Breeding with wild tomato species

[Andrew Barney]

Though there is a non-introgression route it would probably lead to a cherry tomato only species for some time.

That is a good point. However from the podcast he says fruit size is the result of one point deletion or mutation. Another idea is to use mutation breeding. If we had lots of seeds to sacrifice there was a free seed radiation service that was mentioned on the old forum. Mutation breeding is not a bad idea if we are having trouble crossing and are trying to domesticate from scratch.

[William S.]

That is a good point. However from the podcast he says fruit size is the result of one point deletion or mutation. Another idea is to use mutation breeding. If we had lots of seeds to sacrifice there was a free seed radiation service that was mentioned on the old forum. Mutation breeding is not a bad idea if we are having trouble crossing and are trying to domesticate from scratch.

Just finished listening to the podcast. His approach is interesting with using only genome editing. It raises the possibility of having 14 domestic tomato species if desirable. I agree about the radiation breeding. There are three approaches here: introgression, radiation breeding, and genome editing. The third may be genetic engineering depending on the legal definition. However, the first two are commonly fair game for organic and open source breeding. If we had the ability of big labs to do genetic testing of seedlings it would be pretty easy to select seedlings that had the desired traits.

However, there is one trait that really stands out and that is large fruit size. So a radiation bred galapagense or Peruvianum would be pretty simple. Create lots of mutants until you find one with big fruits.

For our rocky Mountain purposes working with pure galapagense might be difficult. Pure pimpinillifolium seems to much like domestic tomato. However to me Peruvianum seems like a likely target for us because it seems pretty straightforward to raise large amounts of seed. We could potentially send in a pound of seed, get it irradiated, and select out a large fruited mutant from resulting seedlings in short order. Which seems like a good alternative if introgression fails to work to bring in desired genes.

It seems like the species we can't grow very well wouldn't work with mutation breeding just because we can't produce enough seed. It would make sense to work with some species in places where they already grow well such as their native range or its equivalent in another part if the world if it exists. Which it may not- for instance how many high elevation salt deserts are there with short day lengths?

I wonder if mutation breeding could create knock out mutants that would actually be easier for us to work with of some of the species? For instance a high elevation Chilense that isn't day length sensitive and blooms continuously?

I've thought that introgression is the key to making some species easier to work with, however it's possible that all the really cool hard to obtain traits we dream of in wild tomatoes are polygenic as discussed in the podcast. By introgressing we would break these traits at least temporarily. The trick would be to keep back crossing to the wild parent until the desired suite of polgenic traits is functional again, but the simple domestic trait like large fruit is transferred. One way to do this might be to be to do the introgression in an environment similar to the native habitat, with galapagense and salt tolerance that could just be seawater. My uncle has a small salt water fish aquarium and salt water for aquaria is readily available. Seedling trays in saltwater anyone? Trichomes, cold tolerance, and others could be a little trickier.

I wonder which of the three techniques is fastest? The example that comes to mind is GMO transgenic blue tomatoes. They are still not readily available a long time after development. Conventionally bred blue skinned introgression  tomatoes are tremendously widespread. So using introgression has potential from that recent historic analogue.

Radiation breeding has some enhanced patentability and has been used to obtain non-GMO herbicide resistances in small grains like wheat that are patented. In this case it's the precise description at the genetic level of the induced mutation that is patentable. Mutation breeding can also be done open source- you just select the big tomato.

GMO technology like transgenes and perhaps gene editing is highly patentable and controlled, we have yet to see much of any GMO tech become available in an open source manner. Though the simple fact that patents do eventually expire suggests that it will eventually all be common use material. When I took a plant genetics course at OSU in Oregon in 2012 gene editing was still a bit of a regulatory unknown. Not sure where it stands legally in 2018. I could see a case for it being as benign as radiation breeding. Even done by universities patentable tech tends to get patented. So I suspect patentability might be part of the draw there. Still for us two open source routes to domestication for additional tomato species are possible.

[Joseph Lofthouse]

Here's a photo of a tomato that showed up among the progeny of [domestic X habrochaites]. I think it is self-compatible. It had closed flowers, so it doesn't match the project goals. It is a tasty fruit. The largest so far from the cross. And the most productive. It was early. The most unusual trait was that it is hollow, sorta resembling a pepper inside. 

Because it produced so much seed, I gave it a name, and intend to include it in my seed catalog this winter.

Fairy Hollow Tomato


A couple days ago, I sent a bunch of the interspecies tomato seeds to a collaborator in a warmer climate. They are making crosses and  F1 hybrids for me during the winter. I'm hyped about that.

