Boyce Thompson Institute Researchers Map Wild Tomato Genetics to Improve Flavor

Scientists at the Boyce Thompson Institute have charted control switches within wild tomato species that might assist breeders in restoring taste and nutrient profiles while preserving decades of progress regarding crop yield, dimensions, and storage durability. This genetic mapping study offers agricultural scientists precise targets for breeding resilient characteristics from wild species into modern cultivars.

Narrowing Genetic Diversity in Cultivated Lines

Generations of selective breeding have made cultivated tomatoes larger, firmer, more productive, and easier to transport. However, this optimization process significantly narrowed their genetic diversity. Wild relatives retain valuable variations in taste and resilience, but introducing those traits often imports unwanted characteristics that disrupt established agricultural performance.

“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. This can be countered with precise information on how the genes responsible for such traits are controlled,” said Carmen Catala, a senior research associate who led the work alongside Professor Zhangjun Fei and adjunct professor and USDA scientist James Giovannoni.

Mapping Cis and Trans Regulatory Controls

The research team examined two distinct ways gene activity is regulated. Changes in nearby DNA, known as cis effects, influence an associated gene directly. Meanwhile, changes elsewhere in the genome, known as trans effects, can influence multiple genes simultaneously.

To distinguish between these two mechanisms, investigators crossed cultivated tomato plants with three wild species. The resulting hybrids carried gene copies from both parents operating within the exact same cellular environment.

“The hybrid gives us a natural controlled experiment. Both versions of each gene sit in the same cells and receive the same regulatory signals. If one version is more active than the other, we know the difference is written into the DNA right next to that gene,” said Fei.

The team measured gene activity across 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 differences in gene activity, affecting up to 23.5% of active genes. By comparison, trans changes affected no more than 4.6% of active genes. Many regulatory differences remained specific to particular tissues and developmental stages.

Cis and Trans Changes Influence Tomato Colour and Taste

The findings clarify why certain wild tomato species remain green as they mature. In those species, specific cis changes increase the activity of genes that direct pigment production away from lycopene, the red pigment standard in cultivated tomatoes. Researchers also identified coordinated regulation of two sugar-related genes, a mechanism enabling green-fruited species to retain higher levels of sucrose.

Regarding bitterness, the team uncovered a distinct developmental shift. Early in fruit development, trans regulation helps maintain bitter defensive compounds known as glycoalkaloids. Later in the cycle, cis changes in cultivated tomatoes assist in converting those compounds into non-bitter forms as the fruit ripens.

Targeting Traits Without Labor-Intensive Cleanup

Wild tomatoes have long been recognized as a source of valuable traits, but utilizing them traditionally required extensive, time-consuming cleanup to eliminate undesirable baggage. Breeders previously lacked a method to identify which specific genetic differences drove individual traits.

“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. What they’ve lacked is a way to tell which of thousands of genetic differences is behind each trait to make selection more targeted. Now we can point to specific genes for selection, with effects in specific tissues, at specific moments in fruit development and ripening,” said Giovannoni.

The study was published in Genome Biology. To facilitate further research and crop development, the investigators have made their data freely available, including two newly assembled wild tomato genomes. The project received financial support from the USDA National Institute of Food and Agriculture and the U.S. National Science Foundation.