CRISPR Can Make Old Tomatoes, New Tomatoes

By Anna Groves | October 4, 2018 4:15 pm
ground tomatoes

Ground tomatoes, still in their papery husks. (Credit: F_studio/Shutterstock)

It’s a big week for CRISPR! Despite being a world apart, two separate research groups had the same idea: to see if CRISPR gene editing can really mimic conventional plant breeding.

One group re-domesticated a wild tomato plant; the other used a similar approach to domesticate an entirely new crop: the ground cherry, a tomato relative.

Together, the new work demonstrates how dramatically gene editing technology could speed up crop improvement efforts worldwide.

How to Make a Crop Worth Growing

In the past few decades, conventional breeding of the tomato plant has dramatically increased its yield, fruit size, and shelf life.

To get a plant from its wild form to something growable as a large-scale food crop is not an easy feat. Conventional breeding requires decades of work from breeders who select the best plants, cross them, and select the best plants again from their offspring.

But this kind of plant breeding leaves quite a bit of room for Mother Nature to get in the way. A good trait and a bad trait might be coded by two genes that are just too close to each other in the DNA to ever hope to keep one while ditching the other.

And breeding for certain traits can let other traits fall through the cracks. Years of focus on breeding red, intact, storable tomatoes can result in red, intact, storable tomatoes that no longer taste like anything.

On top of all that, conventional breeders have to constantly fight to keep a certain level of genetic variation in their plants. If all the genes in their population end up the same, all the plant traits end up the same, and there are no longer any “best plants” to choose from.

To combat this, breeders traditionally have to cross-breed crop plants with wild relatives. This comes with its own challenges, including a risk of losing important crop genes in the process.

But advances in gene editing technology might make those worries disappear.

Researchers have learned a lot about which genes in the modern tomato are responsible for which traits. They can point to specific places in the DNA and say, changes here and here are what made the fruits bigger. This allows them to pinpoint, for example, which genes changed a sprawling vine into a compact plant with fruits that ripen all at the same time.

With CRISPR, changes to genes could be made in a single generation, and with a gene-level precision that doesn’t cause unintended effects.

Tom-ay-to, Tom-ah-to

But this idea hadn’t been thoroughly tested. In Nature Biotechnology, researchers from the State Key Laboratory of Plant Cell and Chromosome Engineering in Beijing attempted to ditch some of the genetic baggage in the conventionally bred tomato and instead “re-domesticate” it from its wild ancestor using CRISPR.

They grew wild tomatoes and engineered the DNA to alter a few key traits. They wanted compact (rather than sprawling) plants, synchronous fruit ripening, larger fruits, and higher vitamin C production, among other things.

The wild plants they used had a few bonus features, either being resistant to bacterial spot disease, tolerant of salt, or both. So when they flipped a few key switches from “wild” to “domesticated,” the resulting plants had a combination of traits that conventional breeding would have taken years to get just right.

The success of this process could have implications for all sorts of crops, dramatically speeding up the continuing quest for improved tolerance to drought, resistance to diseases, and other traits that will be critical for crops to survive future climate.

A Brand New Tomato

Meanwhile researchers from the Howard Hughes Medical Institute in Maryland domesticated, for the first time, a tomato relative — the ground cherry. Their work is published in Nature Plants.

The team wanted to see if they could use what we know about tomato genetics to achieve a similar result in a related species with untapped crop potential.

The ground cherry, a species of Physalis, is a weedy plant native to the Americas. Sometimes called a “strawberry tomato,” the sweet-and-sour fruit is already available commercially. But it’s relatively rare: you might come across it in a U.S. farmers market, but it hasn’t achieved the breeding attention or commodification that other crops have. Plants like this are called “orphan crops” — quinoa is probably the most well-known right now.

After quite a bit of genetic and genomic legwork, the team engineered the DNA to alter a few key traits, using tomatoes as a guide. Some of the traits will sound familiar: they wanted compact (rather than sprawling) plants and larger fruits. They also fixed a few other wild tomato problems, like stems that drop their fruits too easily.

So, should we watch for new-and-improved ground cherries in stores?

Not quite yet.

“We are not at the end yet,” says Zak Lemmon, lead author on the study. “What we were able to do is rapidly show some very rapid improvements in key traits that will be needed for a larger scale adoption into the mainstream agriculture market.”

“(Physalis) was a lot of fun to work on. I think it’s a really interesting specialty crop that has a lot of promise and potential for some bigger impact,” says Lemmon.

MORE ABOUT: biotechnology
  • OWilson

    Maybe the biggest obstacle to overcome, will be the anti-GM folks, who may be inspired by the recent rise to power of anarchism in the resist, persist and insist movement.

    After all, it’s one small step from ejecting Republican voters from restaurants to MAM gangs throwing out all food they perceive as not being “Real Food for Real People!” :)

    • Robert Sorel

      A stretch to compare the two, since they have nothing to do with one another. Though I have no interest in eating modified food, I recognize that CRISPR could, and likely will, assist with developing increased nutrition, disease resistance, and drought tolerance in crops. Monsanto is a different story with it’s vertically integrated crop-pesticide business, and methodology in suing farmers who’s crops have been infected with GMO genes. Their practices have resulted in tens of thousands of farmer suicides in India, and have become increasingly susceptible to root fungal infections. Their practices are reprehensible.

