Supermarket tomatoes could be about to get much tastier, according to new research which has identified a rare gene that relates specifically to flavour.

During the domestication process, commercial tomato growers favoured traits such as yield, shelf life, disease resistance and stress tolerance.

But these were at the expense of other genes that expressed important qualities like flavour.

“How many times do you hear someone say that tomatoes from the store just don’t quite measure up to heirloom varieties?” said Dr Clifford Weil, programme director of the National Science Foundation’s Plant Genome Research Programme, which supported the work.

Now scientists think they can make cultivated tomatoes taste like their wild relatives again, following research on the tomato’s pan-genome which includes all genes from 725 different cultivated varieties and their closely-related wild relatives.

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While cultivated tomatoes come in a wide range of varieties, they have a narrow genetic base, according to the study published in Nature Genetics.

Researchers mapped nearly 5,000 new genes and identified a rare version of a gene called TomLoxC that makes tomatoes tastier. This is present in 91.2 per cent of wild tomatoes but only 2.2 per cent of older domesticated tomatoes.

“The rare version of TomLoxC now has a frequency of seven per cent in modern tomato varieties, so clearly the breeders have started selecting for it, probably as they have focused more on flavour in the recent decades,” said Professor James Giovannoni from the Boyce Thompson Institute (BRTI) in Ithaca, New York state.

“We found it also produces flavour compounds from carotenoids, which are the pigments that make a tomato red. So it had an additional function beyond what we expected, and an outcome that is interesting to people who enjoy eating flavourful tomatoes”, he said.

Tomatoes are one of the most eaten vegetables – although they are actually botanically fruit – with a worldwide annual production of 182 million tons, worth more than $60bn (£46bn).

Scientists say breeders should be able to use this genetic information to quickly increase the flavour of store-bought fruit while preserving the genes that make them economically advantageous.