Nestled in the fertile floodplains of the Skagit Valley is a raspberry field like no other. Some 270 different varieties of the fruit fill the plot operated out of Washington State University’s Mount Vernon Research and Extension Center, but these berries are not destined for market.
It’s a type of research field called a diversity panel, and it may help catapult Washington’s raspberry breeding into the age of genomics.
Northwest Washington is the raspberry capital of the state. In 2023, Whatcom County produced 58,614,626 pounds of raspberries — that’s 99.3% of the state’s entire production. It also leads the nation in frozen raspberries, a result of the grown varieties’ unique ability to be machine harvested en masse. To maintain that status, however, Washington raspberry growers must wage an unceasing war against disease and pests.
Particularly insidious are nematodes: microscopic worms that live in soil and feed voraciously on the roots of raspberry plants. Over time, this root feeding can leave plants sickly, decrease fruit quality and put a severe dent in production. While some pesticides can treat nematode infestations, the most effective ones render the fruit unsafe to eat.
Breeding raspberry plants with natural nematode resistance or tolerance* can lessen the need for harsh chemicals, but creating a variety that has both resistance and the right set of traits for commercial production can take decades with traditional methods. That’s where genetics research can help.
Savannah Phipps, a plant pathology Ph.D. student at Oregon State University, is one of the researchers using the diversity panel of 270 different varieties of raspberry and raspberry relatives. Phipps’ will explore the diverse array to find genes associated with natural nematode resistance, shortening the breeding timeframe significantly.
“There were like four [people] back in the ’70s, early ’80s that looked into it, but no one’s looked into it again since,” Phipps said. “But the [genetic] technology that we had then versus the technology we have now … it’s progressed wildly.”
By planting many varieties of raspberry together, infecting them with nematodes, then measuring the amount of damage caused, Phipps hopes to first grade each varieties’ resistance (less damage equals more resistance).
Next, Phipps will sequence the DNA of each variety. The DNA sequence of each differs slightly, almost like a fingerprint. The key behind the diversity panel is to see which of those tiny genetic differences are always found in plants with nematode resistance, because they likely correspond to resistance genes that can be passed down to offspring via conventional breeding.
Once they know what parts of the genetic “fingerprint” confer resistance, all breeders have to do is check a given plant for those particular sequences of DNA to see if it has natural protection against nematodes.
Wendy Hoashi-Erhardt, director of the small fruit breeding program at WSU, said it’s a major step up from traditional methods which require vast numbers of seedlings to be grown to maturity and tested manually for resistance.
“If we can throw out the [seedlings] that we know are not going to have the qualities we want and not need to grow them up in the field, that saves us a lot of money and can make our breeding both more time and cost efficient,” Hoashi-Erhardt said.
The best part about the diversity panel, Hoashi-Erhardt added, is that it can be used to explore the genetics behind other traits beyond just nematode resistance. In the future, the same method could be used to improve disease resistance, fruit quality and even berry yield.
Phipps said it’s an exciting step forward for a fruit that’s lagged behind larger crops such as grains and apples in genetics research.
“Most of our raspberry production is targeted in very specific regions of the U.S., and as a result there’s not as much money as other crops like wheat, soybean or even apple bring in,” Phipps explained. “[You] have to accumulate not only the financial resources but also the brains behind being able to look at that genetic data.”
While genetic methods can speed up breeding, they can’t work miracles. For example, Phipps said not every trait can be improved using the diversity panel, especially highly complex ones like machine harvestability that are likely influenced by lots of different genes. It also can’t replace traditional breeding: even if the researchers find a variety with nematode resistance, they still will likely need to breed in other desirable traits from commercial varieties using old-fashioned crosses.
Even so, Hoashi-Erhardt, Phipps and the others on their team remain optimistic their work will end with better berries for a region where raspberries are king.
“We’re super excited to see the diversity in this planting,” Hoashi-Erhardt said. “The opportunity to further our genetic resources of this crop for all these breeders is really exciting.”
*Author’s note: Resistance and tolerance are technically different concepts when talking about nematodes, although we use “resistance” in this article to refer to both. Resistance is how well nematodes can feed/reproduce on a plant, while tolerance is measured by how severely nematodes affect a plant’s growth. The researchers are using the diversity panel to investigate both traits.
Ben Long is an environmental/science reporter, placed at CDN through the American Association for the Advancement of Science (AAAS) Mass Media Fellowship. Reach him at benlong@cascadiadaily.com.
