Author Topic: Funding Blight Resistance Breeding in Heirloom Tomatoes  (Read 1373 times)

William S.

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #15 on: 2019-01-07, 09:42:34 PM »
It says it is resistant to both kinds.  -  " Impressive resistance to late blight, early blight,"

"Must be planted away from other tomatoes to prevent early blight transmission."

But the odd cultural separation recommendation is for the early blight.
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Diane Whitehead

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #16 on: 2019-01-08, 10:41:02 AM »
There is a very interesting thread on Tomatoville,    'Mountain Gem' F1 hybrid tomato,  started by RandyG,   Dr. Randy Gardner
from North Carolina, who bred a lot of the tomatoes with "mountain" in their names.
« Last Edit: 2019-01-08, 11:00:19 AM by Diane Whitehead »
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nathanp

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #17 on: 2019-01-08, 07:37:41 PM »
Mountain Gem looks like a good potential parent, though it appears to be heterozygous for both Ph2 and Ph3.  Having a homozygous version of it would be ideal, but it might be a better starting point for using to cross with heirlooms if it has good flavor.  In my opinion, most of the LB resistant tomatoes have poor taste.

William S.

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #18 on: 2019-01-08, 08:47:30 PM »
That's why Carol points out Iron Lady F1 is homozygous for the resistances in her book. The dehybridization of it is homozygous and the F1 cross with it and any heirloom gets all three genes.

My goal of crossing an ultra early with it would be unaffected. Most ultra early tomatoes are reds and have pretty unremarkable flavor.

Someone said Skykomish a Tom Wagner creation is also homozygous and being his work and a bicolor may have better flavor. If true, that would be a better starting point. Here is a blog post about it on bifurcated carrots https://bifurcatedcarrots.eu/2010/09/genetic-sequence-for-late-blight-resistant-tomatoes-cracked/
« Last Edit: 2019-01-08, 10:04:04 PM by William S. »
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nathanp

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #19 on: 2019-01-09, 07:05:14 PM »
From RandyG

Quote
NC 1GEM is homozygous for Ve, I, I-2, Ph-2, and Ph-3 genes. NC 4GEM is homozygous for Ve, I, I-2, Sw-5, and Tm-2 genes. Also, both NC 1GEM and NC 4GEM are homozgous for the recessive crimson gene, ogc, which is necessary to have in both parents for expression of crimson fruit color in the F1 hybrid.

The hybrid Mountain Gem (NC 4GEM x NC 1GEM) is therefore homozygous for Ve, I, and I-2 and heterozygous for Ph-2, Ph-3, Sw-5, and Tm-2

It's still about as good of a parent as you will find with the combination of other resistance genes combined.  Even if it is heterozygous for Ph-2 + Ph-3.  If it was crossed with something homozygous with those traits, you get something where 3/4 will be homozygous for them, and heterozygous for all Mountain Gem's other homozygous traits.

Regarding the question of Skykomish, yes I believe it is homozygous for both Ph-2 + Ph-3.   I've been growing it for about 5 years now and am slowly selecting for earlier selections.  It is fairly long season, and the first year I grew it only had 2 tomatoes mature before frost.  It's a very good tasting tomato too, which is rare of having LB resistance.

Carol Deppe

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #20 on: 2019-01-09, 08:20:02 PM »
Re funding my own breeding, especially the tomato project--Asking directly for donations, doing crowdfunding, and going for grants are not mutually exclusive. I'll probably try em all before I'm done.

As for the reference to Raul Robinson--this refers to the idea that there is "horizontal" and "vertical" resistance, that these are actually different from each other, and that "horizontal" is slower to be overcome by the evolution of the pathogen. It's additionally assumed that horizontal resistance is dependent upon multiple genes with small affects, and vertical resistance is dependent upon one gene with major effects (the sort of gene university breeders transfer into their varieties). It's normally assumed that heirlooms have horizontal resistance, but this is only until someone actually does some crosses and looks.

