Open Source Plant Breeding Forum

General Category => Plant Breeding => Topic started by: William S. on 2018-12-02, 09:31:11 AM

Title: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2018-12-02, 09:31:11 AM
Darrel Jones and Joseph Lofthouse have spent some time and energy on frost and cold tolerant breeding of tomatoes. We just did some discussion of this in the climate change breeding thread but I thought a dedicated thread might be useful here.

There is a history of some strains of domestic tomato having more cold or frost tolerance. There are also wild tomato species with more cold and frost tolerance. So through both epigenetic and genetic means we may be able to produce more cold/frost tolerant tomatoes to extend the growing season.

There has been a lot of discussion about epigenetic change in Tomatoes over on the homegrown goodness forum and possibly another forum like tomatoville especially in regards to Darrel Jones initiated cold/frost tolerant tomato breeding project, Josephs trays full of frosted seedlings, some Russian tomatoes, and the wild tomato species with better cold and frost tolerance.

In 2018 I got no spring frosts after planting tomatoes. However in 2017 I got two frosts after transplanting at least the latter of which impacted much of my direct seeding experiment as well. Most plants that were frosted twice died. Most plants frosted once survived by resprouting from the base. One Peruvianum complex plant survived both frosts with top growth intact. Habrochaites survived by resprouting.

I included some of the Russian genetic strains in this. They did not impress particularly if they had resistance I think it must have been epigenetic and inactive in 2017. It's possible that the shock of being frozen once or twice may have activated some epigenetics.

A few rare plants planted between the two frosts survived with top growth intact despite every plant surrounding them succombing. These results were pretty nonsensical. For instance one Blue Gold plant a Brad Gates variety not chosen for frost tolerance survived with top growth intact while many many frost or cold hardy strains succombed and every other Blue Gold individual. However the frozen to the ground plants resprouted and did set fruit as well.

I also learned that most inch high tomatoes direct seeded survived.

I also direct seeded more tomatoes the next day. Ultimately I had too many tomatoes in 2017.

I am pretty willing to flirt with that last spring frost or two because I now know I can reseed immediately, that most tomatoes will survive being top killed once, and if there are epigenetics at play they may be being activated, and soil moisture is great I can transplant without watering anything but the flats or direct seed without watering, which means I may not need to water until July.

In 2017 my fall killing frosts weren't very telling. A single big very hard fall frost killed everything. 2018 I had weaker fall frosts and they took out domestic tomatoes first then wild tomatoes like Peruvianum complex and habrochaites lived longer both from top growth and resprouting. Though even domestics were sometimes killed in layers.

It would be interesting to have a bit of an experimental facility to test and play with both epigenetic and genetic cold and frost tolerance in tomatoes. A dedicated refrigerator would work for cold tolerance- Darrel Jones suggested that a refrigerator test would quickly separate strains there by turning non-cold tolerant strains to mush. However freezing is trickier. It would be nice to be able to freeze tomato plants under controlled conditions. Darrel also explained go us that the moisture with the frosts is important- leaf dry vs. Leaf Wet frosts.

Joseph, when you are growing stuff you know is outside it's comfort zone, do you direct seed, or start it in a greenhouse?

I'm suspicious that some, maybe most of what we experience when we adapt varieties to our region is epigenetic rather than genetic change. I speculate that most plants have a basic adaptation that is fairly wide, but this adaption is narrowed and optimized for any specific environment by heritable epigenetic modifications. Essentially a program on top of a program. I speculate that what gets you from one epigenetic subprogram to another is a serious shock of some sort. Heat shock, cold shock, etc. Something extreme enough to make the plant stop growing for a while but not so extreme it kills the plant. Maybe the nature of the shock induces a specific change to the correct alternate epigenetic program. Or maybe it just causes the plant to try a different one of it's epigenetic programs at random, with some plants hitting the right one.

If something like this is going on, Joseph's transition year might be the year that causes enough of a shock to trigger change in epigenetic program but not so much it kills unaltered plant first.

So if all this speculation was actually truth, we might be able, for example to get a tomato variety to become more freeze-hardy by subjecting seedlings to cold shocks and then saving seeds. Shades of Lysenko. However not for the reasons he supposed. No inheritance of acquired characters. Just an environment induced epigenetuc program change.

This is all speculation. I set it out because it we can test these ideas. And they have a whole lot of plant breeding implications.

