Tomato's wild ancestor is a genomic reservoir for plant breeders
Humans turned a weedy plant with tiny fruit into the tomato that we know today. That wild ancestor could lead to tomatoes that taste better, are more nutritious and more resilient.
IMAGE: THE FRUITS OF SOLANUM PIMPINELLIFOLIUM, THE WILD ANCESTOR OF MODERN CULTIVATED TOMATOES, ARE ABOUT THE SIZE OF BLUEBERRIES. view more
CREDIT: SCOTT PEACOCK AND THE C.M. RICK TOMATO GENETICS RESOURCE CENTER.
ITHACA, NY, December 1, 2020 -- 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 on November 16.
"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 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.
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 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."
CAPTION
The fruits of Solanum pimpinellifolium, the wild ancestor of modern cultivated tomatoes, are about the size of blueberries.
CREDIT
Scott Peacock and the C.M. Rick Tomato Genetics Resource Center.
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 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.
About Boyce Thompson Institute:
Boyce Thompson Institute is a premier life sciences research institution located in Ithaca, New York. BTI scientists conduct investigations into fundamental plant and life sciences research with the goals of increasing food security, improving environmental sustainability in agriculture, and making basic discoveries that will enhance human health. Throughout this work, BTI is committed to inspiring and educating students and to providing advanced training for the next generation of scientists. BTI is an independent nonprofit research institute that is also affiliated with Cornell University. For more information, please visit BTIscience.org
Tweaking carotenoid genes helps
tomatoes bring their a-game
A research team led by the University of Tsukuba shows that modern gene editing techniques can help tomato breeders introduce diversity and improve the nutrition and environmental impact of tomato crops
IMAGE: TOMATOES USED IN THE EXPERIMENT view more
CREDIT: UNIVERSITY OF TSUKUBA
Tsukuba, Japan - Cooked, fresh, sun-dried, or juiced, whichever way you prefer them, tomatoes are arguably one of the most versatile fruits on the planet--and yes, despite mainly being used in savory dishes, tomatoes really are a fruit.
The popularity of tomatoes has led to the development of more than 10,000 cultivars of various sizes, shapes, and hues. Interestingly though, there is little genetic diversity among modern tomato varieties. This lack of diversity, coupled with the fact that many traits are controlled by multiple genes, makes improving plant yield and quality a major challenge for tomato breeders.
But in a study published this week in Scientific Reports, researchers led by the University of Tsukuba explain how modern gene editing technology may be able to give tomato breeders a helping hand.
"The tomato was the first genetically modified food to be approved for human consumption," says senior author of the study Professor Hiroshi Ezura. "However, many early transgenic varieties contained genes derived from other species, raising safety concerns among consumers. Therefore, coupled with the fact that most transgenic varieties showed only moderate improvements in quality, tomato breeding has, for the most part, moved away from transgenics."
Unlike traditional genetic modification, modern gene editing techniques leave no trace in the genome and can introduce small changes within a native gene, mimicking natural variation.
Tomatoes contain relatively high levels of carotenoids, the yellow, red, and orange pigments found in many plants. Carotenoids are precursors to vitamin A and demonstrate antioxidant and anti-cancer properties, making them hugely important to human nutrition. Several natural mutations that enhance carotenoid accumulation in tomatoes have been documented, but their introduction into commercial varieties is a complicated and time-consuming prospect.
The University of Tsukuba-led team therefore set about reproducing carotenoid accumulation mutations in tomatoes using gene editing technology.
"Single nucleotide changes in individual tomato genes had previously been achieved using Target-AID gene editing technology," explains Professor Ezura. "However, we designed a system whereby changes were simultaneously introduced into three genes associated with carotenoid accumulation."
Among 12 resulting tomato lines, 10 contained mutations in all three target genes. Further examination of two lines with the dark green fruit and purple roots of natural carotenoid accumulation mutants revealed high levels of carotenoids, particularly lycopene, in the gene-edited plants.
Professor Ezura explains, "This shows that it is possible to improve multigenic plant quality traits using gene editing technology, and opens up a whole range of options for improving the yield, shelf-life, nutrient content, and disease resistance of different crop plants, which has obvious benefits for both human health and the environment."
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