Modern tomatoes are very different from their wild ancestors

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Modern tomatoes are very different from their wild ancestors and we find missing links in their evolution. Researchers have long thought that the tomato’s path from the wild plant to the household staple is much more complicated.

The Big Idea: Tomatoes’ path from wild plant to household staple is much more complicated than researchers long thought. For many years, scientists believed that humans domesticated the tomato in two main stages.

Modern tomatoes are very different

First, the natives of South America grew wild tomatoes the size of blueberries about 7,000 years ago to produce a plant with fruits the size of a cherry. Later, the people of Mesoamerica advanced this middle group to create the large-scale grown tomatoes that we eat today.

But in a recent study, we showed that the cherry-sized tomato originated in Ecuador about 80,000 years ago. No human group domesticated the plant long ago, so this means that it started out as a wild species, although Peru and Ecuador probably cultivated it later.

We also found that two subgroups of this intermediate group extended north into Central America and Mexico, possibly as vulnerable companions for other crops. As soon as this happened, the characteristics of its fruits changed radically. They began to look like wild plants, with smaller fruits and higher levels of citric acid and beta-carotene than their South American counterparts.

We were surprised to learn that modern cultivated tomatoes are most closely related to this group of wild tomatoes, which is still found in Mexico, although it is not intentionally grown by farmers. Average fruit size of a cultivated tomato compared to its semi-domesticated and totally wild relatives. Hamid Raziford, CC BY-ND

Why it Matters?

This research has a direct impact on crop improvement. For example, some intermediate groups of tomatoes contain high levels of glucose, which makes the fruit sweet. Breeders can use those plants to make grown tomatoes more attractive to consumers.

We also observed that some varieties in this intermediate group had traits that promote resistance to disease and tolerance to drought. Those plants can be used to grow hard tomatoes.

What is still unknown: We do not know how the intermediate group of tomatoes spread from South America to Central America and Mexico. Birds may have eaten the fruits and dumped the seeds elsewhere, or humans grew or traded them.

Fruit development and taste

Another question is why this intermediate group “bounced back” after spreading north and losing so many domesticated traits. Natural selection may have actively favored termites with more wild traits in the new northern habitats. It may also be that humans were not breeding these plants and were not selecting for domestication traits such as large fruits.

Which may require the plants to use more energy than they would naturally produce fruit. How we do our work: We reconstruct the history of the tomato by sequencing the genomes of wild, intermediate and domesticated tomato varieties. We also perform population genomic analyzes, in which we use models and data to extract changes in the tomato over time.

This job involves writing a large amount of computer code to analyze large amounts of data and look for patterns of variation in DNA sequences. We also work with other scientists to develop tomato samples and record data on a number of characteristics, such as fruit size, sugar content, acid content, and flavor compounds.

Plants to flower

What else is happening in the field? Crop yields and quality will need to be improved to feed a growing human population. To do this, scientists need to learn more about plant genes that are involved in events such as fruit development and taste, and resistance to disease.

For example, research led by Zachary Lippman at the Cold Spring Harbor Laboratory in New York is using genome editing to manipulate traits that could help improve tomato yield. Modifying native genes of two popular varieties of tomato plants. They have devised a faster way for plants to flower and produce ripe fruit more quickly.

This means more planting per growing season, which leads to an increase in yield. It also means that the plant can be grown at higher latitudes than is currently possible. For example, research led by Zachary Lippman at the Cold Spring Harbor Laboratory in New York is using genome editing to manipulate traits that could help improve tomato yield.

Modifying native genes of two popular varieties of tomato plants. They have devised a faster way for plants to flower and produce ripe fruit more quickly. This means more planting per growing season, which leads to an increase in yield. It also means that the plant can be grown at higher latitudes than is currently possible.

History of domestication

An important feature as Earth’s climate warms. What’s next for you? Our research provides an atlas of candidates for future studies of tomato genetic function. Now we can identify which genes were important at each stage in the history of domestication and find out what they do.

We can also discover beneficial alleles, or specific types of genes, that were lost or diminished by the domestication of the tomato. We want to find out if some of those missing types can be used to enhance growth and desirable traits in cultivated tomatoes.

