MAY 2019. DISCOVER 11EARLY IN THE 20TH CENTURY, a strange
tomato plant took root in the northeast-
ern United States. Because of a random
genetic mutation, the plant’s branches
were shorter than normal. The result was
a more compact crop that was easier to
harvest. “Breeders started using it,” says
Joyce Van Eck, a plant biologist with
Boyce Thompson Institute in New York.
“Over time, the trait revolutionized com-
mercial tomato production.”
Most other qualities we associate with
tomatoes also arose by chance. Over mil-
lennia of selective breeding, the fruit grew
from the size of a pea to that of an apple,
and ripening was streamlined to ensure
supermarket tomatoes were uniformly
red. The farmers who had laid claim to
these desirable traits inadvertently lost
others, such as flavor, nutritional value
and drought resistance — dropped by
the same random processes that made
the fruit commercially viable.
The tomato’s genetic history is typical
of produce: Accident has driven the
domestication of practically every fruit
and vegetable. But Van Eck is one of a
growing number of geneticists who envi-
sion an alternative approach to cultiva-
tion. Labs like hers throughout the world
want to reboot history. They’re starting
with wild ancestors and relatives of mod-
ern crop plants, which have their own
appealing features. Then, using a novel
gene-editing technology called CRISPR-
Cas9, they’re deliberately introducing
commercially desirable traits.
The idea was first floated in 2016
when a group including University of
São Paulo plant physiologist Lázaro
Eustáquio Pereira Peres revealed a plan
to re-domesticate tomatoes. In their paper
published in Plant Science, they identi-
fied several crucial traits, such as fruit
size and branch length, and found thatthe desirable, modern versions of these
traits arose when certain genes changed
their functions. If they could deliberately
edit those genes, they’d essentially get to
redo domestication — on their terms.
The CRISPR-Cas9 system, successfully
launched in 2013, was perfect for the job.
Injected into a cell nucleus, the system
finds and removes a predetermined
genetic sequence. All Peres had to do was
use CRISPR-Cas9 in a wild
tomato plant to whittle
away the DNA guiding
the growth of long shoots.
Then he’d have the best of
both worlds: A compact
plant with ancient traits,
like flavor and nutrients.
So, Peres tried it out
in the lab. Late last year
in Nature Biotechnology,
he and several colleagues
revealed they’d success-
fully controlled branch
length and improved fruit
size and yield. Essential
nutrients such as lyco-
pene, an antioxidant, were
boosted. And as for flavor?
“It’s an intense experience,”
says University of Münster
geneticist Jörg Kudla, who led the study
with Peres. “It’s very aromatic.”
The viability of the technique was
verified by another, independent study
by researchers at the Chinese Academy
of Sciences, also published last year. Using
essentially the same technique, they
introduced commercially valuable traits
while retaining drought resistance in wild
tomato plants. These more resilient ver-
sions might better withstand the effects
of climate change. “The biggest advantage
of de novo domestication is the [ability
to harness] the numerous natural wildplant resources,” says Chinese Academy
of Sciences geneticist Caixia Gao.
But ancestral relatives of modern crops
are only the start. In fact, while Kudla and
Peres were wrangling tomato plants, Van
Eck enlisted CRISPR to improve the com-
mercial prospects of ground cherries.
A distant tomato relative sold in
farmers markets, the ground cherry is
intensely flavorful, highly nutritious
and extremely impractical.
The fruit is minuscule and
drops off the branch when
ripe, making it nearly
impossible to harvest. Van
Eck’s group fixed these
problems by comparing
genes of ground cherries
with genes of domesticated
tomatoes, singling out
ones that were similar, and
altering them. “Instead of
waiting for happenstance,
we fast-tracked domestica-
tion,” she says.
Meanwhile, people have
started contacting Van Eck
with other prospective
crops. “I was approached
by somebody from Nigeria
who said they have an
indigenous grain that’s naturally drought
resistant,” she says. It doesn’t produce
many seeds, and the plant has an unwieldy
growth pattern that makes it tricky to har-
vest. Her lab is now investigating muta-
tions that would make it more suitable
for harvesting.
With the ability to guide plants down
different paths of cultivation, or to explore
what would happen if our ancestors had
picked different crops, CRISPR has turned
speculation into reality — just in time for
a future that will have more mouths to
feed than ever before. – JONATHON KEATSDomestication 2.
How CRISPR is helping experts cram millennia of agricultural progress into the blink of an eye.
BIG IDEAOver millennia
of selective
breeding, the
tomato grew
from the size of
a pea to that of
an apple, and
ripening was
streamlined
to ensure
supermarket
varieties were
uniformly red.DIG
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