Wild tomato genome will benefit domesticated cousins
A team of researchers has assembled a reference genome for Solanum lycopersicoides, a wild relative of the cultivated tomato, and developed web-based tools to help plant researchers and breeders improve the crop.
Solanum lycopersicoides (S. lycopersicoides) harbors a gene that makes the plant resistant to a particular strain of bacterial spot disease. The gene could be introduced into cultivated tomatoes to protect them from the pathogen.
That discovery prompted researchers at the Boyce Thompson Institute to sequence the plant’s genome and create online resources to facilitate the discovery of more genes that could improve tomatoes.
“There wasn’t even really a discussion about whether or not to sequence Solanum lycopersicoides, it was just plain to do it,” said Susan Strickler, director of the BTI Computational Biology Center (BCBC). Strickler is co-corresponding author of the paper describing the S. lycopersicoides genome, which was published in The Plant Journal on May 18.
Wild crop relatives are becoming increasingly valuable to plant researchers and breeders. During the domestication process, crops tend to lose many genes, but wild relatives often retain genes that may be useful, such as genes that resist drought and disease.
In their study, the researchers demonstrated the value of the new genome by finding several candidate genes associated with compounds — phenols and carotenoids — that contribute to the species’ color, taste and nutrition, as well as other genes associated with disease resistance.
Perhaps more importantly, a larger goal of the project was to make the reference genome of S. lycopersicoides as widely accessible and useful as possible to the scientific community.
“This kind of data is being added to the National Center for Biotechnology Information repository as a common requirement, and that’s important, but not everyone is a bioinformatician or has access to bioinformatics resources to analyze the data,” said Adrian Powell, deputy director of BCBC and a lead author on the paper.
“To increase access and ease of genome exploration, we have developed web-based tools and components for researchers outside of our project team to use and add,” he said.
One resource is a S. lycopersicoides genome browser available on the Sol Genomics Network website, which serves as a community resource and repository for tomatoes and other species in the Solanaceae family. Powell said the browser could help early exploratory studies of the wild tomato variety, as well as more advanced studies.
Another tool is a S. lycopersicoides expression atlas, which allows users to analyze RNA sequencing data and visualize which genes are expressed in different plant tissues and under different conditions. “The atlas is based on code that was first developed for the cultivated tomato, but now we have a version for the wild varieties,” Powell said.
These tools, combined with the new reference genome, will help researchers analyze hybrids of the wild tomato and cultivated tomato more easily than before, and they will also help researchers who study the wild species for its own sake, he said.
For example, the reference genome could facilitate genome-wide association studies (GWAS) on multiple S. lycopersicoides entry, to assess the genetic diversity of the species and identify candidate genes for the traits that breeders would like to introduce into cultivated tomatoes, such as drought tolerance, Powell said.
Genome sequences for two wild tomato ancestors
Adrian F. Powell et al, A Solanum lycopersicoides reference genome facilitates insights into the specialized metabolism and immunity of tomatoes, The Plant Journal (2022). DOI: 10.1111/tpj.15770
Quote: Wild tomato genome benefits domesticated cousins (2022, June 28) retrieved June 29, 2022 from https://phys.org/news/2022-06-wild-tomato-genome-benefit-domesticated.html
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