Hamid Raziford is a postdoctoral researcher in biology at the University of Massachusetts Amherst. Ana Cassado is an associate professor of biology at the University of Massachusetts Amherst.

Disclosure statement: Hamid Raziford receives funding from the US National Science Foundation Ana Cassado receives funding from the US National Science Foundation (NSF) and the US National Institute of Food and Agriculture (NIFA).

Modern tomatoes are very different
Modern tomatoes are very different

The researchers looked at the genome sequence of the tomato’s wild ancestor. Scientists at the Boyce Thompson Institute have produced a high-quality chromosome-scale genome sequence for today’s tomato Solanum pimpinellifolium. The wild ancestor of the modern cultivated tomato Solanum licarsicum. Botanisc Tidschrift, Solanum pimpinellifolium in 1872.

Tomato is the world’s leading vegetable crop with a total production of 182 million tons and exceeded $ 60 billion in 2018. Solanum penicillifolium, bearing small, round, red fruits, he is a cultivator of wild ancestors. It was domesticated in South America to give rise to the variant Solanum lycopersicum.

Cerasiform. Which was later improved with the large-fruited tomato Solanum lycopersicum var. Lycopersicum in Mesoamerica. However, other groups had previously sequenced Solanum pimpinellifolium. The new reference genomes are more complete and accurate thanks to state-of-the-art sequencing techniques that can read very long DNA fragments and according to researchers from the Boyce Thompson Institute and Robert W. co-lead author Dr. Zhangjun Fei said.

Hawley Center for Agriculture and Health at the US Department of Agricultural Research Services. Older sequencing techniques that read small pieces of DNA can identify mutations at the single base level, said postdoctoral scientist Dr. Doyce of the Boyce Thompson Institute. Shan Wu said. But they are not good at finding structural differences.

Such as insertions, deletions, inversions or duplications of large parts of the DNA. Many of the known traits of tomatoes are caused by structural adaptations. So we have focused on them, said Dr. Fei. Structural adaptations are also understood because they are more difficult to identify. The scientists found their reference Solanum pimpinellifolium genome compared to cultivated tomatoes, known as Heinz 1706.

Researcher from the Boyce Thompson Institute

And more than 92,000 structural genetic variants. They then battled the tomato pangenome, a database of more than 725 closely related wild tomato genomes and genomes, and discovered structural variants related to several important traits. For example, modern cultivated tomatoes have some genomic deletions that reduce their levels of lycopene.

A red pigment with nutritional value, and an insert that reduces their sucrose content. A co-author researcher from the Boyce Thompson Institute and Robert W. Drs. Jim Giovannoni said: The identification of additional genetic diversity captured in the Solanum pimpinellifolium genome provides opportunities to recover some of these important characteristics from store-bought tomatoes.

Holly Center for Agriculture and Health at the Agricultural Research Service of the United States Department of Agriculture. The authors found a number of other structural variants that may be of interest in many disease-resistant genes to include variants involved in variants and fruit shape, ripening, hormonal regulation, metabolism, and flower, seed, and leaf development.

They also found structural motifs associated with the regulation of the expression of genes involved in lipid biosynthesis in the skin of the fruit, which may help improve the subsequent yield of the fruit. “Dr. Fei said,” A lot of genetic diversity was lost during tomato domestication. These figures can help bring back some of the tomato variety and result in tomatoes taste better, more nutritious and more flexible.

The results appear in the journal Nature Communications. The tomato is a genomic reservoir for responding wild plant breeders. Thousands of years ago, people in South America began to domesticate Solanum pimpinellifolium, a vegetable plant with a small, intense flavor. 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.

Cornell University

They are less resistant to disease and environmental stresses, such as drought and saline soils. Researchers at the Boys Thompson Institute, led by Zhangjun Fei, created a high-quality reference genome for S. pimpinellifolium and discovered parts of the genome that reduce fruit taste, size and ripening, stress tolerance, and resistance to The diseases. The results are published in Nature Communications.

For example, Fei said, “This reference will allow genome researchers and plant breeders to improve traits such as fruit quality and stress tolerance in tomatoes.” Pimpelinlifolium yes. It faded over time in the form of Lycopersicum. Fei is a member of the BTI faculty and a related co-author on the paper, as well as an assistant professor in the School of Integrative Plant Science (SIPS) at Cornell University.

