Humans eat a lot of tomatoes—around 182 million tons of the fruit (and yes, they technically are a fruit) are produced around the world each year. But the varieties that we buy in the supermarket are notorious for not tasting all that great, due to years of tinkering by breeders. Now, as Roni Dengler reports for Discover, scientists have identified a flavor-making gene variant that is absent from most cultivated tomatoes, which in turn may help growers develop more tasty varieties in the future.

The discovery stemmed from a wider project to establish a tomato “pan-genome,” which describes the entire set of genes of all members of a species. The first tomato gene sequence, derived from a modern variety known as Heinz 1706, was published in 2012 and pinpointed around 35,000 genes. Heinz 1706 has since been used as a reference example for other tomato genomes, hundreds of which have been sequenced over the years.

For the new investigation, researchers looked at the genetic data of 727 cultivated and closely related wild tomatoes; 561 of the sequences had been previously published, and the researchers generated an additional 166 sequences “to obtain broader regional and global representation,” they write in Nature Genetics. The team was ultimately able to identify 4,873 previously undocumented genes.

“The pangenome essentially provides a reservoir of additional genes not present in the reference genome,” explains Zhangjun Fei, study co-author and plant pahtologist at Cornell University.

It was breeding that led to the disappearance of these genes, as growers focused their efforts on selecting for traits like increased shelf-life, bigger yields and larger sizes, which are important to modern methods of production. But along the way, other important traits were lost; the new study found that genes involved in defense responses to various pathogens were the ones most commonly missing from domesticated tomatoes.

The researchers also identified a rare allele, or variant, of a gene called TomLoxC, which is likely to be of particular interest to breeders who hope to bolster the taste of their crops. “The gene influences fruit flavor by catalyzing the biosynthesis of a number of lipid-involved volatiles—compounds that evaporate easily and contribute to aroma,” says study co-author James Giovannoni, a molecular biologist at Cornell and USDA scientist. Through their investigation, the researchers also discovered that TomLoxC facilitates the production of a group of organic compounds called apocarotenoids, which have a number of fruity and floral odors that influence tomato taste.

Some 90 percent of wild tomatoes had this rare version of TomLoxC—but only two percent of older domesticated tomatoes did. The allele seems to be making a comeback, however; the researchers found it in seven percent of modern tomato varieties. “[C]learly the breeders have started selecting for it, probably as they have focused more on flavor in the recent decades,” Giovannoni says.

The new pan-genome ultimately offers breeders the opportunity to look for other genes that they might want to selectively breed for in the future—which may in turn result in a more robust selection of tasty tomatoes landing on supermarket shelves.

“How many times do you hear someone say that tomatoes from the store just don’t quite measure up to heirloom varieties?” asked Clifford Weil, program director of the National Science Foundation’s Plant Genome Research Program, which supported the research. “This study gets to why that might be the case and shows that better tasting tomatoes appear to be on their way back.”