Scientists at Boyce Thompson Institute have produced a high-quality chromosome-scale genome sequence for the currant tomato Solanum pimpinellifolium, the wild progenitor of the modern cultivated tomato Solanum lycopersicum.

Solanum pimpinellifolium in Botanisk tidsskrift, 1872.

Tomato is the worlds leading vegetable crop with a total production of 182 million tons and a worth over US $60 billion in 2018.

Solanum pimpinellifolium carrying red, small, and round fruits is the wild progenitor of the cultivated tomato.

It was domesticated in South America to give rise to Solanum lycopersicum var. cerasiforme, which was later improved into the big-fruited tomato Solanum lycopersicum var. lycopersicum in Mesoamerica.

Although other groups had previously sequenced Solanum pimpinellifolium, the new reference genome is more complete and accurate, thanks in part to cutting-edge sequencing technologies that are able to read very long pieces of DNA, said co-lead author Dr. Zhangjun Fei, a researcher at Boyce Thompson Institute and Robert W. Holley Center for Agriculture and Health at the U.S. Department of Agricultures Agricultural Research Service.

Older sequencing technologies that read short pieces of DNA can identify mutations at the single-base level, said co-lead author Dr. Shan Wu, a postdoctoral scientist at Boyce Thompson Institute.

But they arent good at finding structural variants, like insertions, deletions, inversions or duplications of large chunks of DNA.

Many known traits of the tomato are caused by structural variants, so that is why we focused on them, Dr. Fei said.

Structural variants also are understudied because they are more difficult to identify.

The scientists compared their reference genome of Solanum pimpinellifolium to that of the cultivated tomato, called Heinz 1706, and found more than 92,000 structural genetic variants.

They then combed the tomato pan-genome, a database with the genomes of more than 725 cultivated and closely related wild tomatoes, and discovered structural variants related to many important traits.

For example, the modern cultivated tomato has some genomic deletions that reduce their levels of lycopene, a red pigment with nutritional value, and an insertion that reduces their sucrose content.

Identification of the additional genetic diversity captured in the Solanum pimpinellifolium genome provides breeders with opportunities to bring some of these important features back to store-bought tomatoes, said co-author Dr. Jim Giovannoni, a researcher at Boyce Thompson Institute and Robert W. Holley Center for Agriculture and Health at the U.S. Department of Agricultures Agricultural Research Service.

The authors found many other structural variants that could be of interest to plant breeders, including variants in numerous disease-resistance genes and in genes involved in fruit size, ripening, hormonal regulation, metabolism, and the development of flowers, seeds and leaves.

They also found structural variants associated with regulating the expression of genes involved in the biosynthesis of lipids in fruit skin, which could help improve the fruits post-harvest performance.

So much genetic diversity was lost during tomato domestication, Dr. Fei said.

These data could help bring some of that diversity back and result in tomatoes that taste better, are more nutritious and more resilient.

The results appear in the journal Nature Communications.

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X. Wang et al. 2020. Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. Nat Commun 11, 5817; doi: 10.1038/s41467-020-19682-0

This article is based on a press-release provided by Boyce Thompson Institute.

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