Breeding for Late Blight Resistant Tomatoes

[William Schlegel]

When I took plant genetics at Oregon State University in 2012 there was a lot of talk about these questions. The professor asked. Philosophically this led me here to try to breed more open-source varieties.

US universities are highly privatized public universities. They cobble together funding from a variety of sources. It isn't fair. I would like to see public university plant breeding well-funded and unpatented. That is not the reality though that universities are currently operating in. Programs are being moth balled as breeders retire, and university breeders work is being commercialized in many ways including this one with the patent.

On the plus side I think this particular patent is a short term one judging by the expiration date.

[William Schlegel]

When I took plant genetics at Oregon State University in 2012 there was a lot of talk about these questions. The professor a barley breeder, asked what we thought about how university breeders should be compensated. I remember responding that I thought they should be funded well and paid well but that the varieties should not be constrained with patents etc. Philosophically this led me here to try to breed more open-source varieties.

US universities are highly privatized public universities. They cobble together funding from a variety of sources. It isn't fair. I would like to see public university plant breeding well-funded and unpatented. That is not the reality though that universities are currently operating in. Programs are being moth balled as breeders retire, and university breeders work is being commercialized in many ways including this one with the patent.

On the flip side huge multinational corporations now may employ perhaps even most plant breeders. So the university breeders are very much an exception now.

On the plus side I think this particular patent is a short term one judging by the expiration date.

[Justin Jardinier]

Sorry William I clicked the link and replied in haste before seeing what you wrote about the patent!

Regarding:

"Ph-3 is the most
effective resistance gene against LB

I wonder if that is true. Like, whether it beats Ph-5 or not, or whether it's just the combined 5.1 + 5.2 only that beats Ph-3. Also, the tomatoes in the Mexican studies beat LA2533, which is I think the source of Ph-3, and itself has greater resistance than Ph-3 alone since it also has additional resistance. I don't know if these superior ones have that from just 1 gene, or more, so they might not count as having a more resistant single gene than Ph-3 though.

Those accessions are V115, 319, and 327. Details are in Identification of sources of resistance in tomato to Phytophthora infestans at Mexico - 2022 - ARELLANO-RODRÍGUEZ, et al. - ECORFAN_Journal_Ecuador_V9_N17 - 2022

I have been trying to track those down, or the lines they made from them, which also seem to beat LA2533 if I remember correctly. If anyone has any insight into this, I would really love to know. Perhaps they are kept at that one Mexican university? I did write to the author whose contact details were given but have not heard back.

Beginning in 2017, newly developed Ph-5 lines were
used in crosses for experimental hybrids containing high-lycopene, EB resistance, and LB
resistance with one, few, or several LB resistance genes. Several hybrids evaluated in this thesis
project are more recently produced in 2018 along with nine other elite 2016 experimental hybrids.

That sounds great! It was also a long time ago already. Do you think there is any hope that they would provide us with any such material to cross with? It would seem a great value to society if they would. It would seem a waste not to, in my view. Especially since many of them are probably very well suited to our crossing needs while they will perhaps be taking lots of time to breed for other needs, for commercial purposes.

When I took plant genetics at Oregon State University in 2012 there was a lot of talk about these questions. The professor asked. Philosophically this led me here to try to breed more open-source varieties.

Awesome.

[William Schlegel]

I think from the materials we found that they are working on commercialization of those crosses. Also, early on when Carol Deppe was posting- Oregon State also was working on a PH-5 tomato. It is strange that none are available yet, but as the professor was explaining in the video- it takes a long time. Longer than expected apparently!

[Justin Jardinier]

Foolad found one "accession," or genetic line, that had four to five times more lycopene — a powerful antioxidant that gives tomatoes their deep-red color — than cultivated varieties.

In the patent it's actually more:

In search of genetic sources of high fruit lycopene content in tomato, we acquired seeds of, and grew and evaluated under field conditions, >300 wild tomato accessions. This experiment led to the identification and selection of one accession of wild species Solanum pimpinellifolium with exceptionally high fruit lycopene content.