I have been pleased with the progress that we have made towards domesticating wild species. I was working with a population that I was calling corneliomulleri. Originally, the fruits were the size of peas. This year, one plant had fruits the size of a grape. Woot! And there were plants that produced tasty fruits, and plants that produced yucky fruits. So yup, I think there is a lot that can be done with plain old selection. So next year, I'm intending to plant a lot of seeds from the grape-sized fruits, and from the lovely tasting fruits.

I still find myself struggling sometimes with the meme of "gotta keep things pure". For example, I've been growing a population that I suspect was 75% habrochaites, and 25% domestic. I call it BC1. This year, I found some fruits with 3 locules in the population, which is  more of a domestic trait than an habrochaites trait.  It took me a good hour of thought to finally merge BC1 into the general habrochaites population. But now, it is done, and cannot be undone. And I grew the [domestic X habrochaites] and [domestic X pennellii] progeny only 20 feet away from the habrochaites patch, hoping that they will cross-contaminate each other. However, I just couldn't bring myself to screen the habrochaites fruits for taste!!!!!!!!!!!!!!!!! Bleck! I'll do that when some non-habrochaites fruit types start showing up.

 

[William S.]

Neat tomato!

Interesting that you call the hollow interior unusual Joseph. I've been researching tomato history and a lot of the original domestic tomatoes bred by indigenous Americans were yellow, hollow, ribbed big heirlooms- and reportedly they had some different flavors.

Kind of like this 80 DTM yellow stuffer from victory seeds.

https://www.victoryseeds.com/mobile/tomato_yellow-stuffer.html

One such effort to create the modern tomato was that of A.W. Livingston of the book which I haven't read "Livingston and the Tomato"

http://blog.seedsavers.org/blog/livingston-tomatoes

[William S.]

Been awhile since we've written anything on this thread. I grew galapagense, chilense, arcanum, and cheesemanii last year for the first time, and penellii successfully for the first time. Though it might actually have been a hybrid if so it was so penellii like it must have been 3/4 penellii. It was from a plant Joseph grew isolated from other penellii but with other species and maybe hybrids. Which it was again this year- plenty of penellii hybrids grew near it. Chilense I did not get seed back from, the rest I did. The cheesemanii and galapagense got a bit buried by more vigorous tomatoes. Also grew the common hybrid cheesemanii that is really a domestic type.

Thinking about the various populations of habrochaites and penellii hybrids I'm curious about the potentialities of some of what grew in my 2019 garden. I had exserted domestics amongst some of the wild patches also. I grew 1/4 wild, 1/2 wild, and 3/4 wild plants in 2019. Perhaps the biggest difference i noticed was that 3/4 habrochaites produced plentiful pollen. Some seeds should grow out 3/8 and 5/8 plants. Though there would be no particular way to tell. I don't think I grew any pure habrochaites last year. The exserted domestics could produce 1/8, 1/4, and 3/8 seedlings. The strain of arcanum I grew has limited fertility as a pollen donor for domestics. It's always possible to find a new species in the interspecies hybrids when growing so many species close together. One of the chilense strains produced pollen but no fruit on one last surviving plant. Though the seed was so different from the other chilense strain I'm not 100% sure it was chilense at all.

I got and grew descendents of that cool Fairy Hollow Joseph found. It segregated massively and I had put it in my direct seeded mix mostly. The ones I grew as transplants proved hard and green- but at least some were hollow. Only edibles showed up direct seeded. Though one yellow plant had pale yellow fruits, but solid, with three radiating green stripes on the fruits. Very mild flavor. No idea if it was a descendent of fairy hollow or a true domestic, it looked pretty domestic. I saved an epic amount of seed last year from the wild species and hybrids. Finally plenty for direct seeding experiments. This year though I think the 1/4 wilds are so close to palatability that I want to do a big grow out of those. However will probably be growing some of the others close by unless my backyard becomes the odds and ends grow out space. I may not grow all the species this year. I will however be growing a new strain of pure habrochaites that's supposed to be arthropod resistant.

[Andrew Barney]

This is great William! Keep up the good work!

I may need to request seed from you if you got plenty from galapagense and cheesmaniae. But I think I have some left. I'm planning on growing out what i can this year.

Fairy hollow crossed to the pennellii line sounds interesting to me. Did you make any fairy hollow x Joseph's exerted domestic line (the name is escaping me right now)?

I really love how the penellii have such vigorous root systems and potato-ish leaves. I hope future edible tomatoes have these traits from pennellii. But one's with lots of pollen would be good. Most of mine seem to be pollen sterile, but we will see what can be separated out in the future.

[William S.]

