Recent research from a North Carolina site of a global plant-development company revealed the tomato has at least 7,000 more genes than humans. And, decoding that genome could make picture-perfect, grocery-store tomatoes taste as good as deformed, homegrown ones.
Since 2008, researchers at Syngenta’s biotechnology hub in Research Triangle Park, along with other scientists worldwide, have analyzed the genetic sequence for two tomato varieties – Heinz 1706, the tomato used in ketchup production, and its closest wild relative, Solanum pimpinellifolium, found in Peru. These investigations revealed tomatoes boast 31,760 genes, many of which scientists are analyzing to determine how they control the fruit’s growth.
Why the tomato?
Although the genetic structures are different, tomatoes are closely related to potatoes, tobacco plants, peppers, eggplant and nightshade – a toxic member of the potato family. According to Rebecca Cade, a Syngenta research scientist, studying the tomato genome can increase the knowledge base around these and many other plants.
“The tomato is an excellent archetype for fruiting plants,” she said. “There’s been lots of research on how it grows, and scientists and breeders will be able to apply the knowledge gained from studying its DNA to other fruiting crops.”
Syngenta’s team has a multifocused goal with this research, looking for genetic answers to the tomato’s shelf-life, size and firmness. However, the company’s chief concern is helping farmers bring a better-tasting product to market.
“Once we have the finished genome sequence, we’ll be able to tell the differences between a beefsteak tomato and a cherry tomato,” Dietrich said. “With that information, we’ll be able to make a beefsteak with a cherry flavor or vice versa.”
Ultimately, Cade said, the goal is to allow breeders to do predictive breeding.
“In this scenario, someone would say, ‘I need a tomato with this maturity date, this sugar content, and resistant to this pathogen,’” she said. “By looking at our tomato genomes, you can take various seed lines, cross them, and get this type of desired outcome.”
Sequencing the code
According to Dietrich, efforts to decode the tomato genome began in 2009. The work was initially geared toward creating a rough draft of the genetic map that would eventually help breeders create more marketable versions of the fruit. In 2010, Syngenta and its partners teamed up to use different technologies that build upon each other’s strengths and weaknesses, he said.
Syngenta’s global collaborators sequenced 70 percent to 80 percent of the tomato’s DNA using technology that focused on longer reads – segments of DNA long enough to identify when gene components (the bases adenine, guanine, cytosine and thymine) begin to repeat. Scientists were able to identify significant differences among cultivated tomato lines with this amount of data.
But the gaps in the genome still left unanswered questions about which genes could control a plethora of tomato characteristics, he said. Using technology from the genetic-analysis company Illumina, Syngenta analyzed the final one-third of tomato genes using a technique that looks at smaller segments of DNA. In this case, Cade said, this short-read sequencing examined DNA strips with up to 800 bases.
“DNA sequencing is really like a puzzle – it takes a lot of work to make sense of it,” she said. “If you have short reads, you can have billions of pieces and maybe 1,000 of them look exactly the same. With longer-read technologies, you can have bigger pieces that show repeat and unique sequences. So, you need long reads to complement the short reads to get a full picture.”
This long/short sequencing technique is beneficial, Dietrich said, because it opens the door for other tomato varieties to be sequenced more easily. Researchers will now be able to analyze the DNA many other types of tomatoes in far less time and for less money.
While knowing which genes could improve the taste and appearance of tomatoes in the grocery store, understanding the fruit’s DNA and how to manipulate it could impact the global food supply, said Jim Giovannoni, Ph.D., plant geneticist at the Boyce Thompson Institute for Plant Research associated with Cornell University. The majority of Giovannoni’s work is also focused on decoding what part of the tomato genome is responsible for ripening.
Toward a ripe future
“Understanding and potentially controlling the ripening process genetically could increase food security for people in other countries who, at certain times, have a lot of food available but can’t eat it due to rot,” he said. “They don’t have the infrastructure and money to store food like we do, so a genetic solution could have a real effect on food security in the developing world. It would also make our First World issue of shipping food around a less expensive process.”
Specifically choosing certain traits that alter taste, color, texture, and ripening does present trade-offs, however, he said. For instance, a tomato bred to last longer on the shelves might not taste as good. Or one bred for a more home-grown flavor might not have a uniformly-colored skin.
“The reality is that, with this research, we understand more about what genes are responsible for what characteristics, and we can give breeders the tools for selecting certain traits,” Giovannoni said. “There can still be negative outcomes, no matter how small, but breeders can now take the selection of characteristics in their traditional breeding programs to a different level.”