Although other groups earlier in the s. Pimpinellifolium was sequenced, Fei said, adding that the reference genome is more complete and accurate, thanks to some of the cutting-edge sequencing technologies that are capable of reading very long pieces of DNA. Older sequencing techniques that read small pieces of DNA can identify mutations at the single base level, said Shen Wu, Fei in the paper and a co-author in the lab.

But they are not good at finding structural adaptations such as insertion, deletion, inversion, or duplication of large parts of DNA. Many known traits of tomatoes are caused by structural adaptations, so we focus on them, Fei said. Structural adaptations are also understood because they are more difficult to identify. Fei’s group compared their reference S. pimpinellifolium genome to cultivated tomatoes, called Heinz 1706, and found more than 92,000 structural variants.

The researchers then searched the tomato pangenome, a database with a genome of more than 725 genomes, and related wild tomatoes, and discovered structural variants related to several important traits. For example, modern cultivated tomatoes have some genomic deletions that reduce their levels of lycopene, a red pigment with nutritional value, and an insert that reduces their sucrose content.

Jim Giovannoni, a BTI faculty member and study co-author, notes that many consumers are disappointed in the quality and taste of modern-grown tomatoes because past breeding efforts ignored those traits in favor of yield and yield. The identification of additional genetic diversity captured in the S. pimpinellifolium genome gives breeders the opportunity to return some of these important characteristics to Stor-Tomato, said Giovannoni and assistant professor at SIPS and also an American scientist.

CM Rick Tomato’s Center

Agricultural Research Service of the Department of Agriculture. The researchers found several other structural variants that may be of interest to grower and including variants in several disease resistance genes and genes involved in fruit size, ripening, hormonal regulation, metabolism, and flower development. seeds and leaves?

The group also found structural motifs associated with the regulation of the expression of genes involved in lipid biosynthesis in the skin of the fruit, which may help improve the subsequent yield of the fruit. Such a wide variety was lost during tomato domestication, Fei said.

These numbers can help bring in some diversity and can result in tomatoes being better, more nutritious and hardier. Reissued courtesy of the Boyce Thompson Institute. The fruits of Solanum pimpinellifolium, the wild ancestor of modern cultivated tomatoes, are about the size of blueberries. Credit: Scott Peacock and CM Rick Tomato’s Center for Genetic Resources.

The researchers looked at the genome sequence of the tomato’s wild ancestor. Scientists at the Boyce Thompson Institute have produced a high-quality chromosome-scale genome sequence for today’s tomato Solanum pimpinellifolium. The wild ancestor of the modern cultivated tomato Solanum licarsicum. Botanisc Tidschrift, Solanum pimpinellifolium in 1872. Tomato is the world’s leading vegetable crop with a total production of 182 million tons and exceeded $ 60 billion in 2018.

Solanum penicillifolium, bearing small, round, red fruits, he is a cultivator of wild ancestors. Tomatoes. It was domesticated in South America to give rise to the variant Solanum lycopersicum. Cerasiform, which was later improved with the large-fruited tomato Solanum lycopersicum var. Lycopersicum in Mesoamerica. However, other groups had previously sequenced Solanum pimpinellifolium.

The new reference genomes are more complete and accurate thanks to state-of-the-art sequencing techniques that can read very long DNA fragments. According to researchers from the Boyce Thompson Institute and Robert W. co-lead author Dr. Zhangjun Fei said. Hawley Center for Agriculture and Health at the US Department of Agricultural Research Services.

“Older sequencing techniques that read small pieces of DNA can identify mutations at the single base level,” said postdoctoral scientist Dr. Doyce of the Boyce Thompson Institute. Shan Wu said. But they are not good at finding structural differences, such as insertions, deletions, inversions or duplications of large parts of the DNA. Many of the known traits of tomatoes are caused by structural adaptations.

So we have focused on them, said Dr. Fei. Structural adaptations are also understood because they are more difficult to identify. The scientists found their reference Solanum pimpinellifolium genome compared to cultivated tomatoes, known as Heinz 1706, and more than 92,000 structural genetic variants.

They then battled the tomato pangenome, a database of more than 725 closely related wild tomato genomes and genomes, and discovered structural variants related to several important traits. For example, modern cultivated tomatoes have some genomic deletions that reduce their levels of lycopene, a red pigment with nutritional value, and an insert that reduces their sucrose content.