I didn't intentionally cross fairy hollow with anything. I wasted most of my Fairy Hollow seed not realizing how much it would segregate. So all I have for certain is hard green seed. Though I did seed save the direct seeded pale mild maybe. Though I may have mixed it with other direct seeded pale yellow milds. I think from this we should realize that in the future any seemingly selfing segregates from the promiscuous project might still self. Also they might still be capable of some crossing as a recipient unless flowers are super inserted. Even when stigma is right at the tip of the pollen cone that's more promiscuous than industrial inserted. We should, in theory, get some selfers with really good exsertion out of this project. I look forward to seeing if that is true this year.

I do have more seed of the galapagense and cheesemanii than you initially sent me Andrew. I wish I was certain I would be able to do an even larger grow out of it this year. Plants are pretty small so filling a whole bed it them would make sense.

I do have a packet of big hill seed that was surrounded by 3/4 habrochaites, 1/2 penellii, a three way cross, the F1 penellii, and the pure or 3/4 penellii. I'm liable to grow out some of its seed densely planted in a flat and prick out any obvious hybrids based on leaf morphology.

[Dominic J]

What's the use of salt tolerance?

Has anyone had any success with cold tolerance? That's certainly a trait that I'd find interesting.

[whwoz]

What's the use of salt tolerance?

Salt tolerance is very important,  enabling plants to be grown in slightly saline soils and watered with brackish water.  Would allow the use of bore water that is just outside of palatable for human consumption leaving higher quality water for drinking. Lots of areas have ground water considered only good enough for stock that could be used for watering salt tolerant plants

[William S.]

What's the use of salt tolerance?

Has anyone had any success with cold tolerance? That's certainly a trait that I'd find interesting.

I agree with Whwoz on the salt tolerance. You might even be able to water with seawater. One of the problems with agriculture is salinization over time where salt builds up in fields because of inadequate flushing with irrigation. Also in North Central Montana the aquifers are saline and rising because of fallow rotations in wheat. Which means that salt can rise up into a field. However the flip side of this is that salt tolerance is multi-gene. It breaks when you hybridize the plants with domestics and no one has ever solved the problem. Except someone recently solved it using gene editing. Newly domesticated the wild plants basically by editing only the important genes for domestication. Unfortunately we can't do that ourselves so it is only possible for the plant patenters at universities and corporations. We might be able to manage a open source version in theory by keeping the domestic percentage low in a population- but so far that is only us theorizing as to how we could replicate that in an open source manner.

The cold tolerance. Some breeders have claimed some things. Big discussions on that around here and over on tomatoville and home grown goodness. http://opensourceplantbreeding.org/forum/index.php?topic=82.0
http://www.tomatoville.com/showthread.php?t=25599
http://alanbishop.proboards.com/thread/6988/tolerant-tomatoes-right-josephs-alley

J and L gardens has worked on the problem some they offer some breeding stock here:

http://jandlgardens.com/xencart/index.php?main_page=index&cPath=81&sort=20a&page=1

One of their recently released edible wild crosses "Wild Child" claims some blight and cold tolerance in the full description http://jandlgardens.com/xencart/index.php?main_page=product_info&cPath=1_8&products_id=577

Their "Weight in Gold" claims some frost tolerance in the full description
http://jandlgardens.com/xencart/index.php?main_page=product_info&cPath=78&products_id=625

LA 1777 which is full habrochaites has shown some cold / frost tolerance for some people.

My peruvianum plants have shown the best cold / frost tolerance in my garden.

In actual frosts weird things survive and die without apparent consistency in my garden. Though I haven't had a useful frost since 2017. Really hard end of the season frosts just murder everything regardless of resistance.

Frost and cold tolerance are two different things according to Darrel Jones who you may notice initiated and or participated heavily in a couple of the threads I linked. So cold tolerance he says you could test for in a refrigerator. Just put a flat in there with variable genetics until most of them die. Frost tolerance you need a freezing event. Hard for an amateur to replicate under controlled conditions which would be optimal. Joseph used to throw a flat with lots of seedlings outside till good portion got frosted. One grower is continuing with that protocol and I think one of the 2020 offerings on EFN is a result of that methodology. I think it was Wild Mountain Seeds in Colorado.

[Dominic J]

Thanks for the links.

Salt tolerance usefulness varies on locale, I guess. No shortage of freshwater around here. Gotta wonder if making plants more resistant to salts is the appropriate answer to overfertilization causing salinity issues, though.

Reminds me that a couple of years back, I had one of my plants stay green after the first frost. It was one of my LB resistant varieties. I didn't have many plants and considered it a fluke, but I think I saved its seeds anyways. I'd have to look to see where I put them.

[William S.]

Might be a fluke, might be epigenetics kicking in, might be regular genetics. Might be some combination.

[William S.]

I've been wondering if any of the historic tomato varieties with Peruvianum and Habrochaites ancestry might have larger chunks of DNA than modern introgressions.

