Juan Zalapa is building a library. But it doesn’t house classic literature or thick textbooks. This one is all about cranberries. Zalapa’s construction materials aren’t what you would imagine either. Instead of wood for shelves, he’s using chromosomes; rather than paper for pages, he’s using genes. And the goal of the library will be to teach plant breeders and growers how to maximize the potential of this popular tart, red fruit.

Zalapa and his research team have become the first to sequence the cranberry genome. In other words, they have discovered the complete list and order of nucleotides in cranberry DNA — the blueprint of all the plant’s genetic material. The genomes of many crops, such as corn, have been known for some time. But fruit crops, such as cranberry, have lagged. Wisconsin produces more than half of the world’s cranberries, so improved breeding is important for the state’s agricultural livelihood. Sequencing the fruit’s genome is an important step toward producing redder, hardier, tastier cranberries.

The accomplishment took some time. Using a sophisticated machine in a lab, the team had to split the chromosomes into millions of shorter bits. Once those bits were sequenced, the researchers reassembled and organized them into the 12 complete chromosomes contained in the nuclei of cranberry cells. This is how Zalapa and his colleagues created a space for their cranberry library.

“Basically, the chromosomes are the bookshelves of our library,” says Zalapa, a professor of horticulture and U.S. Department of Agriculture scientist. “The first thing we had to do when setting up the library was to build those bookshelves, the scaffold that holds the information.”

Number Crunching

Wisconsin is the number one cranberry-producing state in the U.S. Its farmers are responsible for bringing in 59% of the nation’s crop. In 2020, they harvested 20,800 acres for a total of 4.64 million barrels and a production value of $178.7 million. No wonder cranberries are Wisconsin’s state fruit.

The scaffold was built through a strong collaboration with the Mexican government, and most of the work was done by Luis Diaz-Garcia PhD’18, a former student in Zalapa’s lab and now a scientist at the National Institute of Forestry, Agriculture and Livestock Research in Aguascalientes, Mexico.

In Mexico, producers and consumers are very interested in blueberries, a popular fruit. But few Mexican scientists study them, so the Mexican government supports students who study fruit crops abroad. Diaz-Garcia earned one of these prestigious scholarships to fund his cranberry research in the United States, which he calls the opportunity of a lifetime.

“I was very lucky to have Juan as a mentor,” Diaz-Garcia says. “He created a great collaborative environment within the lab and externally with growers and the industry. We were able to publish research articles that are now the foundation for more research.”

Those future projects will essentially stock the shelves in the cranberry library. The books will be the genes and traits associated with different areas of the chromosomes. And organizing and sharing those books will greatly benefit breeders as they look to improve cranberry and related fruits.

Traditional breeding involves the selection of better plants over time. Breeders may look for crops with higher yield, superior taste, or lower acidity, for instance. However, cranberries don’t grow fruit immediately: It can take five to six years to yield a crop. But if breeders can look up the location of certain traits on a chromosome and know which genes are linked to better fruit color, for example, they won’t have to wait for fruit to develop to select the best plants. Instead, they can sample the leaves of seedlings and keep just those plants that contain the gene or genes they want.

“In simple terms,” Diaz-Garcia explains, “a piece of a leaf can be used to predict if a cranberry fruit is going to be sweet or not, even before the plant produces fruit.”

This ability will greatly speed up breeding and allow growers to choose precisely what traits they want in their fruits. One of the characteristics they are most interested in is anthocyanin content. Anthocyanin is an important chemical for human nutrition, and it gives cranberries their color. Sometimes color doesn’t develop or develops at the wrong time; environmental cues can have a big impact on this process. An understanding of which genes affect how and when plants color, then, would be very useful for growers and breeders.

“What we’re looking for are plants that are consistent in their color development, despite the elements,” Zalapa says. “We can really try to understand how this color changes and hopefully put the right combinations of genes together to produce colors that are better for our growers here in Wisconsin and across the country.”

The cranberry genome is already available online. Genes and traits will be added to the site after they are uncovered, giving breeders and researchers access to the complete cranberry library.

“This work can lead to the development and release of better-tasting varieties with higher fruit quality characteristics and improved adaptation to environmental stresses,” Diaz-Garcia says. “All of that will be beneficial for the cranberry industry, growers, and consumers.”