Scientists have discovered why store-bought tomatoes taste so bland: they are missing a version of a gene that gives tomatoes their flavor.

In a study, an international team including researchers from Boyce Thompson Institute has created a pan-genome that offers the complete genetic information of 725 cultivated and closely related wild tomatoes. This, they believe, can help breeders grow more flavorful tomatoes.

How Tomatoes Lost Some Of Its Genes

In the past, Tomato breeders valued traits that will improve yield. Somewhere along the way, other equally important qualities, like flavor, disappeared.

To find out what disappeared, the team compared the genome of the domesticated tomato called Heinz 1706 to its pan-genome. They discovered that the Heinz 1706 was missing nearly 5,000 genes that were present in other varieties of tomatoes.

Some of the genes that were absent in domesticated varieties of tomatoes are those that are involved in the plant's defense against pathogens.

"These new genes could enable plant breeders to develop elite varieties of tomatoes that have genetic resistance to diseases that we currently address by treating the plants with pesticides or other cost-intensive and environmentally unfriendly measures," said James Giovannoni, a faculty member at the Boyce Thompson Institute.

Putting Flavor Back To Store-Bought Tomatoes

The scientists also identified a rare version of TomLoxC, a gene that gives tomatoes their flavor. TomLoxC is present in 91.2 percent of wild tomatoes, but only 2.2 percent of the older domesticated variants.

"We found it also produces flavor compounds from carotenoids, which are the pigments that make a tomato red," explained Giovannoni.

However, the researchers added that flavor might already be coming back in style among tomato breeders in the United States. The rare gene was found in about 7 percent of modern tomato varieties in recent decades.

The researchers hope that tomato breeders will take advantage of the pan-genome and select genes that will result in tastier produce.

Clifford Weil, the program director of the National Science Foundation's Plant Genome Research Program, said the findings could benefit both the consumer and the economy. Tomatoes are the second most-consumed vegetables in the United States, although, technically, people eat the plant's fruits, and an average American is estimated to consume about 20.3 pounds or 9.2 kilograms of fresh tomatoes every year.

The study appears in the journal Nature Genetics.