Author Topic: Tomato CRISPR for Urban tomatoes  (Read 1192 times)

William S.

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Tomato CRISPR for Urban tomatoes
« on: 2019-12-23, 05:03:25 PM »
Here is an interesting article on CRISPR edited tomatoes.

https://www.sciencedaily.com/releases/2019/12/191223122820.htm

They manipulated three genes to produce short, abundantly, fruiting plants that produce in less than forty days.

This sounds familiar to me. Many of my new favorites are super compacts and extreme short season. I bet that a clever geneticist could find naturally occurring mutations on these same three genes. I would start looking in those ultra compact short season plants.

However, given this innovation. How, what, where, why, and when might this become available to open source breeding? ~50 years? It doesn't particularly sound unsafe or unnatural. I like the idea of CRISPR editing a lot more than transgenes so far.
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Diane Whitehead

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Re: Tomato CRISPR for Urban tomatoes
« Reply #1 on: 2019-12-23, 06:37:19 PM »
 40 days - from sowing, from germination?  from transplanting, from flowering?

My tomato seeds take a week to 10 days to germinate, and that's a good chunk of 40 days gone.

« Last Edit: 2019-12-23, 06:39:46 PM by Diane Whitehead »
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William S.

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Re: Tomato CRISPR for Urban tomatoes
« Reply #2 on: 2019-12-23, 06:43:21 PM »
I would assume from transplant.

Notably that would put them in a very rarified category. With traditional breeding we have Sweet Cherriette and a few others in the low 40's. So if they've achieved less than 40 days from transplant AND decent fruit size, this is something fairly impressive.
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Diane Whitehead

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Re: Tomato CRISPR for Urban tomatoes
« Reply #3 on: 2019-12-23, 07:02:41 PM »
I'm in the process of moving 125 of Dan Follett's multiflora dwarf seedlings from 4.5 cm pots to 9 cm ones.
This is the first time I've tried them under lights for the winter - the seeds are from ones I grew outside.
 
I don't know whether they will fruit in these pots or whether I will have to pot them again.  I will keep
track of when I do that, when they flower, and when they fruit.  Then I can compare them to the CRISPR
urban ones, as they will be growing in similar conditions

Diane
« Last Edit: 2019-12-23, 08:09:01 PM by Diane Whitehead »
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Steph S

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Re: Tomato CRISPR for Urban tomatoes
« Reply #4 on: 2019-12-24, 09:38:51 AM »
That's a great idea, Diane.   I also thought of Dan's micros, and wondered if the multiflora lines would be very close to this crispr thing, with the advantage of being selected for taste, beauty and other fruit qualities.
I have worked on earliness and 40 days is out of the park for days from seed.  40 from transplant to the bundle of ripe tomatoes is also impossible I think, they can only mean to first ripe.    A cherry tomato can set and mature a first fruit in as little as 28-30 days in my cool climate spring.  It takes 12-15 days or longer (up to 24 days in cold weather)  from the time a flower opens until it sets.    I don't have the data in front of me but I think 7 days is the earliest I've seen from flower open to a pea sized set.   So 40 days from flower opening is doable for the first fruit .
The Crispr plants were tweaked for stem lengths as well as the sp genes, but they probably started with something early (was it Tiny Tim again?). No manipulation of basic time from flower to set to ripe, only internode length and frequency of flowers, which would make the plant get its flowers out quicker.

William S.

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Re: Tomato CRISPR for Urban tomatoes
« Reply #5 on: 2019-12-24, 10:24:10 AM »
Just thinking of our PH2 PH3 discussion and the sole Lizzano F2 plant I grew in 2019 was very much in the ultra early vein. Suspect Lizzano could be dehybridized with attention to shortness of season like Anmore Dewdrop was.

Shortest season varieties I know are things like Tim Peters Sweet Cherriette 35 days from transplant and the variety 42 Days. Would be interesting to intercross some of them. Sub 40 from transplant is extremely rare.

If I were an organic university breeder with the ability to test for these things I would check the gene variants in all the existing ultra earlies.

I wonder how closely related the ultra earlies we have now are? If we cross ultra earlies but they rely on the same exact mutations we are just spinning our wheels.

Steph, it at least seems plausible to me that they may not have started with an early. If so, this technique would be producing new ultra earlies from scratch and that would be intriguing.
« Last Edit: 2019-12-24, 10:30:00 AM by William S. »
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Andrew Barney

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Re: Tomato CRISPR for Urban tomatoes
« Reply #6 on: 2019-12-25, 06:16:11 AM »
My terminology may or may not be perfectly accurate, but basically the new crispr stuff is really exciting because it may fix all the things wrong with traditional genetic engineering.

Basically from a legal standpoint in the U.S. we make a distinction between Genetically Modified and Genetically Engineered. Whereas in Europe they make no legal distinction.

The difference in a nutshell is that traditional genetically modified uses modified agrobacterium and that DNA remains in the modified plant and is thus Transgenic (even though the DNA portion is small). Also there is some degree of random placement in the genome.

The cool thing about crispr is that we now have the potential to engineer specific modifications in targeted genes and then after a few generations of plant selection we can select out a plant that has these modifications but does not have any of the virus or bacterium genetics so it is not actually transgenic. In theory should be safer and much more accurate.

The question about being released public domain and/or being allowed in an organic farm system is still up for debate (or up the the universities that create them). But as of now there is a good possibility that both could happen! Which I think is good. I'm not anti genetic technology,  but I am cautious in some instances. Crispr really sounds Like a promising leap forward.

