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In ‘Nature': The science of a perfect strawberry

  • Garden-variety genetics:
    Garden-variety genetics:  William & Mary Assistant Professor of Biology Josh Puzey (right), undergraduate Scott Teresi (center) and grad student Ron Smith joined a team of researchers to complete the first chromosome-scale assembly of the strawberry genome. Their work, recently published in the journal "Nature Genetics," identifies a quirk in the genome that could fundamentally change how the fruit is bred.  Photo by Adrienne Berard
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The old-fashioned strawberry is having a renaissance thanks to new genetic research.

“I always hear, ‘Oh these strawberries today aren’t like the ones from my grandma’s garden,’” said William & Mary Assistant Professor of Biology Josh Puzey. “So we built a tool by sequencing its genome. Now we can drill down and understand how flavor is produced, how texture is produced, how size is produced. It will help us understand other crops, but one outcome would hopefully be that you could find strawberries in the store that actually taste like your grandmother’s strawberries.”

Puzey and two of his students joined a team of researchers to complete the first chromosome-scale assembly of the strawberry genome. The newly sequenced genome offers a window into global crop development and highlights the lesser-known power of “junk DNA” to influence gene expression.

Their work, recently published in the journal Nature Genetics, traces the origin of the North American strawberry and identifies a quirk in the genome that could fundamentally change how the fruit is bred. The other partner institutions include Michigan State University, University of California – Davis, University of Alabama, University of Arizona and the University of Nebraska. 

{{youtube:medium:left|ZYG7RzGNkVY, Junk DNA and the strawberry genome}}

The garden strawberry (Fragaria × ananassa) is extremely sensitive to weather and thrives only in certain climate conditions, Puzey explained. California is currently the world’s top strawberry producer, according to the U.S. Department of Agriculture. The state accounts for a third of the total global strawberry production, meaning the berries have to be bred to withstand world travel.

Selectively breeding for jetsetters comes at a cost to flavor and nutrition, Puzey explained. By sequencing the full strawberry genome, Puzey and the research team are a step closer to identifying the subset of the genome that accounts for other desired attributes like taste and smell. The findings could open the door to new breeding techniques that could select for both durability and flavor.

“Our analyses revealed that certain metabolic pathways, including those that give rise to strawberry flavor, color and aroma, are largely controlled by the dominant subgenome,” the paper states. “Thus, we anticipate that this new reference genome, combined with insights into subgenome dominance, will greatly accelerate molecular breeding efforts in the cultivated garden strawberry.”

It may sound simple, but it’s a long road to shortcake. Reproduction is a complex process for the cultivated garden strawberry. Depending on the individual strawberry, it either has a lot of parents or no parents at all. Some baby strawberries are the product of four different parental lineages, while others are just a clone of the same strawberry.

“Imagine if you could stick your arm out, put it in the ground and then chop it off and make another you,”Ron Smith said. “That’s essentially what it’s doing. The clone just an appendage of the first strawberry plant.”

For the strawberries created through breeding, traits are passed down from four parents. Geneticists call this phenomenon octoploid, when an organism has a complete set of homoeologous chromosomes from all four parents residing within a single nucleus. The strawberry Book of Genesis would feature not only Adam and Eve, but Barbara and Steve.

“Imagine you have Parent A,B,C and D,” Puzey said. “They all hybridize to produce an individual. Now, within that individual, all these parents each have their unique evolutionary trajectory and that entire history is within a single nucleus inside the larger genome of that one plant.”

Each of those parental lineages is called a subgenome, Puzey explained. Together, the four lineages hybridized to create the full Camarosa strawberry genome that we eat today. Puzey and the research team wanted to understand the individual attributes of each subgenome. Specifically, they were interested in which of the four parents was more dominant.

To solve that problem, they needed a numbers guy. Smith, a graduate student in Applied Science, fit the bill. He has a degree in mathematics from Farmingdale State College and, as part of his graduate work at William & Mary, he developed a statistical test to evaluate subgenome dominance.

“Let’s say I’ve got genes from multiple different lineages and I want to know what happens when I hybridize with another individual that has multiple lineages,” Smith said. “If we want to know what gene is dominant, there is a mathematical method for solving that problem. Any time you have a polyploid question, a question about which gene from which genome will win out, this method applies.”

With plants, as with people, certain traits are passed down to offspring through dominant genes. A baby born from a brown-eyed father and blue-eyed mother is much more likely to have brown eyes because the brown-eye gene is more dominant. The small piece of DNA that codes for brown eyes will more likely be activated, or expressed, in the baby’s genome and odds are the child will have brown eyes.

Strawberries carry the genomes of four different parents, which make up the offspring’s’ subgenomes. Puzey and his team found that one of the four parental genomes is more active and, therefore, more expressed than the other three. If humans had four parents like strawberries, our offspring would be more likely have the eye color of just one mother. That mother’s genome, in this hypothetical case, would be the dominant subgenome in the baby.

The dominant subgenome in the garden strawberry is called the F. vesca subgenome. The researchers found F. vesca has about 20 percent more protein-coding genes than the other three subgenomes. They also found F. vesca may control for disease resistance and other vital aspects of strawberry survival.  

“Once we made this discovery, the question became, how is a single genome more dominant over the other?” Puzey said. “What we find evidence for in this paper is these things called transposable elements, what people often refer to as junk DNA, actually has an impact on subgenome dominance in ways we didn’t previously anticipate.”

The researchers found that the F. vesca subgenome has about 20 percent fewer transposable elements – DNA that doesn’t functionally contribute to a gene product like a protein – than the strawberry’s other three subgenomes. That lack of transposable elements may be what makes F. vesca so dominant, Puzey explained.

“We found that this so-called ‘junk DNA’ might actually have a regulatory role in gene expression,” he said.

Understanding the real regulatory role of transposable elements requires a staggering amount of data analysis. Undergraduate Scott Teresi has spent much of his junior and senior year doing just that. He’s currently building a dataset detailing the types of transposable elements and their distance relative to every single gene in the strawberry genome. The code he’s writing to track “junk DNA” can be run on any genome.

“A transposable element, or transposon, is a mobile genetic element that can copy and move itself around the genome, for this reason they are sometimes referred to as jumping genes,” Teresi said. “Historically they’ve been thought of as parasitic genes because they were purported to have no function other than their own proliferation. Consequently, this has led them to contribute to significant portions of genome size. Your genome is riddled with them.”

Almost half of the human genome is made up of transposons, Teresi said. Corn’s genome is about 85 percent transposon. In fact, the multi-colored kernels of Indian corn are a direct result of transposons.

“The reason one kernel looks so different from the kernel next to it is because a transposon landed on or near the pigment gene and basically blew it up,” Teresi said.

Like corn, strawberries are polyploid. They contain the genomes of multiple parents, carrying more than two complete sets of chromosomes. The researchers believe that the connection they found between transposons and gene expression in strawberries may hold true for many other polyploids. The more transposons a subgenome has, the less likely gene expression is, so another subgenome will win out. 

“This is the type of finding we can’t really explain through classical genetics,” Teresi said. “We’re now in the realm of epigenetics, when there are changes to the accessibility of the DNA but not to the code itself. It’s exciting because this goes towards developing a new paradigm for the functions and consequences of transposable elements.”

If the team’s discovery can be put into practice, we’ll have strawberries that are colorful, durable and taste like they just came out of Grandma’s garden.