At first glance, it looked like any other plant that can be found growing in the corners of offices or on the windowsills of university laboratories. But this particular tomato plant, grown in 2018 at the University of Minnesota, was different. The bushy tangle of elongated leaves and small red fruits were characteristic of a wild species of tomato plant native to Peru and Ecuador called Solanum pimpinellifolium, also known as the red currant tomato. A closer inspection, however, made the plant's uniqueness more apparent.
This particular plant was more compact, with fewer branches but more fruits than the wild tomato. Its fruits were also a little darker than was usual, a sign of increased lycopene – an antioxidant linked to a lower risk of cancer and heart disease. It had, in fact, been designed that way.
The plant was created by geneticist Tomas Cermak and his colleagues with the use of Crispr gene editing, a Nobel Prize-winning technology which works like a "cut and paste" tool for genetic material. The technique is now revolutionising agriculture and helping create crops for the future.
The robot that picks ripe tomatoes
Vermak himself is on a mission to find a perfect tomato, one that would be easy to cultivate, nutritious and tasty, yet more adaptable to a changing climate. "The ideal plant would be resistant to all forms of stress — heat, cold, salt and drought, as well as to pests," he says.
Climate change spells trouble for many crops, and tomatoes are no exception. Tomatoes don't like heat, growing best between 18C (64F) and 25C (77F). Cross either side of that threshold and things start going downhill: pollen doesn't form properly, the flowers don't form into berries in the way they should. Once the mercury goes over 35C (95F), yields begin to collapse. A 2020 study showed that by mid-21st Century up to 66% of land in California historically used for growing tomatoes may no longer have temperatures appropriate for the crop. Other modelling studies suggest that by 2050 large swaths of land in Brazil, sub-Saharan Africa, India and Indonesia will also no longer have optimal climate for cultivation of tomatoes.
Of course, as average temperatures rise, other, previously too chilly regions, may become tomato-friendly. Yet observations in Italy show that weather extremes are something to consider, too. The 2019 growing season in northern Italy was marred by hail, strong winds, unusually high rainfall, and both exceptional frost and exceptional heat. The result was stressed tomato plants and poor harvests.
And there is more. Water scarcity, which forces farmers to use lower quality irrigation water, often containing salt, leads to increases in soil salinity – something commercial tomato cultivars don't like. Higher ozone levels, meanwhile, make tomatoes more susceptible to diseases such as bacterial leaf spot.
That's all troubling, especially considering that tomatoes are currently the largest horticultural crop in the world – humanity produces 182 million tons of the fruit every year, equivalent to the weight of almost 32 Great Pyramids of Giza. What's more, our appetites for tomatoes are growing fast – over the last 15 years global production of tomatoes rose by more than 30%.
Besides being humanity's favourite fruit, tomatoes also happen to be a model crop: they are fast to grow, easy to breed and relatively simple to manipulate on a genetic level. "There is more funding available for research than there is for other plant species to develop resources like genome sequences, genetic engineering, and gene editing for tomato," says Joyce Van Eck, plant geneticist at Cornell University in New York. Taken together, this makes tomatoes perfect for study of novel gene editing technologies such as Crispr, which could bring us many climate-adaptive crops in the near future.
Once the climate-smart genes such as these are identified, they can be targeted using Crispr to delete certain unwanted genes, to tune others or insert new ones
Crispr is a molecular toolbox scientists have repurposed from bacteria – when bacteria are attacked by viruses, they capture and cut the viral DNA to prevent the aggressor from being able to replicate and so fight it off. In use in plants since 2013, Crispr now allows researchers to modify genome with extreme precision and accuracy to obtain traits they desire. You can insert genes, delete them, and create targeted mutations. In non-human animals Crispr is being used for the study of human disease models, for improving livestock, and could even potentially be used to resurrecting extinct species. In plants, it can help create better, tastier, more nutritious and more resistant crops.
The first step is finding the right genes to target. "We need to identify the genes responsible or involved in being able to withstand abiotic and biotic stress because otherwise we cannot alter, modify or knock them out by using gene editing," says Richard Visser, plant geneticist at Wageningen University, the Netherlands.
Domesticating crops, tomatoes included, has led to a huge loss of genetic diversity. Modern commercial cultivars may be fast to grow and easy to harvest, but genetically speaking they are plain vanilla. Just four highly homogenised crops – soybeans, rice, wheat and corn – dominate global agriculture, accounting for more than half of all the world's agricultural land.
In contrast, their wild cousins – as well as so-called landraces (traditional varieties adapted to specific locations) – are a treasure box of genetic diversity. This is why scientists now search this genetic pool to identify traits that can be reintroduced into commercial plants – a process much helped by fast-dropping costs of DNA-sequencing technologies.
