The wild ancestor of the tomato is a genomic reservoir for plant growers

Thousands of years ago, people in South America began domesticating Solanum pimpinellifolium, a herbaceous plant with small, intense flavor fruits. Over time, the plant evolved into S. lycopersicum, the modern cultivated tomato.

Although today’s tomatoes are larger and easier to grow than their wild ancestors, they are also less resistant to disease and environmental stresses such as drought and salty soil.

Boyce Thompson Institute researchers, led by Zhangjun Fei, created a high-quality reference genome for S. pimpinellifolium and discovered sections of the genome that underlie fruit flavor, size and ripeness, and stress tolerance. and disease resistance. The results were published in Nature Communications on November 16.

“This reference genome will allow researchers and plant growers to improve characteristics such as fruit quality and stress tolerance in tomatoes,” Fei said, “for example, by helping them discover new genes in modern tomatoes and reintroduce genes from S. pimpinellifolium which were lost over time when S. lycopersicum was domesticated. “

Fei is an ITV faculty member and corresponding co-author of the paper, as well as an adjunct professor at Cornell University’s School of Integrative Plant Science (SIPS).

Although other groups had previously sequenced S. pimpinellifolium, Fei said this reference genome is more complete and accurate, thanks in part to cutting-edge sequencing technologies that are capable of reading very long DNA fragments.

“Older sequencing technologies that read short DNA fragments can identify mutations at the single base level,” said Shan Wu, a postdoctoral scientist in Fei’s lab and corresponding co-author of the paper. “But they are not good at finding structural variants, such as insertions, deletions, inversions or duplications of large pieces of DNA.”

“Many known traits of the tomato are caused by structural variants, so that’s why we focused on them,” Fei said. “Structural variants are also poorly studied because they are more difficult to identify.”

Fei’s group compared the reference genome of S. pimpinellifolium with that of the cultivated tomato, called Heinz 1706, and found more than 92,000 structural variants.

The researchers then sifted through the tomato pan-genome, a database with the genomes of more than 725 closely related cultivated wild tomatoes, and discovered structural variants linked to many important traits. For example, the modern cultivated tomato has some genomic deletions that reduce their lycopene levels, a red pigment with nutritional value, and an insert that reduces their sucrose content.

Jim Giovannoni, a BTI faculty member and co-author of the study, notes that many consumers are disappointed with the quality and flavor of modern-grown tomatoes because past farming efforts have ignored those traits in favor of performance and yield.

“Identifying the additional genetic diversity captured in the S. pimpinellifolium genome offers farmers the opportunity to bring some of these important characteristics back to store-bought tomatoes,” said Giovannoni, who is also an adjunct professor in SIPS and a scientist in the United States. United States. Agricultural Research Service of the Department of Agriculture.

Researchers found many other structural variants that could be of interest to plant growers, including variants in numerous disease resistance genes and genes involved in fruit size, ripening, hormone regulation, metabolism and development of flowers, seeds and leaves.

The team also found structural variants associated with the regulation of the expression of genes involved in the biosynthesis of lipids in the peel of the fruit, which could help improve the fruit’s post-harvest performance.

“So much genetic diversity was lost during the domestication of the tomato,” said Fei. “This data could help bring back some of that diversity and lead to tomatoes that taste better, are more nutritious and more resilient.”