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Consumers want great tasting fruit with few or no blemishes. Growers want that, too, but they also need fruit trees to be easier to grow and, specifically, to be resistant to diseases that can decimate an orchard.

A national team of scientists aims to tie those goals together by applying modern genomics to deliver new cultivars that carry both the disease resistance desired by producers and the horticultural qualities demanded by the marketplace.

It is no simple task, but researchers have some success with which to build upon their efforts: The RosBREED project enabled researchers to develop the infrastructure to conduct DNA-informed breeding to improve the efficiency of the breeding process.

By using molecular markers, researchers are able to identify and keep plants that contain multiple desirable traits — a process called gene pyramiding — and discard those that don’t.

From that project, researchers now have access to genetic markers for some ideal horticultural traits, such as fruit color or crispness, and are using these DNA markers to select for those traits early in the breeding process.

The next generation of the project, called RosBREED 2, goes a step further by combining those efforts with new research to increase the efficiency of breeding new cultivars that have excellent horticultural traits and disease resistance.

Two years into the five-year project, many of the researchers have finished phenotyping, which means they’ve established which trees are disease resistant in their respective research blocks for different crops.

The tart cherry breeding selection, left, exhibiting the sweet cherry derived tolerance to cherry leaf spot, right, at Michigan State University's Botany Farm, East Lansing, Michigan pm July 24, 2015. This orchard was not sprayed for cherry leaf spot in 2015. <b>(Courtesy Kristen Andersen)</b>

The tart cherry breeding selection, left, exhibiting the sweet cherry derived tolerance to cherry leaf spot, right, at Michigan State University’s Botany Farm, East Lansing, Michigan pm July 24, 2015. This orchard was not sprayed for cherry leaf spot in 2015. (Courtesy Kristen Andersen)

The next step is to gather genetic data from those plants and use this information to locate the positions of the genes responsible for the disease resistances on the plant’s chromosomes.

“The goal is to, in future generations, use DNA information to choose parents more effectively and choose seedlings more effectively,” said Amy Iezzoni, cherry breeder for Michigan State University and the project’s co-leader. “And ultimately, to choose seedlings that are resistant for not just one disease but two.”

Pyramiding disease resistance is most efficiently done using DNA markers, Iezzoni said. “Many times you can’t subject the same seedlings to multiple diseases.

Then if it is a fruit disease you are breeding for, with DNA markers you don’t have to wait for the seedling to flower and fruit to know whether it is disease resistant. Using DNA information to predict its phenotype is the next step.”

RosBREED history

A $14 million grant from the Specialty Crop Research Initiative created the first RosBREED project, which involved nearly three dozen scientists from 14 U.S. institutions to focus on five crops: apple, peach, strawberry, sweet cherry and tart cherry.

RosBREED 2 has been expanded to include blackberry, pear, rose and prunus rootstock, as well as the efforts of a team of plant pathologists to help research diseases. As with the first project, information gleaned from individual projects will be shared across crops.

Jim McFerson, director of Washington State University’s Tree Fruit Research and Extension Center, said the standardized approach allows researchers for each crop to benefit from the synergies in their research techniques.

“We really have had to build a network in the national and international community so that our growers are benefiting from the antennae that are out in the world trying to get information and translate it to something meaningful,” he said. “Breeding takes forever, but we’re making rapid progress because of RosBREED. We’re not all trying to build our own disease factory and breeding program. We’re sharing a lot of information.”

In the future, once DNA markers associated with disease resistance are identified, people in the field will be able to screen seedlings for disease by conducting a DNA test rather than by challenging the plant to the disease to determine if it carries resistant traits, said Jay Norelli, a plant pathologist at the U.S. Department of Agriculture’s research station in Kearneysville, West Virginia.

“We won’t rely on the DNA tests 100 percent in the end, but the big cost in the breeding program is growing material out in the field,” he said. “This way, we can start out with a much, much larger number of seedlings, screen them by DNA tests, and then have fairly good confidence that the plant materials we’re taking out in the field and spending the money on are going to have the traits we want.”

Practical applications

The genomic information gained from the RosBREED project is already being used to enhance breeding efforts for targeted crops across the country.

Breeders now routinely use genetic testing to verify parentage — some programs have even discarded individuals in their programs after these tools showed unintended parentage.

Parents are being selected using genetic tests in RosBREED breeding programs, for such things as fruit texture, firmness and size, storability, acidity and color, and some programs are already using genetic tests to cull seedlings.

Researchers are trying the same approach to identify tolerance to 16 diseases in seven different crops, as well as prunus rootstock.

Among them: Erwinia amylovora (fire blight) in apple and pear, Podosphaera clandestina (powdery mildew) in sweet cherry and Blumeriella jaapii (leaf spot) in tart cherry.

Iezzoni, who is leading tart cherry research, noted that while most tart cherries are highly susceptible to leaf spot, sweet cherries are tolerant. The fungus still enters the leaves of sweet cherry; however, the leaves simply do not yellow or fall off the tree as quickly.

“There definitely is, in this genetic background, a cherry leaf spot tolerance, and the plant can continue photosynthesizing. It’s just been remarkable,” she said.

She said she altered her breeding strategy this year to include the gleaned information.

Ultimately, cultivars resistant to cherry leaf spot could translate to fewer sprays for a grower and less of a negative impact if they miss a spray for some reason.

“Sometimes, this disease is not very forgiving if you miss a spray as the fungus gets well established in the tree,” she said. “And this impact from disease resistant cultivars could be repeated again and again thanks to help from RosBREED.”

RosBREED has provided breeders a new path forward to make breeding more effective and efficient, she said. “We’ve learned about genetics, how to make changes in how we’re breeding, and we’re making progress that we would not have made without the grant.”

The results achieved already are proving the project very worthwhile, said Bill Dodd, an Ohio peach and apple grower and president of the Ohio Fruit Growers Marketing Association who serves on the RosBREED industry advisory panel.

“I look at it from the big picture. We’re headed down this highway, and our destination is better apples. We’re making better stops along the way and gathering data along the way and gathering tools along the way, and from an overall view, it’s doing what it’s intended to do,” he said. “The work they’re doing is incredibly exciting.” •

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– by Shannon Dininny