Genetic markers fast-track breeding of seedless muscadine grapes

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Using new genetic markers, fruit breeders can now tell whether grapes will be seedless and self-pollinating even years before vines bear fruit. The approach will save time and resources in the pursuit of creating flavorful new grape varieties, including the major challenge of developing seedless muscadines on self-pollinating vines. A paper on this work appears in Journal of the American Society for Horticultural Sciences.

Margaret Worthington, associate professor of horticulture and director of the Fruit Breeding Program for the Arkansas Agricultural Experiment Station, joined colleagues at Cornell University, the U.S. Department of Agriculture, Gardens Alive! and E&J Gallo Winery in publishing the study validating a system for predicting flower sex type and seedlessness in muscadines and other grapes.

The study was conducted in association with the VitisGen3 Project and Vitis-x-Muscadinia. The researchers made their predictions using a genotyping platform that tests muscadine plant DNA for genetic markers—like signposts in the DNA pointing to specific traits.

The same genetic markers, which are publicly available, can also be used by wine and table grape breeders.

"This is a resource for the global breeding community," Worthington said.

The experiment station is the research arm of the University of Arkansas Division of Agriculture, and Worthington is also part of the Dale Bumpers College of Agricultural, Food and Life Sciences at the University of Arkansas.

Broadening the scope

Scientists discovered and published the genetic mutations causing seedlessness and male sterility in grapes a few years ago. In this new study, low-cost diagnostic markers targeting those mutations were developed and validated in more than 900 Vitis–Muscadinia hybrid grapes from the Arkansas Fruit Breeding Program and about 200 cultivated and wild grapes.

Isabella Vaughn, a graduate student in the department of horticulture, was the study's first author.

"She did a great job," Worthington said of Vaughn. "She scored a lot of plants, coordinated a lot of logistics and helped us to start using the markers in our program."

KASP, short for Kompetitive allele-specific PCR, is a proprietary but common and cost-effective genotyping platform used to detect specific genetic traits.

The researchers collected leaf samples from the plants, conducted the DNA testing, and then compared the predictions from the DNA testing with what was directly observed on the plants.

Worthington and her team correctly predicted flower sex and seedlessness with 100% and 99.7% accuracy, respectively.

"We took leaf samples from mature vines with fruit for the validation," Worthington explained. "The DNA will stay the same regardless of plant age. So, this is proof that it will work for young seedlings, too. We started culling seedlings in 2024 in our applied program and this will be our third year using the markers."

A century-long breeding quest

Over the past 100 years, fruit breeders have sought to create fertile crosses of muscadines—a native North American grape—with Vitis vinifera, the species behind most commercial table and wine grapes.

Muscadines are prized for their disease resistance, adaptability to the southeastern United States and distinctive flavors. Vitis vinifera offers superior fruit quality, consumer appeal, and seedlessness, Worthington said.

But combining the two has proven difficult. Chromosomal differences and compatibility barriers often prevent viable, fertile hybrids, Worthington explained.

"Muscadines are in a different subgenus of grape than Vitis. They're related, but not that closely related. It's like a horse and a donkey," she said.

Like horses and donkeys producing sterile mules, crosses between these grapes often result in infertile offspring.

Muscadines are not widely consumed outside of the U.S. South, but Worthington said seedlessness is key to expanding their appeal, especially for fresh markets and kids.

"What we really want is to make something that has a good size, a dry stem scar so that it can be easily picked, good post-harvest qualities and a really good texture, while keeping that muscadine flavor," Worthington said.

Despite the challenges in developing fertile, seedless muscadines, extensive traditional breeding efforts have paid off. In 2017, Jeff Bloodworth of Gardens Alive! developed the seedless RazzMatazz muscadine hybrid grape. That was followed in 2022 by Oh My!, another seedless muscadine variety that is also powdery-mildew resistant.

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Practice makes 'perfect'

Beyond seedlessness, Worthington also seeks "perfect-flowered" vines for growers to allow for self-pollination and more consistent fruit production.

Wild grape species, including muscadines, are typically dioecious, meaning individual vines produce either male or female flowers. Female flowers require pollen from a nearby male plant to produce fruit. In muscadines, the discovery of two perfect-flowered selections by chance in the mid-20th century provided the foundation for all perfect-flowered cultivars of muscadines grown today.

While crosses between perfect-flowered parents might seem an ideal map to get to that seedless, perfect-flowered muscadine, Worthington said they are not always practical in breeding programs. Muscadines have very small flowers, which makes removing the male parts from perfect-flowered plants and making controlled crosses extremely difficult, Worthington said. The preferred method, to avoid having to do a costly and difficult embryo rescue, is to make crosses between seeded females and seedless perfect-flowered vines.

"The ones we want to keep, we'll put out in the vineyard at the Fruit Research Station in Clarksville and then we'll look at those and see how it goes," Worthington said. "Not everything we keep is going to be good, but the markers tell us if it's perfect-flowered and if it is seedless. It doesn't tell us whether it tastes good and has a thin skin and is productive."

But, with roughly half as many plants needing to be grown out for field evaluation, Worthington will put more resources into the candidates and make more crosses.

More information

Isabella Vaughn et al, Diagnostic KASP Markers for Flower Sex and Stenospermocarpic Seedlessness in Diverse Vitis, Muscadinia, and Wide Hybrid Populations, Journal of the American Society for Horticultural Sciences (2026). DOI: 10.21273/jashs05580-25

Key concepts

sexing (plants & animals)genotype

Provided by University of Arkansas