Research from the Boyce Thompson Institute shows how wild tomato relatives may help breeders recover flavour and nutritional traits without sacrificing yield, fruit size or shelf life. The study maps regulatory switches tied to tomato fruit quality.
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Researchers have mapped regulatory switches in wild tomato relatives that could help breeders recover flavour and nutritional traits without undoing decades of improvement in yield, size and shelf life.
Researchers at the Boyce Thompson Institute have mapped genetic controls influencing tomato fruit quality, offering breeders more precise targets for incorporating useful traits from wild relatives.
Generations of breeding have made cultivated tomatoes larger, firmer, more productive and easier to transport, while narrowing their genetic diversity. Wild relatives retain valuable variation, but introducing those traits can also bring characteristics breeders do not want.
The study, published in Genome Biology, compared gene activity in cultivated tomato and three wild relatives across different fruit tissues and stages of development.
“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.
Separating Two Types of Genetic Control
The researchers examined two ways gene activity is regulated. Changes in nearby DNA, known as cis effects, influence an associated gene. Changes elsewhere in the genome, known as trans effects, can influence multiple genes, according to a press release.
To distinguish between them, the team crossed cultivated tomato with each wild species. The resulting hybrids carried gene copies from both parents operating within the same cells.
“The hybrid gives us a natural controlled experiment,” said Fei. “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.”
The team measured gene activity in the fleshy outer fruit wall, placenta and jelly surrounding the seeds, at up to four developmental stages.
Across the species, tissues and stages examined, cis changes were the main driver of differences in gene activity, affecting up to 23.5% of active genes. By comparison, trans changes affected no more than 4.6%. Many regulatory differences were specific to a particular tissue and developmental stage.
Tracing Colour, Sugar and Bitterness
The findings help explain why some wild tomato species remain green. In these species, cis changes increase the activity of genes that direct pigment production away from lycopene, the red pigment found in cultivated tomatoes.
Researchers also identified coordinated regulation of two sugar-related genes that allows green-fruited species to retain more sucrose.
For bitterness, the team found a developmental shift. Early in fruit development, trans regulation helps maintain bitter defensive compounds called glycoalkaloids. Later, cis changes in cultivated tomato help convert those compounds into non-bitter forms as fruit ripens.
More Precise Targets for Breeders
“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,” said Giovannoni. “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.”
The researchers have made their data freely available, including two newly assembled wild tomato genomes, to support further research and breeding.
The study received support from the USDA National Institute of Food and Agriculture and the U.S. National Science Foundation.
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