It's no secret that tomatoes plucked from the supermarket aisles just aren't as tasty as those fresh from your garden patch or a local market. That difference is tomato growers select for genes that help the fruit survive the long journey, sacrificing taste in the process. To find taste genes that could be spliced back into commercial crops, researchers have now complied a pan-genome of all cultivated and related wild tomato species, uncovering almost 5,000 previously-unknown genes.

The domestic tomato genome was fully sequenced back in 2012, but that was only one particular breed, known as Heinz 1706. More recent work has gone into studying other varieties, including heirloom tomatoes that are more flavorful, before they were bred out of the modern commercially produced fruit in favor of appearance and shelf life.

The new work has expanded that view out to a full genome of all regularly-grown tomato breeds and their closest relatives. That includes all genes from 725 different types of tomatoes, and in doing so the team discovered an extra 4,873 genes that weren't included in the base Heinz 1706 genome.

That gives growers plenty of new tools to work with for growing tastier, healthier or longer-lasting tomatoes. And in terms of flavor, one gene in particular caught their attention. TomLoxC was found to add floral and fruity notes to tomatoes by producing more of a certain group of apocarotenoids.

"One of the most important discoveries from constructing this pan-genome is a rare form of a gene labeled TomLoxC, which mostly differs in the version of its DNA gene promoter," says James Giovannoni, co-author of the study. "The gene influences fruit flavor by catalyzing the biosynthesis of a number of lipid (fat)-involved volatiles — compounds that evaporate easily and contribute to aroma."

This form of TomLoxC turned up in only two percent of heirloom tomato breeds, but it was found in over 90 percent of the smaller, wild tomatoes. Interestingly, the team discovered that this version of the gene was starting to appear more in new varieties of tomato. Although the gene's role has only just been discovered, it seems that breeders have a nose for these things.

"It appears that there may have been strong selection pressure against or at least no selection for the presence of this version of TomLoxC early in the domestication of tomatoes," says Giovannoni. "The increase in prevalence of this form in modern tomatoes likely reflects breeders' renewed interest in improved flavor."

The researchers say that having access to such detailed data on the genomes of so many tomato varieties will help breeders design tastier crops that still retain the genes allowing them to be shipped long distances to supermarkets. And if scientists want to get really creative, they might also start making spicy tomatoes.

The research was published in the journal Nature Genetics.