Then, my impression is that the heirloom usually turns out to have no measurable resistance--or it actually has one of those major resistance genes, exactly the same ones involved in "vertical" resistance. Ph1 is a good case in point. It was present in a number of heirlooms, which would undoubtedly, in the absence of serious genetic investigation, been called "horizontal" resistance. It conferred serious resistance in its day. However, it was overridden by more modern lines of late blight, and now doesn't confer useful resistance.

Whether a variety's resistance is easily out-evolved by the pathogen is not any such simple thing as one-gene-bad, more-genes good, either. For example, Jim Baggett's pea varieties that carry one gene for resistance to pea enation virus and one for powdery mildew and one for wilt--which let's them be grown all the way from spring to fall--are still nicely resistant to the respective diseases, though they have been around for decades.

Generally, though, from first principles you can guess that if you have two different major genes for resistance to something, your variety is less vulnerable to evolution of the pathogen than just one.

Ph2 and Ph3 show a different repertoire of what lines of late blight they are sensitive too. However, both genes act as codominants and act quantitatively with respect to each other. So varieties that are homozygous for both generally show strong resistance to all strains of blight; varieties that are homozygous for just one, or heterozygous for both show less resistance, with levels more dependent upon specific strains.

Another way of looking at it. Let's suppose that after we've developed a new generation of heirlooms with Ph2 and Ph3 in them, whether someone who didn't know what we did would call them "horizontal" or "vertical" resistance. Well, before they did serious genetics, they would probably just assume they had horizontal resistance. If they then went and did the serious genetic analysis in the absence of testing specifically for Ph2 and Ph3, they would probably still think the resistance was horizontal. Because it would look quantitative under field conditions.

One thing that is very valuable about working with wild material is you might discover additional genes conferring serious resistance to late blight. To show up as a QTL in something as hard to evaluate as disease resistance, especially in variable material, you pretty much would be talking about genes with major effects, by the way. Various university breeders are still "mining" wild material looking for new genes. Additional new genes would be valuable. Could you test for them using marker assisted selection? No. Marker assisted selection is based upon someone having identified a distinctive DNA sequence in or near the gene for resistance. So you could test wild-derived late-blight resistant material to see if it contains Ph2 or Ph3. But not PhX, something new. Of course, if your material doesn't have either of those genes and is resistant, it presumably is something new. So then you'd just give some to one of the university groups which is spending day and night looking for new Ph genes, and they would undoubtedly be very happy to do the molecular biology and identify a marker for the gene.


Carol Deppe

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #21 on: 2019-01-09, 08:48:31 PM »
"Must be planted away from other tomatoes to prevent early blight transmission."

But the odd cultural separation recommendation is for the early blight.

 So take Iron Lady which is homozygous for three of these traits.

That's cool becase we can cross any tomato to Iron Lady and our resulting cross is going to get all three traits.



My understanding is Iron Lady is homozygous for 2, not 3, late blight resistant genes, Ph2 and Ph3. I've seen it reported as having hard resistance to late blight but intermediate resistance to early blight. Note that early blight is an unrelated disease. It's actually more important here than late blight, as if the plants die of early blight before yielding anything, it's irrelevant whether they would have lived through late blight if they lived long enough to see any.

I'm guessing that Iron Lady is heterozygous for early blight resistance. Apparently that level of resistance to early blight is proving inadequate, hence the info added to the variety description suggesting growing the variety separate from other varieties so it doesn't catch early blight from them.

You may actually select more for new late blight strains with a population variable for resistance genes than one that uniformly carries homozygous resistance at two or more major genes. Blight already can infect plants having two of the 4 possible lb resistant alleles at Ph2 and Ph3. The less resistant plants would serve as a selective system for mutations to overcome both genes, with there being plenty of plants with just one or the other. But with all plants being homozygous for both genes, the blight might die instead of living long enough to be selected for resistance. Something like taking the full dose of the antibiotic versus cutting it to 1/4 to 1/2 the recommended dose. The latter is a very good way to select for bacteria resistant to the antibiotic.

If a pathogen has to have two mutations simultaneously to overcome the resistance of a variety, that can be pretty powerful, as exactly the right two mutations aren't nearly as likely to happen simultaneously as just one.

