Scientists Discover Why Store-Bought Tomatoes Taste so Bad and How to Fix It

Constructing the pan-genome for the cultivated tomato led to the discovery of 'taste genes.'
Jessica Miley

Everyone knows store-bought tomatoes pretty much suck. While deceptively good looking - more often than not they lack any real flavor. That’s all about to change thanks to the hard work of scientists who have isolated genes for flavor.


Scientists from the Agricultural Research Service (ARS) and the Boyce Thompson Institute (BTI) have worked together to construct the pan-genome for the cultivated tomato and its wild relatives.

James Giovannoni with the ARS Plant, Soil and Nutrition Research Laboratory and BTI bioinformatics scientist Zhangjun Fei, both in Ithaca, New York, mapped almost 5,000 previously undocumented genes including the genes for that elusive flavor.

Understanding missing genes will lead to more flavor

A genome is a biological map of an organism's genes and their functions. While a genome is usually of a single variety, this pan-genome includes all of the genes from 725 different cultivated and closely related wild tomatoes. The project revealed 4,873 genes that were absent from the original reference genome.

There have been difficulties in the domestication of tomatoes that has led to the tomatoes we know today having a really narrow genetic base. The pan-genome helps figure out what genes are missing from the original model genome to help with crop breeding and overall improvement.

Tomatoes mean big bucks

Typically breeders of modern vegetables have placed emphasis on traits such as yield, shelf life, disease resistance, and stress tolerance, rather than flavor in order to meet economic demands. Tomatoes are among the most popular crop in the world.

More than 182 million tons are produced annually with a gross value of more than $60 billion dollars. In the US alone, the average consumption per person tops over 20 pounds per year.

Breeders ready to bring back taste

"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. 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," explained Giovannoni.

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The rare version of TomLoxC was found in over 91 percent of currant-sized wild tomatoes but in only 2 percent of older or heirloom cultivated large tomato varieties.

"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," Giovannoni added.

"The increase in prevalence of this form in modern tomatoes likely reflects breeders' renewed interest in improved flavor."

Armed with this new genome information, breeders should be able to work quickly on ways to improve the flavor of commercially grown tomatoes while maintaining the other necessary qualities to make them an economically advantageous crop.

"These novel genes discovered from the tomato pan-genome added substantial information to the tomato genome repertoire and provide additional opportunities for tomato improvement. The presence and absence profiles of these genes in different tomato populations have shed important lights on how human selection of desired traits have reshaped the tomato genomes," said Fei.

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