Scientists at the Agricultural Research Service (ARS) and the Boyce Thompson Institute (BTWI) have completed mapping the pan-genome (the entire gene set of all strains of a species) for the cultivated tomato and its wild relatives. In the process, they have identified almost 5,000 previously undocumented genes. With the availability of this vast array of specific genetic information, the researchers say breeders should be able to increase the flavor of store bought, mass-produced tomatoes while preserving the traits that make them an economically advantageous crop.

“One of the most important discoveries from constructing this pan-genome is a rare form of a gene labeled TomLoxC, which mostly differs in the version of its DNA gene promoter. The gene influences fruit flavor by catalyzing the biosynthesis of a number of lipid (fat)-involved volatiles – compounds that evaporate easily and contribute to aroma,” explains Molecular Biologist James Giovannoni, an author of the study.

Through their research, published in Nature Genetics, the scientists were able to identify a new role of TomLoxC. The gene facilitates the production of a group of apocarotenoids – organic chemicals derived from carotenoids including vitamin A precursors – that work as signaling molecules influencing a variety of responses in plants, including environmental stressors. The compounds have a variety of floral and fruity odors that are important attributes in tomato flavor.

Mapping the pan-genome of 725 species of tomato
While cultivated tomatoes have a wide range of physical and metabolic variation, the researchers note that there have been several severe bottlenecks during its domestication and breeding – meaning that today’s tomatoes have a narrow genetic base. 

A genome is a biological map of an organism’s genes and their functions. But a genome is usually of a single variety, which then acts as a reference genome for the rest of the species. This pan-genome includes all of the genes from 725 different cultivated and closely related wild tomatoes, which revealed 4,873 genes that were absent from the original reference genome.

The rare version of TomLoxC was found in only 2 percent of older or heirloom cultivated large tomato varieties, although the version was present in 91 percent of currant-sized wild tomatoes, primarily Solanum pimpinellifolium, the wild predecessor of the cultivated tomato. The genetic variant is now is becoming more common in newer species.

“It appears that there may have been strong selecion pressure against or at least no selecion for the presence of this version of TomLoxC early in the domestication of tomatoes,” Giovannoni adds. “The increase in the prevalence of this form in modern tomatoes likely reflects breeders’ renewed interest in improved flavor.”

“These novel genes discovered from the tomato pan-genome added substantial information to the tomato genome repertoire and provide additional opportunities for tomato improvement. The presence and absence profiles of these genes in different tomato populations have shed important lights on how human selecion of desired traits have reshaped the tomato genomes,” says Zhangjun Fei, a BTI Bioinformatics Scientist and co-author of the study.

The scientists expect the addition of nearly 5,000 genes to the tomato genome repertoire to provide additional opportunities for improvement as their roles in tomato biology and fruit quality are determined.

FoodIngredientsFirst has reached out to the authors of the study for comment on how new knowledge acquired from these findings can be applied in genetic modification practices.

Old crop, new tricks
The tomato crop is no stranger to agricultural innovations. This is primarily due to the fact tomato plants are easy to propagate, and that genetically modified tomato plants show immediate evidence of trait changes. As such, developments in the space of novel breeding practices may prove beneficial to producers who seek to expand their flavor portfolios with the goal of meeting and exceeding consumers’ current expectations of traditional tomato flavors. The mainstay status of tomatoes as a pantry staple is driven by a powerful health association that continues to inspire an array of NPD.