Mapping plant mutations could boost food security

Almost 75% of the world’s food comes from just 12 crops, but trying to diversify this isn’t easy.

Genetic changes that can increase the yield of one crop don’t necessarily work for others, even if they’re close relatives. It’s a particularly prickly issue in the nightshade family, which includes important plants in the genus Solanum like the potato, the tomato and the aubergine.

This is because traits that increase the yield of a crop might be caused by one gene in the potato, but a completely different one in the tomato. This is complicated further by gene duplications, which can shuffle these traits around the genome.

New research, published in the journal Nature, aims to simplify matters. By sequencing the genome of 22 different Solanum plants, researchers have put together a pan-genome ‘map’ that reveals where crucial genes for plant breeding are in different species.

Dr Sandra Knapp is our Solanum expert, who worked with geneticists on the new research. She says that the study will help to provide new insights into the potential foods of the future.

“Plant breeding has been happening for thousands of years to increase yields, but this comes at a cost,” Sandra explains. “The focus on production has narrowed the genetic basis of many crops, making it harder for them to adapt to challenges like climate change.”

“The pan-genome allows us to look more in-depth at how wild relatives might be able to help improve our crops, and how easy or difficult that might be.”

Seeing double

Solanum is one of the largest plant genera on Earth, and contains many species that are grown as crops on small and large scales. But the complex relationships between these different species can cause a headache for those trying to breed new varieties.

“Solanum is one of the few plant genera which has more than 1,000 species in it, which can be challenging,” says Sandra. “When you breed plants, you cross your crop with its closest relatives. In this case, all of Solanum’s members are relatives of each other and potential resources for new traits.”

One of the complications of breeding these plant species with each other are what are known as paralogues. These are genes which start off as identical copies of each other, but over time evolve in different ways that can result in them doing different things.

“Paralogues can evolve along different pathways,” Sandra explains. “They can lose their function, becoming what we call pseudogenes, or sometimes take on new roles. Other paralogues split the function of the original genes between them.”

“In Solanum, you get a lot of duplication where the same characteristics re-evolve in these paralogues. This means that there can be quite fundamental change in a plant over millions of years, which is quite a short timescale in evolutionary terms.”

The intricacies of plant breeding

As different Solanum plants have evolved, their characteristics have ended up being controlled by a variety of different paralogues. For this new paper, the researchers wanted to investigate a gene that is known to control the size of fruit in some of these plants.

This gene, called CLAVATA3, is one of the reasons that a beef tomato is much larger than a vine tomato. This is because CLAVATA3 causes the beef tomato to form more seed compartments, so the fruit grows much bigger.

While it might seem logical that breeding this gene into other Solanum crops would also create bigger fruits, that’s not the case. The results are unpredictable, and paralogues seem to be one of the reasons why.

Having assembled a pan-genome of Solanum, the team looked at what insights it could offer about the scarlet eggplant. This is an important crop in Africa and Brazil, where its fruit and leaves feed millions of people.

Working together with local breeders, the team combined Indigenous knowledge and the Solanum pan-genome to investigate what CLAVATA3 and its paralogues do in the scarlet eggplant. They uncovered a complex series of genetic changes which culminated in a previously unknown gene that affects the size of its fruits. Crucially, however, it’s not the same gene that causes this in tomatoes.

The team recommend that if breeders want to improve the yield for the scarlet eggplant further, they should look at how it flowers. Producing earlier flowering varieties would help produce more fruits for subsistence farmers, while delaying flowering would stimulate the production of more edible leaves.

Sandra adds that the study demonstrates the importance of taxonomy, and finding out more about the relationships between different species. Without it, advances in food security, medicine and so much more would simply not be possible.

“Taxonomy in a big genus like Solanum is a challenge, and it took a lot of effort to get high-quality genomes so that the team could do this work,” Sandra says. “But it was worth it, as every time we do something like this we understand how the world works a little better, even if it is more complicated than we thought before.”