A little later after a couple hrs reading about plant epigenetics on internet. Lots of people have approximately same ideas as outlined above, with much work on biochem of epigenetic changes on DNA. And there is much enthusiasm for potential in plant breeding. And much work happening attempting to get plants to produce "epilleles".. However there seems to not be a single variety developed based upon an epigenetic change yet.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Kai Duby on 2019-01-12, 04:50:30 PM
I really appreciate seeing epigenetics being discussed alongside breeding efforts!

I recently came across some research on Goji berry breeding, which indicated that there is the potential to cross tomatoes and other Solanaceae with Lycium sp. It's mentioned under Hybridization here:  https://www.researchgate.net/publication/325759407_Gojiberry_Breeding_Current_Status_and_Future_Prospects

The study states that out of seven lines from 21 cross combinations they were able to obtain two flowering and fruiting plants.

This may not necessarily count as a true tomato breeding project but given the cold hardiness of many Lycium sp. it may be worth looking into. There are certainly many more factors to consider but it seems like a potential path toward a perennial zone 4 tomato-like plant. Perhaps a tomoji?

I hope this doesn't diverge too drastically from your original subject but I thought it should be mentioned.


Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Diane Whitehead on 2019-01-12, 08:08:18 PM
I wonder what conditions are best for cold tolerant tomatoes.

I live on the Pacific coast of Canada.  Our summers are what most everyone else in North America would call 'cool'. Both days and nights too. We don't have air conditioning, and I don't sit around outside in the evening.

However, we don't have late frosts.  Our usual time to plant tomatoes is late in May, but that is not to avoid frost, but to hope for some warmth.   I have planted out tomatoes in April in years that I have been travelling in May, and they've grown as usual. 

Are Russian tomatoes like the Saraev ones bred to do well in these conditions?

Or do they withstand the occasional night frost but then revel in hot days to compensate?

Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2019-01-12, 08:31:02 PM
I wasn't impressed by any of the Saraev tomatoes I tracked down. I suspect it was epigenetic. Darrel Jones seems to be the Guru on this. He has a bit of something in the works. I was recently visiting relatives in Vashon WA and they had a live but unproductive tomato plant in november. A cold tolerant tomato could be huge there.

Have you seen that new cloudy day hybrid? That could be a good dehybridization project.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Diane Whitehead on 2019-01-12, 09:05:49 PM
Well, I will have to try that one.  Has everything I need:  Variety thrives in cooler temperatures; plants laugh off early and late blight. 

Well, almost everything - comments on its looks, but there is no mention of it being delicious.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2019-01-12, 09:35:04 PM
Yeah it could be perfect for one of our colder cloudier summers here. Some years it's hot and the skies fill with smoke, some years it rains alot... Never know what your going to get.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Joseph Lofthouse on 2019-01-12, 11:41:33 PM
A summary of what I think I have learned about cold/frost tolerance in tomatoes....

There seems to be two different traits that may be useful, and don't seem to be closely related to each other: 1- frost tolerance. 2- ability to grow in cool temperatures. The winner of my frost tolerance trials was Jagodka (Ягодка) a variety from the Vavilov Institute of plant science in Russia. It has low tolerance to frost, but a high ability to grow well during cold weather, and in my garden with intense radiant cooling at night. Most of the Russian varieties that I trialed were a bust -- My continental desert climate is radically different than the maritime climate of Saint Petersburg. The runner up in my cold/frost trials was a variety named Matina.

Some years, my domestic tomatoes have been frozen for two months before the Solanum habrochaites plants finally get frozen.

There seem to be large differences in early spring frost tolerance between varieties.

Tomatoes in my garden would benefit from developing resistance to flea beetles, because plants are severely damaged by them first thing in the spring. The earlier I plant them, the more predation there is, so increased frost tolerance would ideally be paired with increased resistance to flea beetles. 

Tomatillos are more frost tolerant than tomatoes. I often use tomatillos as a control in my seedling frost tolerance trials, because if the tomatillos also get killed, then I know it was a really hard frost.

I think that frost tolerance of seedlings may not be closely related to cold tolerance of end-of-season plants.

Some of the wild species, and some of the interspecies hybrids can have their tops killed by frost or winter weather, but they have the ability to survive and re-sprout from the basal stem.