William S.

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Re: Tomato CRISPR for Urban tomatoes
« Reply #7 on: 2019-12-25, 06:30:04 AM »
Intrigued by this particular paper for a couple reasons and one is simply the intended audience. Who grows urban tomatoes? Uh us? Seems like a cats out of the bag scenario as soon as the tomatoes are released. Tomato seeds are too easy to save and dessiminate. Sell it as fresh fruit and it's full of seed. The other option is kind of like those GMO transgene purple all the way through tomatoes. They've just sat on the shelf all this time essentially unused.
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Steph S

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Re: Tomato CRISPR for Urban tomatoes
« Reply #8 on: 2019-12-25, 05:37:26 PM »
I guess my next questions about crispr would be:
(1) how stable (heritable and breedable) are the edited genomes, and
(2) what kind of patents will be applied.

I just feel that my optimism would be wasted on a product that someone paid high tech money to produce and will therefore (in the vast majority of cases) do something to recoup the high costs and make a profit.   If it can be privately owned it's a problem and I wouldn't touch it.

As for stability, I just wonder about the modified genomes.  Not just in the first generation and its heritability, but how well would those edits hold up in a breeding context, where by nature the arrangement can be challenged via transposable elements etc. 

William S.

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Re: Tomato CRISPR for Urban tomatoes
« Reply #9 on: 2019-12-25, 07:12:07 PM »
With breeding I would worry about simple segregation as they are editing in multiple traits.

Sooner or later some of this stuff will be public domain. I wish we could create a legal framework and funding system that poured all university plant breeding directly into the public domain.
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Steph S

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Re: Tomato CRISPR for Urban tomatoes
« Reply #10 on: 2019-12-25, 07:44:27 PM »
Re: segregation,  I expect the two modifications to sp would segregate together if it is stable, so it would be similar to any two trait search, to find the third modification together with these at expected ratio 1/16. 

Re: christmas wish list... I see your public domain and raise you one peace on earth.  ;) ;D


William S.

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Re: Tomato CRISPR for Urban tomatoes
« Reply #11 on: 2021-04-25, 08:09:42 AM »
https://m.youtube.com/watch?v=Jem3hP734uA

Not sure how related this double determinate crispr video is but seems like the same thing. Or part of it.

It talks about a trait that helped tomatoes move north and how they modified it further to get even shorter season tomatoes.

Still wonder if there are existing mutations that do the same thing in existing ultra early tomatoes.
« Last Edit: 2021-04-25, 08:25:48 AM by William S. »
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William S.

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Re: Tomato CRISPR for Urban tomatoes
« Reply #12 on: 2021-04-25, 09:05:25 AM »
Just some thoughts on a few things:

Dwarfism in the dwarf tomato project sense seems to be compatible with earliness but not necessarily early.

Dwarfism in the micro dwarf sense seems similar. Some of the plants are surprisingly longer season but can be very early.

The F3 or so Lizzano dehybridization I grew out last year was uniformly compact very short plants. Lizzano itself is spreading. My guess is the hybrid has one compact parent.

Anmore Dewdrop is pretty compact compared to tumbler F1.

Sweet Cherriette has 35 DTM from transplant the earliest I've found but is not compact just small. It's been described as an "Indeterminate Dwarf" I don't think it's a dwarf in the dwarf tomato project sense. It isn't that upright. The fruit is very small but bigger than pimpinillifolium. One possibility might be to back cross to pimpinillifolium to bring the fruit size down to shave off days. Combined with a more compact growth form such as that in my Lizzano ~F3 could probably shave off days? They don't have small seedlings unless the seedlings have tough growing conditions. Small size kicks in later.

Coyote is pretty early but pretty normal. Combined with compactness you could probably shave off days.

My 2020 growout of my blue bicolor had some of the earliest tomatoes I got. This year the seedlings are notably shorter than many other varieties. Some kind of dwarfism or determinance must be at play.

So I think I see room for improvement in ultra earliness. They don't seem to all rely on the same traits. So if we wanted to I suspect we could push back DTM more than currently available by decreasing fruit size and crossing micro dwarf plants with small spreading plants. I bet some of the genes at play in existing ultra early varieties are mutations similar to the crispr edits made by researchers.

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Steph S

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Re: Tomato CRISPR for Urban tomatoes
« Reply #13 on: 2021-04-25, 09:16:56 AM »
There are some OP varieties with 'precocious flowering'.   Kimberley is one.  Beaverlodge Plum is another.  Both were bred in Canada.
They flower about 15 days earlier than other early tomatoes - that is about 45 days from seed, compared to about 60 days from seed for the usual earlies like Stupice.   

This might be a natural occurrence of the same mutation that he's talking about, ie completely deactivated gene for daylength sensitivity.
Very interesting work...  I didn't know that all of our northern hemisphere tomatoes depended on this mutation to flower in our long days.


William S.

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Re: Tomato CRISPR for Urban tomatoes
« Reply #14 on: 2021-04-25, 10:24:17 AM »
I bet the precocious flowering trait you mention would combine well with some other traits like the extreme compactness of micro dwarf types to bring down DTM even more.
Western Montana garden, glacial lake Missoula sediment lacustrian parent material and shallow 7" silty clay loam mollisoil topsoil sometimes with added sand in places. Zone 6A with 100 to 130 frost free days