A co-author researcher from the Boyce Thompson Institute and Robert W. Drs. Jim Giovannoni said: The identification of additional genetic diversity captured in the Solanum pimpinellifolium genome provides opportunities to recover some of these important characteristics from store-bought tomatoes.

Holly Center for Agriculture and Health at the Agricultural Research Service of the United States Department of Agriculture. The authors found a number of other structural variants that may be of interest in many disease-resistant genes to include variants involved in variants and fruit shape, ripening, hormonal regulation, metabolism, and flower, seed, and leaf development.

They also found structural motifs associated with the regulation of the expression of genes involved in lipid biosynthesis in the skin of the fruit, which may help improve the subsequent yield of the fruit. Dr. Fei said. A lot of genetic diversity was lost during tomato domestication.

These figures can help bring back some of the tomato variety and result in tomatoes taste better, more nutritious and more flexible. The results appear in the journal Nature Communications. The tomato is a genomic reservoir for responding wild plant breeders. Thousands of years ago, people in South America began to domesticate Solanum pimpinellifolium.

A vegetable plant with a small, intense flavor. 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 less resistant to disease and environmental stresses, such as drought and saline soils.

Researchers at the Boys Thompson Institute, led by Zhangjun Fei, created a high-quality reference genome for S. pimpinellifolium and discovered parts of the genome that reduce fruit taste, size and ripening, stress tolerance, and resistance to The diseases. The results are published in Nature Communications.

For example, Fei said, “This reference will allow genome researchers and plant breeders to improve traits such as fruit quality and stress tolerance in tomatoes.” Pimpelinlifolium yes. It faded over time in the form of Lycopersicum. Fei is a member of the BTI faculty and a related co-author on the paper, as well as an assistant professor in the School of Integrative Plant Science (SIPS) at Cornell University.

Although other groups earlier in the s. Pimpinellifolium was sequenced, Fei said, adding that the reference genome is more complete and accurate, thanks to some of the cutting-edge sequencing technologies that are capable of reading very long pieces of DNA.

92,000 structural variants

Older sequencing techniques that read small pieces of DNA can identify mutations at the single base level, said Shen Wu, Fei in the paper and a co-author in the lab. But they are not good at finding structural adaptations such as insertion, deletion, inversion, or duplication of large parts of DNA.

Many known traits of tomatoes are caused by structural adaptations, so we focus on them, Fei said. “Structural adaptations are also understood because they are more difficult to identify. Fei’s group compared their reference S. pimpinellifolium genome to cultivated tomatoes, called Heinz 1706, and found more than 92,000 structural variants.

The researchers then searched the tomato pangenome, a database with a genome of more than 725 genomes, and related wild tomatoes, and discovered structural variants related to several important traits. For example, modern cultivated tomatoes have some genomic deletions that reduce their levels of lycopene.

A red pigment with nutritional value, and an insert that reduces their sucrose content. Jim Giovannoni, a BTI faculty member and study co-author, notes that many consumers are disappointed in the quality and taste of modern-grown tomatoes because past breeding efforts ignored those traits in favor of yield and yield.

The identification of additional genetic diversity captured in the S. pimpinellifolium genome gives breeders the opportunity to return some of these important characteristics to Stor-Tomato, said Giovannoni and assistant professor at SIPS and also an American scientist.

Agricultural Research Service of the Department of Agriculture. The researchers found several other structural variants that may be of interest to growers and including variants in several disease resistance genes and genes involved in fruit size, ripening, hormonal regulation, metabolism, and flower development.

Seeds and leaves?

The group also found structural motifs associated with the regulation of the expression of genes involved in lipid biosynthesis in the skin of the fruit, which may help improve the subsequent yield of the fruit. Such a wide variety was lost during tomato domestication, Fei said.

These numbers can help bring in some diversity and can result in tomatoes being better, more nutritious and hardier. Reissued courtesy of the Boyce Thompson Institute. The fruits of Solanum pimpinellifolium, the wild ancestor of modern cultivated tomatoes, are about the size of blueberries. Credit: Scott Peacock and CM Rick Tomato’s Center for Genetic Resources.

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