Montana Tomato Project

[Carol Deppe]

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

[William Schlegel]

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.

[Tim DH]

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

[Carol Deppe]

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.

[William Schlegel]

It is funny because I absolutely loved the graduate non-degree plant genetics course I took at Oregon State in 2011-2012 which was probably the culmination of genetics in high school, college, and reading plant breeding books like Carol's. Then in actual practice I just use the first principles. Very simple understandings like knowing that blue skinned tomatoes are likely a little bit partially expressed in the F1 and then segregate out in the F2 and subsequent years. In many ways a lot of my breeding is very simple. Though I do think I have grown out some F2's that were perhaps too large! If I did a little bit more planning I could have right sized my growing efforts. However, I also think that there is great value in some other techniques. As my skill at making crosses has gone up- and the number of my own crossed lines I'm growing as well. Now I think my new plan may be to grow a clump of each cross (maybe 10 or 20 plants of each line all in a clump), hope for a segregant I like- but also, I can cross with something like my line 303 that has already segregated back to one of the phenotypes I like- it is a blue bicolor potato leaf cherry. Then the odds are more in my favor that the cross with 303 will segregate back to that same phenotype in a small grow out. With my line 294 on the other hand, I want to do some larger grow outs of the F2 crosses with it. 294 has everything I want except for some genes from wild and indigenous tomatoes from mostly South America. So, my plan is simply to cross it with those and then get it to segregate back to its phenotype which is striped, green when ripe (with amazing flavor), and blue. When I crossed one of my blue bicolor lines with Brad's Atomic Grape to get 294 the F2 was amazing and had a lot of diversity. So, I know that once I get the 294 phenotype in a tomato that like 303 has everything I want, I can make lots of crosses with it and get a wide variety of fancy tomatoes in relatively small grow outs of each given line. I don't know if I stated that very clearly, but it is my plan to turn my 75 or so 50% or greater wild and indigenous lines into at least that many very fancy lines that meet all my criteria. Which can be summed up as: wild and indigenous x adapted x fancy x open source. Double crosses being necessary in all cases. This plan has gradually changed over the course of this project. For example, I've realized recently that one key thing of import is that I want my lines to contain at least 50% wild and indigenous genetics- and those mostly from South America. Last year's crosses made that a practical goal. Then my released lines and varieties should support the conservation of tomato genetic diversity for years to come while at the same time making the Montana tomato fancy and modern!

[William Schlegel]

Tomato season is gradually picking up. Most of my plants still seem to mostly have leaves and flowers with little fruit. However seven F1 lines are producing ripe fruit.

Line 523 is an F1 of 294 x PI129143 and it has precisely one small red fruit with anthocyanin shoulders. The F2 seed within has the potential to produce some really wonderful cherry tomatoes. Given that 294 is a fancy tasty green when ripe with anthocyanin skin and stripes. The specific plant this cross was made on was potato leaf- which I find a helpful marker for cross takes.