of anything, because growing and evaluating 1000 F2s of anything is too many to be fun. And I would probably not notice totally unexpected things that might turn up that may be as important or more important than what I thought I wanted. So I might figure out different parents that share one or two of the recessives.

Or I get what I want by selecting in stages. I will grow as many as I can grow and evaluate so it will still be fun. And then, for example, I select for just one of the recessives and ignore the others. Then the next year I can select for another recessive. Doing it that way, if I plant 40-80, the number of most projects that I find manageable and fun, I can fix (make homozygous) one gene per season and have odds of 1/4 each year. That is roughly 10 to 20 plants of the type I want each year.