QTL, by the way, are always in the context of a particular cross, usually of inbred lines. Do a different cross, and you'll usually get a different repertoire of QTL showing up. As for QTL in a variable population, not sure that can be done at all. (You can only identify alleles that are different in the specific cross. If some gene matters hugely but is in both lines that went into the cross, it is invisible and doesn't show up.)

I suggest crossing your favorite heirlooms to a source of disease resistant genes, THEN BACKCROSSING ONCE TO THE HEIRLOOM, and only then choosing the best offspring of the backcross and taking them to the F2. The source of disease resistant genes is usually full of genes we want to get rid of. And most heirlooms have more than one major gene needed for their distinctive colors/flavors, usually more than one recessive. You greatly increase the probability of getting something similar to the heirloom with great flavor if you go to the F2 with material that is genetically 3/4 the heirloom rather than 1/2.

I have a huge section outlining this sort of tomato project in Tao of Vegetable Gardening, along with a big section on the major genes in heirlooms we care about and how they are inherited. That book also has sections on genetically rejuvenating heirloom varieties, creating landraces, etc.
« Last Edit: 2019-01-10, 03:47:52 AM by Carol Deppe »

Carol Deppe

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #22 on: 2019-01-09, 08:53:57 PM »
My most blight tolerant tomato aside from some crossed up currents is one I call "Hoosier Rose" a dehybridized version of the commercial F1 "Red Rose". It is a cross between Brandywine and Rutgers, it segregated into normal and potato leaf versions, the best one "Hoosier Rose" has lobed green shoulders and is also the best flavored. It's flowers are semi-open, that is open enough to be attractive to the micro-bees.

The original F1 was not advertised as having any special blight tolerance, having none that I know of the blight resistant genes but it's descendants are  more resistant  than any I'v tried that are advertised as such. How can that be?

Two others that hold on better than most are an heirloom called Mr. Stripy and one I call Utah Heart, from a mix of Joseph's seeds. They also have semi open flowers and I pant them all together.

Interestingly an old local heirloom I grew for many years gets diseased so bad I stopped growing it. it used to be my primary juice tomato, now replaced by Utah Heart.

Hoosier Rose might have picked up a mutation for resistance to exactly whatever line of late blight that is your problem.

Carol Deppe

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #23 on: 2019-01-09, 09:02:44 PM »
Quote and link from Carol:

http://www.caroldeppe.com/Donate.html

"believe that because of changes in late blight lines, it's going to become impossible to grow all heirloom tomatoes outdoors almost everywhere in North America within the next 5 to 10 years. None of the heirlooms have adequate defenses against late blight. There are commercial late blight resistant varieties produced by university breeders and big seed companies. But these are all in the form of hybrids, not open pollinated varieties. Worse yet, they pretty much all taste awful. They are bred to have uniform gorgeous color, which requires the u gene (uniform shoulders). The u gene actually causes sugar content and aromatics (flavor) to drop. In addition the commercial varieties usually have tough, unpalatable skins for resistance to damage in handling and shipping, and additional genes associated with slow ripening that confer longer shelf life, but also destroy flavor. That is not what most gardeners want to grow and eat.


I've begun a major project that involves crossing major genetics for late blight resistance as well as resistance to other major diseases into a large repertoire of heirloom varieties. My basic plan is to cross resistant hybrids to each of a couple dozen heirlooms, backcross once to the respective heirlooms, choose the offspring that carry an appropriate repertoire of late blight and other disease resistance genes, take those to the F2, OSSI-Pledge these lots as breeding material, then distribute that material far and wide for hundreds of gardeners and farmers and seed companies to use to select hundreds of new varieties of heirloom-quality open-pollinated OSSI-Pledged tomato varieties with late blight and other disease resistance combined with heirloom-quality flavor. I hope in this fashion that we can replace all the current heirlooms with equally delicious late blight resistant versions before the late blight situation gets so bad that our current heirlooms become ungrowable. This project is going to require major resources in land and labor. In addition, the step of "choosing the offspring that carry an appropriate repertoire of late blight and other disease resistant genes" from which to get the F2s to distribute will involve marker assisted selection. That alone will require several thousand dollars in lab fees per year for a number of years. However, the result of this project should be a new generation of heirloom-quality tomatoes that are not only resistant to late blight, but also carry the other important genes for disease resistance that most heirloom tomato varieties currently lack"

This sounds great to me then we can get the F2 populations we want from OSSI. We could also do similar work in parallel to Carol and pledge our own F2's to OSSI. It would be good not to duplicate. Carol is talking about doing about ~24 varieties, IF she can get the necessary funding. The marker assisted selection is a big funding need, I could cross my intended lines but could not do the Marker assisted selection. Would just need to freeze the F2 and wait for blight which would also preclude the back cross for better flavor retention.

