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Genetic Variants Affect Tomato Flavor Through Sugar Production, Other Pathways

Tomato slice

NEW YORK (GenomeWeb) – An international team has identified genetic and metabolic clues to tomato flavors expected to find favor with consumers.

As they reported in Science today, researchers from the Chinese Academy of Agricultural Sciences, the University of Florida, and elsewhere gathered whole-genome sequence and targeted metabolomic information on hundreds of modern, heirloom, and wild tomato plant accessions. In their subsequent search for genetic loci associated with compounds implicated in tomato flavor in consumer taste tests on some of the accession, they narrowed in on variants and genes that seemed to coincide with the production of sugars and other flavor-related compounds.

"Together, these results provide an understanding of the flavor deficiencies in modern commercial varieties and the information necessary for the recovery of good flavor through molecular breeding," co-first authors Denise Tieman and Guantao Zhu and their colleagues wrote.

The Tomato Genome Consortium presented the genome sequence for the domesticated tomato plant, Solanum lycopersicum, in a paper published in Nature in 2012. But though there have been hints that commercial tomato breeding and storage approaches may have inadvertently altered tomato fruit flavors, "most breeders focus on yield, disease resistance, and firmness, which are essential for shipping, long-term storage, and external appearance rather than flavor quality," the authors wrote.

Consequently, the team argued, research on flavor-related features has come in second to studies of more easily tallied and tested tomato fruit features, including those related to production and transport.

For their new analysis, the researchers focused on 398 accessions of modern, heirloom, or wild tomato accessions — a set that included representatives from the domestic tomato plant S. lycopersicum and a related wild plant called S. pimpinellifolium. They used the Illumina HiSeq 2000 to re-sequence tomato plant genomes, and used gas chromatography and/or mass spectrometry to profile volatile compounds, sugars, and acids in tomato fruits from the different varieties.

The team also gauged consumers' responses to 160 ripe tomatoes from 96 varieties, which the individuals rated during focus groups held from 2010 to 2016. Analyses narrowed in on 33 compounds coinciding with favorable consumer ratings overall and more than three-dozen compounds with apparent ties to flavor intensity. The group also detected declining consumer favorability for some modern, commercially grown varieties.

When the investigators compared modern and heirloom tomato compounds, they identified differences in content for more than a dozen volatile compounds. And a genome-wide association study aimed at finding genetic variants associated with flavor-favoring compounds led them to 251 genetic variants that had apparent associations with four non-volatile and 15 volatile flavor-related chemicals — results that the investigators followed up on in two additional tomato plant collections.

For example, the team's results suggest that several genetic loci linked to sugar content may be negatively associated with tomato fruit size, meaning a preference for larger tomatoes might unintentionally curb their flavor in some cases. Other genetic loci appeared to influence volatile compound metabolism, fruit coloring, acid content, and more.

"Our results provide a roadmap for improvement of flavor," the authors concluded. "The genes and pathways identified here in the tomato almost certainly point to pathways worth investigating for improvement of flavor quality in other fruit crops."

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