An international team of researchers led by Boyce Thompson Institute for Plant Research and the U.S. Department of Agriculture- Agricultural Research Service has created a pan-genome that captures all of the genetic information of 725 cultivated and wild tomatoes, establishing a resource that promises to help breeders develop more flavorful and sustainable varieties. The team found 4,873 new genes and identified a rare version of a gene that can make tomatoes tastier.
Tomatoes are one of the most eaten vegetables — although they actually are fruit botanically — with a worldwide annual production of 182 million tons, worth more than $60 billion.
U.S. tomato consumption per capita was 9.2 kg (20.3 pounds) for fresh tomatoes in 2017 plus an additional 33.2 kg (73.3 pounds) of processed tomatoes eaten per person. They are the second most consumed vegetable in the United States after potatoes.
While cultivated tomatoes have a wide range of physical and metabolic variation, there have been several severe bottlenecks during its domestication and breeding. This means today’s tomatoes have a narrow genetic base.
The tomato pan-genome helps identify what additional genes beyond the reference might be available for crop breeding and improvement. It 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 pan-genome essentially provides a reservoir of additional genes not present in the reference genome. Breeders can explore the pan-genome for genes of interest, and potentially select for them as they do further breeding to improve their tomatoes,” said co-lead author Dr. Zhangjun Fei, a researcher with Boyce Thompson Institute for Plant Research and the U.S. Department of Agriculture-Agricultural Research Service.
“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,” added co-lead author Dr. James Giovannoni, a molecular biologist with Boyce Thompson Institute for Plant Research and the U.S. Department of Agriculture-Agricultural Research Service.
“The gene influences fruit flavor by catalyzing the biosynthesis of a number of lipid-involved volatiles — compounds that evaporate easily and contribute to aroma.”
In addition, the researchers found a new role of TomLoxC — it facilitates production of a group of apocarotenoids that work as signaling molecules influencing a variety of responses in plants including environmental stresses. The compounds also have a variety of floral and fruity odors that are important in tomato taste.
The rare version of TomLoxC was found in only 2% of older or heirloom cultivated large tomato varieties, although the version was present in 91% of currant-sized wild tomatoes, primarily Solanum pimpinellifolium, the wild predecessor of the cultivated tomato. It is becoming more common in newer varieties.
“It appears that there may have been strong selection pressure against or at least no selection for the presence of this version of TomLoxC early in the domestication of tomatoes,” Dr. Giovannoni said.
“The increase in prevalence of this form in modern tomatoes likely reflects breeders’ renewed interest in improved flavor.”
The results are published in the journal Nature Genetics.
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Lei Gao et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics, published online May 13, 2019; doi: 10.1038/s41588-019-0410-2