Grape plant breeders are always striving to develop new varieties that satisfy growers, producers and consumers.

To do this, they use genetic markers to bring desirable traits from wild species into their cultivated cousins. But transferring those markers across species, though, has been difficult at best.

A team of grapevine breeders, geneticists and bioinformatic specialists at Cornell have come up with a powerful new method.

The team used new, automated DNA sequencing technology to create a “core genome” for grapevines, matching important regions shared between 10 species’ genomes. Using new rhAmpSeq genetic mapping technology, they targeted those regions to develop robust DNA markers. Of the 2,000 markers the team developed, 92% matched with four grape families spanning the diversity of the Vitus (grapevine) genus, including related species that diverged 20 million years ago.

Finding traits quicker

The team’s new technique for developing genetic markers improves markers’ transfer rate across grapevine species from 2% to 92%. With it, breeders can screen their collections and find out immediately what vines have the traits they want, regardless of what varieties they are, where they came from or what species their parents were.

“This new marker development strategy goes well beyond grapes,” says co-author Bruce Reisch, professor of horticulture in the College of Agriculture and Life Sciences and leader of Cornell’s Grapevine Breeding and Genetics Program. “It’s applicable for breeding and genetic studies across different grape breeding programs, plant species and other diverse organisms.”

Breeders bring desired traits from native species into cultivated ones by identifying DNA markers that point to trait-associated genes, selecting plants that carry them and then breeding across species.

But evolution has reshuffled the genetic deck to the point that markers developed using certain grapevine species don’t work with wild species or their hybrids.

It’s essential, though, that breeders have reliable markers for creating new varieties with improved flavor, weather- or disease-resistance, especially as climate change increases disease pressure and alters the growing range for many varieties.

The researchers have already applied these new markers to more than 22,000 grapevines, including those within the USDA’s national grapevine collection. The markers also map muscadine grapes, a subspecies native to the Southeast and a major source of disease-resistant gene.

Other grape species native to North America and Asia also are better adapted to varied climate and soil conditions, in addition to disease resistance.

New breeding opportunities

“This tool is much more powerful than we realized,” says co-author Lance Cadle-Davidson, adjunct professor in Cornell’s School of Integrative Plant Science and a research plant pathologist with the USDA’s Grape Genetics Research Unit in Geneva. “It opens up so many new opportunities to make connections where none existed before. Now, we’re all speaking the same language.”

The breakthrough is central to the mission of VitisGen2, the second iteration of a multi-institution research project from which the new marker development strategy emerged.

“This is game-changing work, and it’s only the beginning,” says Donnell Brown, president of the National Grape Research Alliance, an industry-led nonprofit. “From here, we can greatly accelerate the genetic exploration that will help us improve fruit and production quality and, ultimately, respond to the threats of pests and diseases, a changing climate, and more.”

Their research is detailed in “Haplotyping the Vitis Collinear Core Genome With rhAmpSeq Improves Marker Transferability in a Diverse Genus,” published Jan. 21 in Nature Communications.

This work was supported by grants from USDA and the National Science Foundation.

Thompson is a freelance writer for Cornell AgriTech.

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