Boyce Thompson Institute Maps Wild Tomato Genetic Switches to Restore Flavor
Researchers at the Boyce Thompson Institute mapped regulatory switches in wild tomato relatives that allow breeders to recover flavor and nutrition without undoing decades of gains in yield, size, and shelf life. Generations of agricultural selection have made cultivated tomatoes larger, firmer, and more productive while significantly narrowing their genetic diversity. Wild relatives retain valuable variations, but introducing those traits often imports unwanted agricultural characteristics that complicate crop development.
Comparing Gene Activity in Cultivated and Wild Tomatoes
The study, published in Genome Biology, examined gene activity across different fruit tissues and developmental stages in cultivated tomatoes and three wild relatives. Researchers investigated two distinct forms of gene regulation to understand how traits are controlled. Changes in nearby DNA, known as cis effects, influence an associated gene directly.
To isolate these mechanisms, the research team crossed cultivated tomatoes with each of the three wild species. The resulting hybrid plants carried gene copies from both parents operating within the same cells. “Both versions of each gene sit in the same cells and receive the same regulatory signals,” said Professor Zhangjun Fei, explaining the natural controlled experiment. “If one version is more active than the other, we know the difference is written into the DNA right next to that gene.”
Tissue-Specific Regulation Across Development
The team measured gene expression in the fleshy outer fruit wall, the placenta, and the jelly surrounding the seeds at up to four developmental stages. Across all species, tissues, and stages examined, cis changes proved to be the primary driver of gene activity differences. These local DNA adjustments affected up to 23.5% of active genes. By comparison, trans changes influenced no more than 4.6% of active genes.
Many of these regulatory differences remained strictly specific to particular tissues and developmental phases. For instance, cis changes increase the activity of genes that direct pigment production away from lycopene in wild species that remain green at maturity. The team also identified coordinated regulation between two sugar-related genes, allowing green-fruited species to retain higher levels of sucrose.
Bitterness followed a distinct developmental shift during ripening. Early in fruit development, trans regulation maintains defensive compounds called glycoalkaloids. Later in the ripening process, cis changes in cultivated tomatoes help convert those bitter compounds into non-bitter forms.
Targeted Breeding for Nutritional Diversity
“Wild tomatoes are an enormous reservoir of diversity for flavor, nutrition, and resilience, but bringing those traits into modern varieties can come at the expense of other traits that breeders have spent decades improving, like yield, fruit size, or shelf life,” said Carmen Catala, a senior research associate who led the work alongside Professor Zhangjun Fei and USDA scientist and adjunct professor James Giovannoni. Precise data on gene control counteracts this trade-off.
“Breeders have always known wild tomatoes hold valuable traits, but their use in breeding introduces undesirable traits as well, necessitating time- and labor-intensive cleanup,” Giovannoni stated. “What they’ve lacked is a way to tell which of thousands of genetic differences is behind each trait to make selection more targeted.”
Researchers Release Wild Tomato Genomes and Dataset
The researchers made their complete dataset freely available to the scientific community, including two newly assembled wild tomato genomes to support ongoing breeding programs.
Questions About Wild Tomato Genetic Mapping
What specific wild tomato tissues did the researchers examine?
The research team measured gene activity in the fleshy outer fruit wall, the placenta, and the jelly surrounding the seeds at up to four developmental stages.
How much influence did cis changes have compared to trans changes?
Cis changes affected up to 23.5% of active genes and drove the majority of differences in gene activity, while trans changes affected no more than 4.6% of active genes.
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