I just found

https://digital.lib.uidaho.edu/digital/collection/ui_ep/id/19060

A actual pedigree for the tomato variety Payette. In short it is 121/128ths the domestic variety Sioux. 4/128ths habrochaites, and 0.25/128ths peruvianum. Leaving only 2.75/128ths of other domestic. If I've tracked this correctly.

Thus, I conclude that even the early crossbreedings were highly introgressed and not very interesting for their wild species content and not likely to have any special crossing potential with say peruvianum at 1/512.

It's great that DNA is out there, but it is not enough content for me to choose a red tomato over a more desirable color or flavor when selecting a domestic parent for an interspecies cross.

[Joseph Lofthouse]

Here's a pedigree of the Beautifully Promiscuous and Tasty Tomato Project.

High resolution image

It shows the ancestors of the varieties that I am currently sharing. It's promiscuous to the core, so I can't possibly show all the interactions. These are the main pollen flow paths that are known, or highly likely.

The F2 and F3 after crosses with wild tomatoes were highly selected for promiscuity and self-incompatible-like traits. The F2 were open pollinated. The F3 were manually pollinated.  In every generation, there was some possibility of wild pollen introgressing into the population. And some possibility of bee-fascilitated crossing among the wild species.

Abbreviations used.

BH =  Big Hill. A super early bicolor beefsteak developed on my farm from a cross between Hillbilly and Jagodka. Super early.

H = Solanum habrochaites

P = Solanum pennellii

W_h = Descended from Domestic X habrochaites.

W_p = Descended from Domestic X S pennellii

W = BH crossed to (Domestic X habrochaites) or (Domestic X pennellii)


BH X W  - XL 2019. Red beefsteak. Very early. Most like a grocery store tomato. One plant out of 250. Self incompatible, so pollinated by something else in the patch with much smaller fruits, mostly by full or half siblings. This is not my preferred phenotype. I'm making seed available, because it was an amazing plant. Earliness from Jagodka. Huge fruits from Hillbilly. Self-incompatibility from S habrochaites. These may segregate for self-fertile/sterile. Interesting traits often skip a generation, so large fruits are expected to segregate out of the 2nd generation. Descendants with yellow fruits are also possible. If I weren't breeding for chefs, I might pursue this line more heavily. Seed is fairly limited. Nominally 25% wild.

BH X W - Best Taste. Chef selected for amazing flavors. Early. Mostly yellow fruited. Self-incompatible, may include some pure S habrochaites pollen donors. Most pollination done by the BH X W sibling group. Up to 250 parents. 3 species hybrids are likely (lycopersicon, habrochaites, pennellii). These may segregate for self-fertile/sterile. Nominally 25% wild.

H X ((BH X Wh) or (BH X Wp)). Most interesting genetically. Highest diversity. More s alleles. 3 species hybrids expected. Fully functional self-incompatibility system.  In the next generation fruits are highly likely to be small, green and not tasty. The F2 may produce red/yellow/white/bicolor fruits with lots of fascinating flavors. Higher resistance to bugs/pests/diseases expected in this population than any other. Nominally 75% wild.

[BH X Wp] X (S habrochaites or (BH X Wh)). Not shown on image. The reciprocal cross to the one above. This cross was done to make 3 species hybrids that are 25% S pennellii, 25% to 50% domestic, and 25% to 50% S habrochaites.  Medium diversity. I recommend doing minimal selection on this population until the 2nd or 3rd generation. Lots of interesting things may show up. Due to the limited availability of s alleles. I recommend recombining with more elite lines after a few generations. Likely to segregate for self-fertile/sterile. 

With any of these seeds, grow as many plants as you can manage, even if that means putting 10 plants into the same hole, or planting them right next to each other.

I've arranged for about 50 collaborators so far, some of them growing up to a couple hundred plants. Should be a fabulous year for the project.

[William S.]

Hmm, I think I will plant close together like I normally do. I was thinking about spreading them out for a change. I can definitely grow more plants close planted. Might be able to do some direct seeding too if I run out of growing space for transplants.

Must Plant:

4 accessions Joseph describes above
BH x W4 from seed I grew last year ~600 seeds
7 seeds of pretty kinda edible habrochaites cross
New Habrochaites Accession

Peruvianum project:
Pure Penellii (with a single Peruvianum)
Arcanum G2 to check for hybrids

Want to Plant:
Pureish Penellii F1 and F2
Three Way from last year's G2
New penellii x domestic F2
Penellii x domestic F2,  F3, and F4?
Trays of exserted domestics I dusted with wild pollen.
Things I am forgetting...
Chilense?

Hmm, I had about 7 rows in the direct seeded field last year. Maybe I could do six rows of ~100 transplants each and one row of a direct seeded wild hybrid mix.