Plant geneticists unmask hidden mutations in tomatoes

After centuries of breeding, tomatoes now take all sorts of shapes and sizes, from cherry-like to hefty heirloom fruit. Scientists are now researching how these physical changes show up at the level of genes — work that could guide modern efforts to tweak the tomato, according to Howard Hughes Medical Institute investigator Zachary Lippman. Lippman and colleagues have identified long-concealed mutations within the genomes of 100 different types of tomato, including an orange-berried wild plant from the Galápagos Islands and varieties typically processed into ketchup and sauce.

The research, published in the journal Cell, assessed the 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. A handful of the mutations identified by researchers alter key characteristics, like flavour and weight. Previous studies have shown that these mutations exist in plant genomes, according to Lippman, a plant geneticist at Cold Spring Harbour Laboratory.

“But until now, we didn’t have an efficient way to find them and study their impact,” said Lippman.

Scientists are teasing out at the level of genes how and why these physical changes show up. Image credit: Lippman Lab/CSHL/HHMI.

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 bigger — they modify DNA’s structure by copying, deleting, inserting or moving long sections of DNA elsewhere in the genome. These mutations, called structural variations, occur throughout the living world. Studies in humans 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. However, limitations in this technology make it difficult to decode long sections of DNA, meaning researchers have not been able to capture a complete picture of structural mutations in the genome. Plant geneticists suspect that these mutations contribute significantly to plant’s traits; Lippman’s team found these mutations in tomato and its wild relatives, and determined how they function within these plants.

The new study, a collaboration with Michael Schatz at Johns Hopkins University and others, identified more than 200,000 structural mutations in tomatoes’ long-read sequencing. Lippman likened it to looking through a panoramic window at large sections of the genome. By comparison, more conventional sequencing offered only a peephole, said Lippman.

The majority of the mutations researchers found do not change genes that encode traits. Many of these mutations alter mechanisms controlling genes’ activity. One such gene, for example, controls tomato fruit size. By modifying DNA structure — in this case, the number of copies of the gene — researchers were able to alter fruit production.

Plants with three gene copies (left) grew fruit 30% larger than those with one (right). Image credit: M Alonge et al/Cell 2020.

Researchers also demonstrated how DNA structure can influence traits, showing that four structural mutations together were needed for breeding a major harvesting trait into modern tomatoes. These insights could help explain trait diversity in other crops and enable breeders to improve varieties. 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.

“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’. The field is making important steps toward this kind of predictable breeding,” said Lippman.

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