I wonder if Carol would be open to working on specific varieties for people with favorites who have money but not time? Wonder what the cost per variety would be?
I'm open to suggestions. However, I plan to come here and invite wide participation as soon as I have F2s of appropriate backcrosses to distribute. I've already got the first cross of Iron Lady to 15 or 20 heirlooms.

Once we have that first batch of foundation material, it will be easier to do more. For example, if I can give you the F2 of a pink offspring that is 3/4 Pruden's purple and carries a useful repertoire of disease resistance, people can use that to cross to additional pink varieties rather than crossing them to Iron Lady or some other commercial source of resistance genes.

But nobody says you have to wait around until I have material distribute. Why not get in there and do some crosses and backcrosses etc yourself, with your favorite varieties?

Carol Deppe

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #24 on: 2019-01-09, 09:21:54 PM »
Variety selection seems key here because being able to agree on specific varieties to undergo this treatment would make it possible to crowd fund the work but also to find collaborators to supply labor and land for specific varieties. What is more, we could bring the costs per variety down potentially if we supplied labor and land. I suspect most of us have access to land and that we are all skilled labor for this sort of thing.
Naw. We don't need to agree on specific varieties. If you love a particular heirloom, get in there and start doing the crosses with it. Once one of us has material to distribute, we can start a thread on the project on this forum. And I'll certainly also distribute it through my seed company.

Part of what I love about plant breeding is being able to do exactly what I want. Create a system that deprived me of that freedom? NEVER!

Carol Deppe

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #25 on: 2019-01-09, 09:39:06 PM »
Somewhere in this thread, someone mentioned that we should avoid redundancy. I don't think so.

For example, let's suppose one of my favorite heirlooms is Pruden's Purple, so I cross it to Fast Lady, backcross once, then grow out about 50 offspring. Half of 'em would be pick. 1/4 of them would be heterozygous for both Ph2 and Ph3. The horrible-flavor conferring u gene would be at worse heterozygous, and invisible because recessive. There are lot's of other disease resistances that are the reason why you usually have to rotate tomatoes, a problem for people with small gardens. I might develop a variety that ends up homozygous for Ph2 and Ph3, is pink, is reasonable large and early, and tastes great. But it might well not be V or F or nemadote resistant, for example. Can't do everything.

But if you do the same cross and you might end up with something with both lb genes, something large, pink delicious, and early. But it would probably lack some of the other resistances that might be desireable. But if we crossed your line and mine, we might...then develop...he he he.

Of course, you would probably produce multiple lines, and so would I. But we would have lots more options with more lines we could share and breed further with.

Criteria for choosing an heirloom to work with? Someone has to love it enough to do the work. Or at least start and get it to the point where others can play with it.

It takes just one plant of each variety to do the first year's work. Just maybe 6 F1 plants and a couple of heirlooms to do the backcross. Then it will take more land and labor, but that's why we need to spread the idea and work around.

Something very similar was done with respect to the Dwarf Tomato Project. There are now more than 100 heirloom-quality compact tomatoes based upon the d gene instead of the sp (determinate) gene. And that taste much better than determinates. And that I feel, given time, will displace the determinate class. And they are all OSSI-Pledged. Craig LeHoullier and Patrina Nuske-Small crossed d containing material with dozens of heirlooms. Then they worked with more than 200 volunteers propagating and selecting that material out into more than 100 OSSI-Pledged dwarf varieties. See the OSSI website SEED page and look up by breeder "The Dwarf Tomato Project".

William S.