      • OWilson

        There are political and legal channels to litigate societal issues.

        On the other hand, you have screaming mobs disrupting due procedure in government, and normal business practices and even law enforcement, verbal abuse and threats, trying to bully and intimidate people and legal businesses into adopting their own particular ’cause celebre’.

        We saw it this week in Washington but the mobs are mobilized all over the country.

        Just today:

        “Whole Foods v vegans: Berkeley store gets restraining order against activists”

        “The order is the latest in a tense standoff with an animal rights group that has staged protests at the store for several years”. – The Guardian

        Intimidation can be very effective, but once mob rule is excused, condoned, enabled, and even funded and encouraged, you can say goodbye to civilized society!

        • Robert Sorel

          There maybe “political and legal channels to litigate societal issues”, and certainly issues such as civil rights have benefitted from legal rulings, if not in reality so much.
          I do not like assaults on people in restaurants or elsewhere, verbal or otherwise, simply because one finds someone’s politics objectionable. This is however, a country in which free speech is well exercised, and “screaming mobs disrupting government”, is as American as Apple pie, and old as the nation. People such as animal rights activists see the killing and often very poor treatment of animals raised for food as murder and torture. They are dedicated to their cause and many believe any action is justified.
          I lived through the sixties and seventies in which there were battles in the streets constantly, gov. institutional, university, and corporate takeovers, sit-ins, and riots. The same criticisms that were leveled then are being used today. This is a different time, as our ensconced position of ‘world leader’ and manufacturing powerhouse are being challenged, as we sacrifice our freedoms and privacy. Mobs should never rule, but what they represent should never be discounted.

          • OWilson

            Do not equate protest movements, or revolutionary uprisings in restrictive dictatorial repressive regimes, with the kind of intimidation and bullying and “in their face” screaming at politicians, even families entering and leaving restaurants and gas stations, as is advised even by politicians on the left!

            In a democratic society, people have a vote, but some people are selfish and undemocratic. They want more than one vote!. They do not accept due process.

            Are threats to rape Senator Collin’s staff, or to encourage waitresses to spit in her food, just disgusting intimidation and bullying, or is it really “seeking justice”? :)

          • Robert Sorel

            In truth only one politician advised that type of confrontation. I don’t get your ‘don’t confuse’ statement as it makes no sense. People have a right to “scream at politicians” should they so choose. Haven’t seen anything about families leaving gas stations or restaurants being screamed at, but it’s possible.
            “In a democratic society, people have a vote, but anarchist mobs are selfish and undemocratic. They want more than one vote!. They do not accept due process”.
            Nonsense, people have every right to protest decisions they don’t like, it says so right in the Constitution:
            The First Amendment’s fifth right will come as a surprise to many. Only 1% of Americans even know that it exists.[1]
            The Right to Petition was central to constitutional law and politics in the early United States. It is the First Amendment’s capstone:
            “Congress shall make no law … abridging … the right of the people …
            to petition the Government for a redress of grievances.”
            Are threats to rape the Senators staff worse than threats to rape and murder an assault victim? Threats are never ok, but are to be expected these days when it’s so very easy to cowardly do it anonymously

          • OWilson

            The Right to Petition? Lol

            Masked and armed street thugs, destruction of government property, burning cop cars, looting of Mom and Pop neighborhood stores, are to be “expected” in a democratic society?

            Tell that to the victims!

            Move along citizen, they are “just blowing off steam”, and “it’s only property”, anyway, are some of the excuses given by politicians in search of a few votes.

            Now it’s just folks exercising their Right to Petition, under the Constitution. :)

          • Robert Sorel

            OK, I see that you’re locked into illustrating extremes that have nothing to do with the subject nor events of the week. I could easily repklie in kind, but It’s a foolish dialogue that can be countered and re-countered, so just a waste of time in the end. Take care, I’m out.

          • OWilson

            You too!

            We are waaaay off topic, anyway!

            But thanks for being civil!

  • Tom Megginson

    This is interesting science, but I prefer conventional methods of achieving new hybrids. For example, traditional potato plots, in the Andes, allow free genetic mixing between multiple cultivars and their wild relatives (which are usually growing nearby). This allows the right amount of chaos to occasionally sprout novel characteristics farmers didn’t even know they were looking for.

    Another interesting one is apples. Our traditional commercial varieties are all clones, but the older lines like McIntosh Red were the result of natural gene mixing.

    I live in the city, and don’t have the space allow my plants to have much of a swingers’ lifestyle, but I do have a mint patch in which several cultivars share space with Canadian wild mint. I’ll let you know how that goes.

    • ligerzero459

      I feel like this process could be mixed in with traditional crop breeding methods. If we have a target version that we like, we can selectively edit for that version while continuing to breed traditionally to identify new traits that we might like to pull into the edited line.

      Best of both worlds :)

  • 7eggert

    While breeding gives a depleted genome pool, gene editing by any means will give a patented single cloned genome as it will be done just once. (And while we are at it, let’s introduce a herbicide resistance gene …)


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