Program Uses Genetics to Bolster Grape Breeding

Program Uses Genetics to Bolster Grape Breeding

Bruce Reisch collects leaf samples for DNA extraction at the New York State Agricultural Experiment Station in Geneva, NY. (Photo: Cornell University Communication Services)

Powdery mildew, downy mildew, and black rot disease are all issues that plague the modern raisin, table, or winegrape grower and are exactly the issues the VitisGen and VitisGen2 projects seek to find solutions for.

In fact, this multi-university project has made leaps and bounds in the first iteration, learning about grape genetics and markers. The project was recently renewed with a $6.5 million USDA National Institute of Food and Agriculture Specialty Crop Research Initiative grant.

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“The industry came to us [at the start of VitisGen] and said there were three major needs: cold-hardiness we were hearing especially from the Eastern parts of the industry, fruit and wine quality, and powdery mildew resistance,” says Bruce Reisch, Professor of Grapevine Breeding and Genetics at Cornell University.

Reisch co-leads the VitisGen2 project with Lance Cadle-Davidson, Plant Pathologist at the USDA-ARS Grape Genetics Research Unit. He says the biggest accomplishment of the first VitisGen project was to develop new DNA marker-trait associations. He says the research team relates a section of DNA with a gene that controls a particular trait either desirable or undesirable.

Early Assessment
Because the VitisGen team is looking at a lot of wild grape strains to help boost powdery mildew and downy mildew resistance, as well as Eastern growers’ desire for cold hardiness, using these marker-trait selections help to assess the new crosses.

“There are some things we can do just by checking the DNA to see if it carries the trait of interest,” he says. “We’re quickly coming to the point where we are able to meet some of our grape breeding objectives very early on, before growing our vines in the field and three or four years before we get fruit, making wine four or five years later.”

Reisch says originally the research team hoped to make around 30 marker-trait associations. Within the first VitisGen project, researchers were able to identify 75.

“We exceeded our goal,” he says. “We discovered new genes for PM resistance, for downy mildew resistance, botrytis bunch rot resistance, and leaf phylloxera resistance.”

The team sends leaf tissue samples from thousands of seedlings to a centralized facility, where the DNA is extracted and analyzed.

“By doing this in quantity, the postdocs on the project analyze the data, and then we use that data to decide which seedlings to keep and which ones to discard,” he says.

Implementation
VitisGen2 will focus on fruit/wine quality and powdery mildew resistance. Reisch says the next steps within the VitisGen2 project are to implement the marker-selected traits in the breeding program with those traits in mind. He’s also hoping to implement a new technology that was a part of the first VitisGen — but came along toward the end of the first project — called AmpSeq.

This low-cost genotyping uses amplicon sequencing to pinpoint genetic variations for marker-trait associations. AmpSeq sequences a large quantity of DNA markers simultaneously. The low cost and speed of AmpSeq will help address some of the barriers to marker-trait assessments of current technology.

With the help of AmpSeq, Reisch hopes to be able to screen several wild species that have traits for cold hardiness and downy mildew, anthracnose, and/or black rot disease resistance at once so that breeders can select and breed at a much faster pace.

“We have the ability in months to put together new genomes, at much, much lower costs,” he says. “Some steps are evolutionary; some steps are revolutionary. I’d put that in the revolutionary.”

Learning about Wine Quality
Reisch says hybrid grapes — which often are more cold-hardy — have low tannins in red wines. So the VitisGen research team determined which factors caused reduced wine tannins in hybrid.

This research was led by Gavin Sacks, Associate Professor in the Cornell University Department of Food Science, and is ongoing as Sacks maps the genetics to control tannins in red winegrapes.

Sacks’ team also used genetic information from apple studies to identify acidity in wild and hybrid grapes, which will also help boost breeding for more palate-pleasing varieties.

“There was a lot of progress [in the first VitisGen] in understanding the control over tannin production in hybrid grapes,” Reisch says. “Hybrids have a problem with low tannins in the red wines, and we’d like to be able to develop Eastern varieties with much higher tannins that would make the production of wine with hybrid grapes possible.”

The Future of the Program
Also within the VitisGen and VitisGen2 programs is a trait-economics component, which helps the research team understand the value these traits would have in the industry. The team assesses what consumers would be willing to pay for desirable table grape traits such as flavor, texture, berry shape and size, and thin skins, in order to help guide the breeding decisions.

The trait-economics group did studies in California to assess what type of savings certain traits might result for growers and Reisch says savings would be seen in materials, applications, etc. He says disease-resistant winegrape varieties may be a solution to Pierce’s disease. However, the challenges to introducing a new winegrape variety in an industry which favors single-varietal wines is a little bit more of a challenge.

“Adopting replacement varieties for ‘Chardonnay’ and ‘Merlot’ — that may take a little more time because the market really wants its ‘Chardonnay ‘and ‘Merlot,’ even though those are susceptible to disease, to have to be sprayed so many times per year,” he says.

But Reisch points to European winegrapes as a future path for disease-resistant hybrids.

“In Italy, France, Germany, Hungary, Spain, and other countries, [growers have] been planting resistant hybrids,” he says. “I don’t think it’ll be long before we see more adoption in California. Certainly, the adoption of table and raisin grapes will likely lead the way.”

For now, VitisGen2 is field testing some of the varieties developed that have some of the marker-selected traits and is learning more and more about market preference.

“These new markers will help us be a lot more efficient about the entire process, but they don’t shave large number of years off the project,” he says. “When a grower makes the decision to plant a newly named variety, they want to know that you have years full of experience. The grower is investing thousands of dollars in a new variety, in a new planting. We need a number of years of field data to show the growers that these new varieties are field-tested and field-proven.”