My frost/cold tolerance project is currently on hold. I am focusing my tomato breeding efforts on creating a genetically diverse, self-incompatible tomato population. Once that is in place, I expect to restart other projects like cold/frost tolerance. The varieties that were previously winners of my cold/frost tolerance trials are being merged into the beautifully promiscuous tomato project.

I'm wondering if something as simple as refrigerating a ripe tomato fruit for a month prior to harvesting the seeds could trigger an epigenetic change towards more cold tolerance. Or how about freezing the fruits before extracting seeds?

I want to focus more effort towards selecting for tomatoes with the ability to volunteer. I think that in my garden, that may also inadvertently be selecting for some measure of frost tolerance, and ability to grow in cool temperatures. 

And finally, just about all of my selection work is done on segregating hybrid swarms. I don't have any good way of differentiating allele-genetic differences from epi-genetic differences. Mendelian genetics doesn't seem to be very applicable to my methods.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: reed on 2019-01-13, 03:55:02 AM
I want to focus more effort towards selecting for tomatoes with the ability to volunteer. I think that in my garden, that may also inadvertently be selecting for some measure of frost tolerance, and ability to grow in cool temperatures. 

I have lots of tomato volunteers both in spring and in late summer/fall. There is definite variation in how much frost they take. I'v seen spring volunteers survive when most didn't as well as some late ones croaking in the first fall frost and some holding on till a harder freeze. I don't have a real need for frost tolerant tomatoes so never gave them much attention. I suspect once you achieve the goal of volunteers the rest will be easier. I have to wonder though, are cold weather tomatoes gonna taste like tomatoes?
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2019-01-13, 06:09:01 AM
I think in my garden our thoughts on domestication of Peruvianum complex lend themselves best towards this. It's a champion volunteer in my, Andrews, and Joseph's gardens. In my garden it's shown interesting frost and cold tolerance. Joseph has started selecting it for flavor. I've decided to focus some on both potential bridge lines and possibly some embryo rescue as it would be neat to A. Cross it into domestics, and B. Cross domestics into it. 
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Andrew Barney on 2019-01-13, 08:18:52 AM

I'm wondering if something as simple as refrigerating a ripe tomato fruit for a month prior to harvesting the seeds could trigger an epigenetic change towards more cold tolerance. Or how about freezing the fruits before extracting seeds?


I think it could be a very good technique. I've thought about it myself. In fact,  it would be nice if we could artificially have a chilled room that was cold but not freezing at the times of growing we wanted to induce an epigenetic change (which I suspect over time epigenetic change can induce more permanent genetic changes), but over several generations.  This I suspect that line would grow better in such conditions.

Simply planting seeds early direct seeded might select naturally for early frost/cold tolerance,  but late cold/ frost tolerance might be a whole separate set of genes or epigenes.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Joseph Lofthouse on 2019-01-13, 08:34:33 AM
I have to wonder though, are cold weather tomatoes gonna taste like tomatoes?

Not in my garden. Any cold tolerant tomatoes that I develop are likely to taste like an exotic tropical fruits, guavas, plums, mangos, etc. I'm pretty much done with lycopene bitterness. One of the great joys of working with the interspecies tomatoes, is that it has taught me that tomatoes don't have to taste like the highly inbred, genetically fragile plants that we inherited from the corporation.

I think in my garden our thoughts on domestication of Peruvianum complex lend themselves best towards this. It's a champion volunteer in my, Andrews, and Joseph's gardens. In my garden it's shown interesting frost and cold tolerance. Joseph has started selecting it for flavor.

I am also selecting the peruvianum complex for fruit size. And I'm growing it next to other wild species, and to the interspecies hybrids, hoping that some natural crossing will occur. Peruvianum doesn't seem to be a good pollen donor to habrochaites, because when I grew a single habrochaites plant in the peruvianum patch, it didn't set seed. 

After I took this photo, comparing the typical small peruvianum fruits to a larger peruvianum fruit, I found a plant that had even larger fruits.... When I grow tomatoes 9 inches apart, it's hard to pay attention to individual plants, until something grabs my attention. Larger fruits certainly did. I saved seeds separately from larger fruited plants, and am intending to do early selection next year by culling plants with small fruits early in the season so that they don't shed pollen for small fruits into the patch.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Andrew Barney on 2019-01-13, 09:01:24 AM

After I took this photo, comparing the typical small peruvianum fruits to a larger peruvianum fruit, I found a plant that had even larger fruits.... When I grow tomatoes 9 inches apart, it's hard to pay attention to individual plants, until something grabs my attention. Larger fruits certainly did. I saved seeds separately from larger fruited plants, and am intending to do early selection next year by culling plants with small fruits early in the season so that they don't shed pollen for small fruits into the patch.

