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Genomic Analysis Finds Lost Tomato Taste Gene

Tomato genetics

(Jack Dykinga, Agricultural Research Service, USDA)

14 May 2019. An analysis of genomes for all varieties of tomatoes, both wild and domesticated, found a rare gene variation that can make tomatoes tastier. A team led by the Boyce Thompson Institute at Cornell University and Agricultural Research Service, or ARS, of the U.S. Department of Agriculture in Ithaca, New York published its findings in yesterday’s issue of the journal Nature Genetics (paid subscription required).

Tomato growers, like other crop producers, often seek out varieties that grow faster, with larger fruit, and more resistance to pests and extreme weather conditions. But along the way, many of the tomatoes available in retail markets lost their characteristic and succulent taste, found today in only a few specialty varieties. Researchers led by Zhangjun Fei , a computational geneticist at Boyce Thompson Institute and James Giovannoni, a plant molecular biologist with ARS — also an adjunct professor at Boyce Thompson — believe they found a genetic variation for restoring that singular taste to tomatoes.

Tomato farming is a large agricultural enterprise, with worldwide production according to ARS of 182 million tons, generating some $60 billion in sales. Moreover, tomatoes are the second-most consumed vegetable in the U.S., after potatoes, with Americans eating 20.3 pounds of fresh tomatoes and 73.3 pounds of processed tomatoes per person per year.

Fei, Giovannoni, and colleagues analyzed the genomes of all 725 known tomato varieties, covering both domesticated tomatoes grown for today’s consumer markets, as well as wild varieties. This pan-genomic analysis revealed 4,873 genes not included in the accepted standard, or reference genome for tomatoes. Many of these genes were considered expendable as growers sought larger, heartier, and faster growing varieties. Over the years, this focus on productivity made the reference genome for tomatoes increasingly more constrained.

“During the domestication and improvement of the tomato,” says Fei in a Boyce Thompson statement, “people mostly focused on traits that would increase production, like fruit size and shelf-life,” so some genes involved in other important fruit quality traits and stress tolerance were lost during this process.”

One of the discoveries in their analysis is an allele, or genetic variation, called TomLoxC. This variation codes for acids that help produce aromas and flavors. Those acids act as catalysts, reacting with lipid, or fat-related compounds to evaporate quickly, producing aromas and influencing flavors. “We found it also produces flavor compounds from carotenoids,” says Giovannoni, “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 flavorful tomatoes.”

TomLoxC contributes still another feature with carotenoids, sending out signals that help protect against environmental stresses. And while present in 91 percent of wild tomato varieties, TomLoxC is found in only about 2 percent of older domestic varieties. Growers of domestic tomatoes, however, began including this gene in their breeding more recently, raising its presence to about 7 percent today in newer heirloom varieties.

“How many times do you hear someone say that tomatoes from the store just don’t quite measure up to heirloom varieties,” notes Fei. “This study gets to why that might be the case and shows that better tasting tomatoes appear to be on their way back.”

Fei and Giovannoni tell more about the study in the following video.

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