The lycopene concentration of this accession is as high as 390 µg/g fresh tomato tissue, approximately 10-fold that of the commercial cultivars of tomato (~30-60 g/g fresh fruit tissue). The Solanum pimpinellifolium selection which was discovered to have exceptionally high fruit lycopene content is designated as LA2093.

The thesis expresses that as:

For example, in a screening of ~300 accessions of the wild tomato species S. pimpinellifolium, one accession (LA2093) was identified for having seven-fold higher fruit lycopene content than commercial cultivars (Hyman et al., 2004).

Also unless I am misunderstanding, the highest lycopene content they got to in their lines from that thesis was:

The lycopene estimates for transformed (a*/b*) 2.5 whole fruit colorimetric data were more within the range of normal values expected for large type, fresh market tomatoes, and there were significant differences among varieties. G49 had the highest lycopene estimate with 59.44 ug/g, and was significantly greater than G4, G9, G73, G81, G40, RD, MF, and MM. G37 (57.37 ug/g) was significantly different from G81 and RD. RD had the lowest lycopene estimate with 40.87 ug/g.

Anyway it sounds like it might be useful to breed directly with LA2093?

The patent continued:

The second approach involved backcrossing the selected F plants, which contained highest fruit lycopene content, with different Solanum lycopersicum genotypes for several generations alternated and followed by several gen erations of self-crossing and intensive selection. This approach, which took about 10 years, resulted in the devel opment of different types of fresh-market (e.g. grape, plum and medium/large round fruit) and processing tomato lines with high fruit lycopene contents (see below for details). The concentration of fruit lycopene in these new lines ranges from 100 to 200 µ/g fresh fruit tissue, much higher than what can be found in current commercial breeding lines and cultivars.

Sounds like it's 2 or more genes involved:

The mapping strategies resulted in the identification and mapping of several QTLS for high fruit lycopene contents on different chromosomes of the Solanum pimpinellifolium accession LA2093, including two consistent and large-effect QTLS on chromosomes 7 and 12. It is the understanding of the inventor that these two QTLS from Solanum pimpinellifolium acces sion LA2093 have major effect on tomato fruit lycopene content and are essential for the development of high fruit lycopene tomatoes, as described in this invention.

This is a strange statement in the paper, especially since we know of many cases of lycopersicum crossed with pimp, which I assume is accessions collected from the wild in the Americas, no? I.e. many of those in the 'cerasiforme' category, as identified in various papers.

It is important to note that Solanum lycopersicum is cleistogamous. Therefore, it is very unlikely in the wild that cross pollination between Solanum pimpinellifolium and Solanum lycopersicum would occur without human technical intervention. It is also unlikely that the identification, selection and backcrossing for the genes (QTLS) for high fruit lycopene content would occur naturally.

[Roland]

Here a presentation about:
Early blight
Late blight ph5 gene
High Lycopene

https://tgc.ifas.ufl.edu/2009/Foolad%20TBRT-2009.pdf

[William Schlegel]

This is a strange statement in the paper, especially since we know of many cases of lycopersicum crossed with pimp, which I assume is accessions collected from the wild in the Americas, no? I.e. many of those in the 'cerasiforme' category, as identified in various papers.

I would say that is a pretty mainstream statement. We with our deliberately exserted style strains and even our ideas about obligate outcrossing tomatoes, we are the counterculture. Doesn't mean we are wrong, because it's clearly a group capable of varied crossing behaviors. However most people, especially when simplified, would think of tomato as obligate selfing with very low rates of outcrossing.

Also obtaining unlikely outcomes is totally what marker assisted selection is all about. This professor though, he is a step beyond that, he is finding the genes and the markers and then using marker assisted selection. So any of us could use MAS for markers for known traits. He is developing those markers. He is also identifying useful traits in specific wild accessions and then finding the markers for them. We are just benefiting from his work. Even if we start paying for genotyping we are still reliant on this prior work.