That's way cool!

That reminds me of another idea I had once. I suspect just growing plants next to each other that epigenetic influence can occur from chemicals leached into the soil.

One year I grew a whole patch of my purple stalked corn. That year and the following year after (maybe two) the grass weeds turned a heavy red shade. It did not seem like a coincidence. Obviously they couldn't have been influenced by pollen. It made me wonder if grinding up dessert adapted plants like yucca and spraying it on as fertilizer could help produce a more desert tolerant domestic crop like corn.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2019-01-13, 10:41:53 AM
That's way cool!

That reminds me of another idea I had once. I suspect just growing plants next to each other that epigenetic influence can occur from chemicals leached into the soil.

One year I grew a whole patch of my purple stalked corn. That year and the following year after (maybe two) the grass weeds turned a heavy red shade. It did not seem like a coincidence. Obviously they couldn't have been influenced by pollen. It made me wonder if grinding up dessert adapted plants like yucca and spraying it on as fertilizer could help produce a more desert tolerant domestic crop like corn.

Course it could just be that corn being a heavy feeder temporarily depleted phosphorous from the area. Google tells me that nutrient deficiency causes red foliage.

Plants use red like sunscreen.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: reed on 2019-01-13, 03:11:09 PM
Not in my garden. Any cold tolerant tomatoes that I develop are likely to taste like an exotic tropical fruits, guavas, plums, mangos, etc.

Ah, you mean like the one pictured below, which came from your seeds. Looks like a tomato but tastes more like something that might be found under a tree in Hawaii. I called it Captain Crunch, cause it's crunchy when chomped on, very juicy and sweet. I think I sent some seeds back to you but don't remember for sure. Unfortunately it had little disease resistance as you can see by the foliage.  I like the flavor of my old red tomatoes but there is room for things like this in my garden too.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Joseph Lofthouse on 2019-01-13, 03:46:28 PM
Ah, you mean like the one pictured below, which came from your seeds. Looks like a tomato but tastes more like something that might be found under a tree in Hawaii.

Yup. Like that!!! Tomatoes are a tropical species after all.

I was especially enthralled by the "high ummami" fruits and by the "fermenty" flavors.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2019-01-13, 07:03:48 PM
I like red tomatoes fine, and yellow ones, and green ones, and bicolor ones, and orange ones, and fruity tomatillos, ground cherries, and tomatoes with new flavors like Brad Gate's Amethyst Cream. So I suspect I will like many of the new flavors Joseph finds for us but still eat some ordinary red ones too. I even like the ice cube flavored ones taco bell chops up and serves on their tacos.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Lauren on 2019-04-14, 10:24:54 AM
As always, I started my tomatoes in regular garden soil, without bottom heat or supplemental lighting. As usual, some croaked. Every year I start them in a similar way and plant out under wall-o-water in March or April. Whether epigenetics or genetics, they seldom die in the spring any more. Those that do I simply replace.

I selected the first to come up, the subset that got secondary leaves while still in dim light (sunny windowsill, no supplemental lighting), and the best of those are now in my garden under milk jugs. Even with snow on the ground they're not complaining. One of the six is easily twice as tall as the rest and I'll be keeping an eye on it. Those six will be my seed tomatoes this year. Two of the other plants have been eliminated--one nearly died when it didn't get watered for a couple days, and the other was covered with aphids in the greenhouse.

Last year I was given a handful of plants. They had a very small survival rate under the same conditions. I think I ended up with fruit on two out of the ten. I was given two tomato plants this year. One croaked in the greenhouse, the other is out under a wall-o-water and getting frost damage even there.

Once I have the spring thing settled, I'll start working on autumn frost tolerance. I have noticed that the plants are much hardier than the fruit. The first frost of the season might not even touch the plants but the fruit bites the dust.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2019-04-14, 05:26:55 PM
Currently watching seedlings germinate in cool soil. Solanum peruvianum, S. Pimpinillifolium, and S. Penelli  x domestic have won the germination race.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Chance on 2019-04-19, 06:15:20 PM
Joseph, do you like acidic flavors in your tomatoes also, or more just sweet and umami?
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Joseph Lofthouse on 2019-04-22, 12:28:41 PM
Joseph, do you like acidic flavors in your tomatoes also, or more just sweet and umami?

