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DNA of the Vine

By Rebekah L. Fraser


Picture this: You're in the vineyard, staring at damaged leaf tissue and fruit that should have ripened by now but hasn't. You wonder whether you'll have a viable crop this year. You apply sulfur, but a week later you're in the vineyard again staring at cracked, rotting fruit with a funky odor that would surely destroy your wine if you tried to salvage your harvest. You didn't catch the disease in time to save your crop. What you're seeing and smelling are the effects of the world's number one fungal disease threat in viticulture: powdery mildew.


We can identify genes of interest before we even send a seedling out to the field.
PHOTO COURTESY OF USDA-ARS.

Although powdery mildew is the most costly disease to grape growers, it's hardly the only threat. In North America, numerous other diseases threaten grape crops. These include black rot, downy mildew, and phomopsis. If you're in a climate with humid summers and intermittent rainfall, your crop may be susceptible to black rot, which causes fruit to shrivel while ripening, or to downy mildew, which under severe conditions completely defoliates vines.

Researchers have spent decades developing varieties that resist downy mildew and powdery mildew. Because these varieties resist the fungi, they don't require sprays and treatments like sulfur or petrochemicals for protection.


NY95.0301.01 is a red wine grape with high disease resistance and potential to produce red wines of good quality.
PHOTO BY NEW YORK STATE AGRICULTURAL EXPERIMENT STATION.
In a new project funded by a U.S. De-partment of Agriculture National Institute of Food and Agriculture (USDA-NIFA) Specialty Crops Research Initiative, researchers are approaching a new generation of traditionally bred, improved varieties developed with the help of DNA markers. In particular, this new generation of varieties will be highly resistant to powdery mildew. Since the sequencing of the pinot noir grape genome began in 2006, researchers have identified over 50,000 genetic markers within the 19 chromosomes of the grape. In Geneva, N.Y., Cornell grape breeder Dr. Bruce Reisch is working with Ed Buckler, USDA Agricultureal Research Service (ARS) research geneticist at Cornell University's Institute for Genomic Diversity, and Lance Cadle-Davidson, a plant pathologist with USDA-ARS Grape Genetics Research Unit, to identify markers predictive of powdery mildew resistance. The project is known as SCRI VitisGen.

The process, called genotyping by sequencing (GBS), allows the team to use the existing reference sequence of the genome to locate DNA markers and tell by the placement of those markers what chromosome they're linked to. "We're looking for the segregation of 10, 20 or 30 markers with this powdery mildew resistance gene," explains Reisch.

Breeders around the country are maintaining a total of 18 different grape populations. These populations of 150 to 200 seedlings carry genes from eight different Vitis species, including Vitis rupestris, Vitis cinerea and other North American wild species. The SCRI VitisGen team depends on these populations for vital information and is working with some DNA directly from the species and seedlings from those populations.

Each seedling has a slightly different set of DNA from the parents. In order to track the genes coming from parent A and parent B and their progeny, Reisch, Buckler and Cadle-Davidson run through the GBS process while characterizing and evaluating the progeny and concurrently correlating those genes and genetic markers with the plant traits. It's a massive correlation process of DNA markers and observations about the traits on those seedlings. "What we really need is to know which marker is always present when, for example, there's resistance to powdery mildew," explains Reisch. "Every year we're making new crosses and evaluating material from crosses made years ago."

Grape breeders typically spend 15 to 40 years developing a new variety, with most of that time spent on evaluating the variety at multiple sites. Once they've identified that a seedling has some potential, they propagate it, wait a few years for the newly propagated vines to start fruiting, and then send it out to cooperating sites and universities for trial. Every year it's a little different. Most of the time is spent gathering additional years of data on new selections. Reisch credits GBS with making him and his team more efficient in their work. "We can identify genes of interest before we even send a seedling out to the field. If we can send the DNA off for evaluating the year we're germinating a new batch of seedlings, we can have the DNA analysis tell us which seedling has multiple resistance for downy mildew, powdery mildew and black rot, etc.," he explains. "There's a list of traits we're shopping for in our breeding program."

The DNA analysis is meant to inform the researchers at a very early stage which seedlings have the greatest potential. The VitisGen team can then focus their efforts on an already elite group of seedlings rather than screening them out over the course of years.

Help for other grape growers

GBS technology isn't just for the wine grape industry. Breeders are also using GBS to develop improved varieties of table and raisin grapes. Cadle-Davidson touts the work of his colleague in Parlier, Calif., USDA-ARS grape breeder David Ramming. Ramming led the way in creating some elite lines being evaluated in replicated test plots for commercial release. These were the first vines to which GBS was applied.

Other USDA-ARS scientists have adopted the technology for the development of future rootstock varieties with improved pest resistance and table grape varieties with large, seedless berries. SCRI researchers are now applying GBS markers in all public U.S. grape breeding programs to help breeders combine multiple powdery mildew resistance genes in advanced breeding lines. In 2012, they expect to identify markers linked with 25 additional traits, including berry size, flavors and cold tolerance.

The author is a freelance writer based in Massachusetts and a monthly contributor to Growing.