Tomato's hidden mutations revealed in study of 100 varieties

Date:
June 17, 2020
Source:
Howard Hughes Medical Institute
Summary:
A new analysis of difficult-to-access genetic variation is the
most comprehensive ever conducted in plants. It could guide the
improvement of tomatoes and other crops.



FULL STORY ========================================================================== [Tomato varieties (stock | Credit: (c) Christian BERND / stock.adobe.com] Tomato varieties (stock image).

Credit: (c) Christian BERND / stock.adobe.com [Tomato varieties (stock | Credit: (c) Christian BERND / stock.adobe.com] Tomato varieties (stock
image).

Credit: (c) Christian BERND / stock.adobe.com Close Human appetites have transformed the tomato -- DNA and all. After centuries of breeding, what
was once a South American berry roughly the size of a pea now takes all
sorts of shapes and sizes, from cherry-like to hefty heirloom fruit.


========================================================================== Today, scientists are teasing out how these physical changes show up at
the level of genes -- work that could guide modern efforts to tweak the
tomato, says Howard Hughes Medical Institute Investigator Zachary Lippman.

He and colleagues have now identified long-concealed hidden mutations
within the genomes of 100 types of tomato, including an orange-berried
wild plant from the Galapagos Islands and varieties typically processed
into ketchup and sauce.

Their analysis, described June 17, 2020, in the journal Cell, is the most comprehensive assessment of such mutations -- which alter long sections
of DNA -- for any plant. The research could lead to the creation of new
tomato varieties and the improvement of existing ones, Lippman says. A
handful of the mutations his team identified alter key characteristics,
like flavor and weight, the researchers showed.

Previous studies have long shown that these mutations exist in
plant genomes, says Lippman, a plant geneticist at Cold Spring Harbor Laboratory. "But until now, we didn't have an efficient way to find them
and study their impact," he says.

A window into the genome Mutations, or changes, in the four types of
DNA letters carried within an organism's cells can alter its physical characteristics. Scientists studying plants have generally focused on
a small, tractable kind of mutation, in which one DNA letter is swapped
for another.



==========================================================================
The mutations Lippman's team studied are much bigger -- they modify DNA's structure by copying, deleting, inserting, or moving long sections of
DNA elsewhere in the genome. These mutations, also called structural variations, occur throughout the living world. Studies in humans, for
example, have linked these variations to disorders such as schizophrenia
and autism.

Scientists can identify mutations by reading out the letters of DNA using
a technique known as genetic sequencing. Limitations in this technology, however, have made it difficult to decode long sections of DNA, Lippman
says. So researchers haven't been able to capture a complete picture of structural mutations in the genome.

Even so, plant geneticists have suspected that these mutations contribute significantly to plants' traits, says Michael Purugganan, who studies
rice and date palms at New York University and was not involved in the
new study.

"That's why this paper is so exciting," he says. Lippman's team not
only found these mutations in tomato and its wild relatives, but also determined how they function within the plants, he says.

A guide for future tomatoes The new study, a collaboration with Michael
Schatz at Johns Hopkins University and others, identified more than
200,000 structural mutations in tomatoes using a technique called
long-read sequencing. Lippman likens it to looking through a panoramic
window at large sections of the genome. By comparison, more conventional sequencing offered only a peephole, he says.



==========================================================================
The majority of the mutations they found do not change genes that
encode traits. But what's clear, Lippman says, is that many of these
mutations alter mechanisms controlling genes' activity. One such gene,
for instance, controls tomato fruit size. By modifying DNA structure --
in this case, the number of copies of the gene -- Lippman's team was able
to alter fruit production. Plants lacking the gene never made fruit,
while plants with three copies of the gene made fruit about 30 percent
larger than those with just a single copy.

Lippman's team also demonstrated how DNA structure can influence traits in
an example he calls "remarkably complex." They showed that four structural mutations together were needed for breeding a major harvesting trait
into modern tomatoes.

These sorts of insights could help explain trait diversity in other crops
and enable breeders to improve varieties, Lippman says. For instance,
perhaps adding an extra copy of the size gene to tiny ground cherries,
a close relative of the tomato, could increase their appeal by making
them larger, he says.

"One of the holy grails in agriculture is to be able to say, 'If I
mutate this gene, I know what the output will be,'" he says. "The field
is making important steps toward this kind of predictable breeding."

========================================================================== Story Source: Materials provided by Howard_Hughes_Medical_Institute. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Michael Alonge, Xingang Wang, Matthias Benoit, Sebastian Soyk, Lara
Pereira, Lei Zhang, Hamsini Suresh, Srividya Ramakrishnan,
Florian Maumus, Danielle Ciren, Yuval Levy, Tom Hai Harel, Gili
Shalev-Schlosser, Ziva Amsellem, Hamid Razifard, Ana L. Caicedo,
Denise M. Tieman, Harry Klee, Melanie Kirsche, Sergey Aganezov,
T. Rhyker Ranallo-Benavidez, Zachary H. Lemmon, Jennifer Kim, Gina
Robitaille, Melissa Kramer, Sara Goodwin, W. Richard McCombie,
Samuel Hutton, Joyce Van Eck, Jesse Gillis, Yuval Eshed, Fritz
J. Sedlazeck, Esther van der Knaap, Michael C. Schatz, Zachary
B. Lippman. Major Impacts of Widespread Structural Variation on
Gene Expression and Crop Improvement in Tomato. Cell, 2020; DOI:
10.1016/ j.cell.2020.05.021 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/06/200617150015.htm

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