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #26 on: 2019-01-09, 10:14:26 PM »
I read The Tao of Gardening recently and my reaction to the tomato section which I skipped ahead to and read first was oh darn. Adding blight resistance is definitely going to complicate my plans. I've figured out in the last two years that some tomatoes are so short season they can be direct seeded here in Ronan Montana. My goal is to add in better flavor maybe some fancy colors. Test for drought tolerance to see if any of them can be direct seeded and dry farmed in my climate. However you have fairly well pointed out with your book and recent posts that none of them are blight resistant and if your prediction holds that would mean all the interesting tomatoes I've found in two years of searching may be useless!

So I have ordered a packet of Iron Lady F1 seed for 2019. I only plan to grow a plant or two and make some crosses with some of my favorites like Joseph's Big Hill, Coyote, Sweet Cherriette, and Amethyst Cream which is long season but has an unusual flavor.

I am also getting increasingly excited about working with wild tomatoes and have several populations from Joseph which might have blight resistance already.

My favorite tomatoes right now that I would like to use for futurent breeding include:

Ultra early reds: Sweet Cherriette, Brad, Jagodka, Forest Fire, Anmore Dewdrop, 42 Days, and Krainy Sever

Flavor and color varieties: Big Hill, Brad x Yellow Pear (unstable), Blue Ambrosia, coyotr, and Amethyst Cream.

Wild Tomatoes: Habrochaites x Domestic (unstable), Penellii x domestic (unstable) and the larger Peruvianum group

Though hopefully the wild tomatoes can fend for themselves with blight.

« Last Edit: 2019-01-10, 07:21:41 AM by William S. »
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William S.

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #27 on: 2019-01-09, 10:22:17 PM »
Naw. We don't need to agree on specific varieties. If you love a particular heirloom, get in there and start doing the crosses with it. Once one of us has material to distribute, we can start a thread on the project on this forum. And I'll certainly also distribute it through my seed company.

Part of what I love about plant breeding is being able to do exactly what I want. Create a system that deprived me of that freedom? NEVER!

I think I was thinking in terms of getting funding for specific varieties especially for some of the more expensive steps like lab testing for resistance genes you proposed. My thought for my favorites is essentially just "cross em with Iron Lady ASAP before the multi strain late blight Carol says is coming gets here" then maybe even freeze the F2 and wait. Late blight is not currently common here. We had a non recurring outbreak about ten years ago or so. Probably a single strain.
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William S.

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #28 on: 2019-01-09, 10:33:15 PM »
[quote author=Carol Deppe
"Once we have that first batch of foundation material, it will be easier to do more. For example, if I can give you the F2 of a pink offspring that is 3/4 Pruden's purple and carries a useful repertoire of disease resistance, people can use that to cross to additional pink varieties rather than crossing them to Iron Lady or some other commercial source of resistance genes. "
/quote]

This makes sense to me. Like I want an ultra early red preserved. I could start with Sweet Cherriette x Iron Lady and then later if I want to try to capture Krainy Sever's upright habit I could use my resistant Iron Cherriette x Krainy Sever. Ultra early reds aren't hugely diverse. Though what I really want is some other color/flavor of ultra early but to get there the germplasm needs to be preserved.
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Andrew Barney

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Re: Funding Blight Resistance Breeding in Heirloom Tomatoes
« Reply #29 on: 2019-01-09, 10:43:12 PM »
. The horrible-flavor conferring u gene would be at worse heterozygous, and invisible because recessive.

Haha,  I like that you call the u uniform-ripening gene as the "horrible-flavor gene" ;)

So true. One of my best tasting tomatoes,  'Anasazi' has green shoulders and I think it tastes amazing. It even won a taste contest a few years ago tieing with 'pineapple' I think. But it does have some sort comings such as cracking and splitting and someone who tried it last summer said he thought it tasted insipid. Lol. I guess everyone has a different idea of what a good tomato tastes like. Some like acid, some like sweet. Some like complex. I have a feeling that color not only affects flavor by chemicals,  but also affects perception which affects flavor in one's mind.

Regardless I really am on the lookout for tomatoes that have green shoulders and do not have the uniform ripening gene as it really does have a big affect. No more cardboard tomatoes for me!