[Justin Jardinier]

https://tgc.ifas.ufl.edu/2009/Foolad%20TBRT-2009.pdf

Wow, seems they were expecting to make the Ph-5 cherry and grape tomatoes available in the fall of that year, 2009! And large ones in 2010~2012. I wonder why they didn't.

I would say that is a pretty mainstream statement. We with our deliberately exserted style strains and even our ideas about obligate outcrossing tomatoes, we are the counterculture. Doesn't mean we are wrong, because it's clearly a group capable of varied crossing behaviors. However most people, especially when simplified, would think of tomato as obligate selfing with very low rates of outcrossing.

But the cross could go the other way more easily. No?

And yes, aside from the patenting and long waits, the work is awesome, it's great people are making ways to make use of the genetic diversity for sure. And he seemed like a nice man in the video, it's nice to watch people share about their research.

[William Schlegel]

I noticed that 2009 date too. Why didn't they release the varieties they developed yet? So curious.

Yes, our exserted tomatoes could easily receive pollen from patented or even GMO tomatoes if they were grown close together.

[Justin Jardinier]

What I meant was, the patent stated:

it is very unlikely in the wild that cross pollination between Solanum pimpinellifolium and Solanum lycopersicum would occur without human technical intervention.

I guess it's all relative. But we do know this happens.

[reed]

Not exactly the wild but that cross happened in my garden, all by itself.

[William Schlegel]

It is kind of like Alan Kapuler said in his article about the tomatoes that occasionally outcross. He didn't have any natural crosses for a very long time. Until he hybridized with wild species and then subsequently had them. We know that tomatoes occasionally outcross. That the style length can range from so short that the stigma is deeply inserted, can be positioned right at the opening of the pollen cone, or can be exserted. We know even from the seed saving literature that tomatoes with exserted styles need to be isolated much further. It is also very clear that TGRC has a clear understanding of the phenomenon of exsertion and there are notes about it on individual accessions.

Most folks though are sitting where Alan was prior to discovering/breeding his occasionally outcrossing tomatoes. Growing and seed saving tomatoes for years without detecting any outcrosses. Many researchers as Carol Deppe mentions in her first book in regard to legumes have very low natural outcrossing rates in their research fields because they are so devoid of pollinators.

Even my deliberate exserted potato leaf tomatoes- I grow them mixed with regular leaf, and then grow out the seed from potato leaf mothers. Sometimes it works great and I find lots of regular leaf crosses but still maybe a few percent, and sometimes I get back a whole tray full of potato leaf seedlings.

[reed]

Because most of my tomatoes have quite open flowers and we have several small bees and flies that visit the flowers, I think crossing probably happens fairly often. I don't find them; I think mostly because I grow such a small number of plants each year and because I haven't really tried to find them. That's changing this year, for example instead of starting ten seeds of my potato leaf Hoosier Rose, I'm going to start a hundred. I figure that should be enough to find some if they exist.

It was just dumb luck that I found my crossed pimps. Pimps are basically weeds in my garden and most are treated that way. As I recall it was sort of late in the season and I was cleaning off a bed to plant a fall crop of something when I noticed the plant pimp looking plant with grape sized fruit. My regular pimps have fruit not much bigger than peas. I assumed that pimp was the original mother side of the cross, but I don't know. After thinking on it, it might have been the other way around because the pimp flowers look to be closed up tight. Seems more likely a little pollen got out than in. 

[Roland]

Wow, seems they were expecting to make the Ph-5 cherry and grape tomatoes available in the fall of that year, 2009! And large ones in 2010~2012. I wonder why they didn't.

Yes, it is very strange that they were ready to release the first varieties in 2009 and now in 2024 they are still not available? Also strange that they have only released 1 variety with high licopene?

[William Schlegel]

Yeah, wonder what keeps pushing their projected release dates back?