I dislike bitter tomatoes. Anything raw, with nasty bitter red-lycopene flavor is close to unpalatable for me. In domestic tomatoes, I pretty much only tolerate yellow or orange tomatoes.

In the wild tomatoes, I am selecting for high ummami, fruitiness, lack of bitters, aromatic, and sweetness. (I'm selecting against red fruits.) People are describing them as guava, tropical, mango, grape, fruity, fermenty, etc... Flavors that might be more typical of physalis: ground cherry, cape gooseberry, etc...   
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2019-04-22, 01:49:41 PM
I've been trying to hand my toddler yellow tomatoes to see if I can get him to eat them. This morning he made a positive comment about how juicy the store bought cherry tomato I handed him was. Still didn't really eat it. Just bit it then rejected. Wanted it though.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: Lauren on 2019-04-23, 07:50:29 AM

That reminds me of another idea I had once. I suspect just growing plants next to each other that epigenetic influence can occur from chemicals leached into the soil.

One year I grew a whole patch of my purple stalked corn. That year and the following year after (maybe two) the grass weeds turned a heavy red shade. It did not seem like a coincidence. Obviously they couldn't have been influenced by pollen. It made me wonder if grinding up dessert adapted plants like yucca and spraying it on as fertilizer could help produce a more desert tolerant domestic crop like corn.

Many years ago I was growing lemon thyme as a groundcover in with the raspberries (bad idea--it choked them out) and for the next couple years I noted that the raspberry leaves had a yellow edge just like the thyme. Again probably a nutrient issue, but interesting nonetheless. It was ONLY the plants closest to the thyme that were affected.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2019-04-23, 09:15:19 AM
Starting my tomatoes in the normally unheated greenhouse this spring. Been unplugging the fan and plugging in a tiny Heuer at night. Been interesting to see which species germinated first. A little worried about one night coming up in the forcast. Low of 29 F. Not sure if the heater can handle that. Might get nervous and bring them in.

Curious though if it affects their epigenetics to keep seedlings relatively cold.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: reed on 2019-04-23, 12:53:14 PM
I start mine in  an unheated cold frame. It's positioned against the south wall of the house, the back and floor are black, a few milk jugs of water take up the extra space.  Hasn't really been much of an issue this year but there have been many times tomatoes sprouted & survived in there when temps at night were intermittently below freezing. It isn't even all that well sealed, I throw a blanket over it on very cold nights but again that hasn't been an issue this year. Maybe I should have started them in February.  ;D

I find this epigenic thing a little hard to swallow but I'm intrigued. The premise being that environmental or other factors  can trigger the same genes to configure themselves in different ways?
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2019-04-23, 01:24:17 PM
Yep, basically as I understand it the epigenome is a system of regulatory switches that turn on and off genes and these changes can be heritable for a couple generations.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: William S. on 2019-05-03, 08:25:44 PM
During some recent cold nights I took most of my tomato starts inside. Save two I left out just for curiosity. One survived a pimpinillifolium directly in line with my small heater. The other a potato leaf froze back badly. Perhaps it will resprout.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: reed on 2019-05-04, 07:21:48 AM
My garden is full of volunteer tomatoes right now, mostly the pimpinillifolium crosses I think.

I'v noticed in some years a dramatic difference in how the early volunteers respond to late frost but we haven't been below 50 F for quite awhile and don't really expect to be so guess there will be no volunteer frost tolerance trial this year.
Title: Re: Frost and Cold Tolerant Tomato Breeding including epigenetic and regular genetic
Post by: PaulJ on 2019-05-04, 11:55:29 AM
I have to agree with what Joseph has said.

Last year I grew some "medicinal plant" varieties that are known as frost tolerant
I sprouted them in a cold windowsill with average ambient day temps (10-15C) and low-ish night temps (4-10C)
they didn't get potted up after 3 inch, they grew great as soon as put out and never got "checked" by the cold ut they seemed to lose their frost tolerance.

Another variety that were sown later straight into warm soil got a few checks but were  much more frost tolerant, although Id never grown this before so its harder to know

All anecdotal but It makes me wonder if maybe at least one of these genes is a one way switch, cold or frost tolerance but not both.