Scientists sequence genome of #1 red wine grape

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Scientists have produced a high-quality draft genome sequence of cabernet sauvignon, the world’s most popular red wine grape variety.

“This will help us understand what makes cabernet sauvignon cabernet sauvignon.”

The findings are the result of new sequencing technology combined with a new computer algorithm that can yield detailed information about complex genomes of various organisms.

Success of the new genome assembly, which allows researchers to assemble large segments of an organism’s DNA, also was demonstrated on the common research plant Arabidopsis thaliana and the coral mushroom (Clavicorona pyxidata). The findings appear in the journal Nature Methods.

“For grapevine genomics, this new technology solves a problem that has limited the development of genomic resources for wine grape varieties,” says the lead researcher of the cabernet sauvignon sequencing effort, Dario Cantu of the University of California, Davis, department of viticulture and enology. “It’s like finally being able to uncork a wine bottle that we have wanted to drink for a long time.

“The new process provides rapid access to genetic information that cabernet sauvignon has inherited from both its parents, enabling us to identify genetic markers to use in breeding new vines with improved traits,” he says.

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The first genome sequence for the common grapevine, Vitis vinifera, was completed in 2007. Because it was based on a grapevine variety that was generated to simplify the genome assembly procedure, rather than a cultivated variety, that sequence lacks many of the genomic details that economically important wine grape varieties possess, Cantu says.

He notes that the new sequencing technology will enable his research group to conduct comparative studies between cabernet sauvignon and other historically and economically important wine grape varieties.

“This will help us understand what makes cabernet sauvignon cabernet sauvignon,” he says.

Grapes in a hotter climate

“The new genomic information that will be generated with this new genomics approach will accelerate the development of new disease-resistant wine grape varieties that produce high-quality, flavorful grapes and are better suited to environmental changes,” Cantu says.

Warmer temperatures attributed to climate change are already being recorded in many prime grape-growing regions of the world. And in California, where the value of grape crops varies widely and is heavily influenced by local climate, it is especially important that new varieties be able thrive despite warming temperatures.

“In a worsening climate, drought, and heat stress will be particularly relevant for high-quality viticultural areas such as Napa and Sonoma,” Cantu says.

A cabernet sauvignon mystery

The new sequencing effort may also answer some of the questions that have surrounded the ancestry of cabernet sauvignon for centuries, Cantu says.

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“Having access to this genomic information is historically fascinating,” Cantu says, noting that the cabernet sauvignon grape variety is thought to date no later than the 17th century. He notes that in 1997 UC Davis plant geneticist Carole Meredith used DNA fingerprinting techniques to identify cabernet franc and sauvignon blanc as the two varieties that had crossed to produce cabernet sauvignon.

“Today, you can find cabernet sauvignon growing on every continent except Antarctica,” Cantu says. “And because grape vines have been propagated by plant cuttings rather than grown from seed, all of the cabernet sauvignon vines are genetically identical, with the exception of some spontaneous, clonal mutations.

“Using this new genome sequencing process, we can now develop the genetic markers necessary to combine important traits into new varieties,” Cantu says. “It’s been 400 years since that was last done for cabernet sauvignon; we can do better than that.”

Funding for the cabernet sauvignon genome sequencing came from J. Lohr Vineyards and Wines. Collaborators on the study are from UC Davis; the University of Nevada, Reno; and the University of Verona, Italy.

The three-pronged, proof-of-concept study used an open-source genome assembly process called FALCON-unzip, developed by Pacific Biosciences of Menlo Park, California. Chen-Shan Chin, the firm’s leading bioinformatician, led the study.

In addition to lead author Chen-Shan Chin, other researchers on the overall sequencing study are from Pacific Biosciences; Johns Hopkins University; Cold Spring Harbor Laboratory; the Department of Energy Joint Genomic Institute; and the Salk Institute for Biological Studies.

Source: UC Davis