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Tomato's wild ancestor is a genomic reservoir for plant breeders

10/05/2021 - François-Xavier Branthôme
Thousands of years ago, people in South America began domesticating Solanum pimpinellifolium, a weedy plant with small, intensely flavored fruit. Over time, the plant evolved into S. lycopersicum – the modern cultivated tomato.

Although today’s tomatoes are larger and easier to farm compared with their wild ancestor, they also are less resistant to disease and environmental stresses like drought and salty soil.

Researchers from Boyce Thompson Institute, 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 ripening, stress tolerance and disease resistance. The results were published in Nature Communications in November.
This reference genome will allow researchers and plant breeders to improve traits like fruit quality and stress tolerance in the tomato,” said Fei, “for example, by helping them discover new genes in the modern tomato as well as by reintroducing genes from S. pimpinellifolium that were lost over time as S. lycopersicum was domesticated.” Fei is a BTI faculty member and co-corresponding author on the paper, as well as an adjunct professor in 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 able to read very long pieces of DNA.
Older sequencing technologies that read short pieces of DNA can identify mutations at the single-base level,” said Shan Wu, a postdoctoral scientist in Fei’s lab and co-corresponding author on the paper. “But they aren’t 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,” Fei said. “Structural variants also are understudied because they are more difficult to identify.”

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

Jim Giovannoni, BTI faculty member and co-author of the study, notes that many consumers are disappointed in the quality and flavor of modern production tomatoes because past breeding efforts ignored those traits in favor of performance and yield.
Identification of the additional genetic diversity captured in the S. pimpinellifolium genome provides breeders with opportunities to bring some of these important features back to store-bought tomatoes,” said Giovannoni, who is also an adjunct professor in SIPS (School of Integrative Plant Science, Cornell University) and a scientist with the U.S. Department of Agriculture’s Agricultural Research Service.

The researchers 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.

The group 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 fruit’s post-harvest performance.
So much genetic diversity was lost during tomato domestication,” 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.”

Researchers can locate novel and useful genes
At the same time at the beginning of the year, the specialized scientific press announced that a team at University of Tsukuba, in collaboration with TOKITA Seed Co. Ltd, have produced high-quality genome sequences of two wild ancestors of tomato from Peru, Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme. They recently published the work in DNA Research.

The team used modern DNA sequencing technologies, which can read longer sequences than was previously possible, coupled with advanced bioinformatics tools to analyze the hundreds of gigabytes of data generated and to confirm the high quality of the data. They assembled the many sequence fragments, showed where sequences matched the known genes in the 12 chromosomes found in cultivated tomatoes, and also identified thousands of sequences of new genes that are not found in modern types. Many of these novel DNA sequences are present in only one or other of the ancestral species.

"The new genome sequences for these ancestral tomatoes will be valuable for studying the evolution of this group of species and how the genetics changed during domestication," says corresponding author Professor Tohru Ariizumi. "In addition, the wild relatives contain thousands of genes not found in modern cultivated tomatoes. With this new information, researchers will be able to locate novel and useful genes that can be bred into tomatoes, and potentially other crops too. This will help plant breeders develop improved future types of tomato with features like better resistance to diseases, increased tolerance for the changing climate, and improved taste and shelf-life."

Some complementary data:
Other BTI faculty members who co-authored the paper include Carmen Catalá, who is also an adjunct assistant professor in SIPS, Gregory Martin, who is also a professor in SIPS, and Lukas Mueller, who is also an adjunct professor in SIPS. Susan Strickler, Director of the BTI Computational Biology Center (BCBC), also was a co-author.

The research was supported by the U.S. National Science Foundation (grants IOS-1855585, IOS-1339287 and IOS-1546625).

The team sequenced the LA2093 accession of S. pimpinellifolium using plant material provided by the C.M. Rick Tomato Genetics Resource Center at the University of California, Davis.

Sources: BTI (,,
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