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Genotyping Study Provides Clues to Domestic Grape History, Diversity

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Current grape breeding programs are exploiting only a fraction of the genetic diversity present in domesticated grape varieties, according to a paper appearing in the early, online version of the Proceedings of the National Academy of Science this week.

By genotyping more than 1,000 grape accessions from the US Department of Agriculture's grape germplasm repository, an international research team was able to learn more about the history of grape domestication and gauge the genetic diversity remaining in grapes today. They found that this diversity has remained high despite thousands of years of domestication — a feature that the team says could be tapped to produce improved grape varieties.

"The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity," senior author Edward Buckler, a researcher affiliated with Cornell University and the United States Department of Agriculture's Agricultural Research Service, and co-authors wrote.

The grape plant was domesticated in the Near East an estimated 6,000 to 8,000 years ago, the researchers explained, and has since become one of the most lucrative crops in the world.

Even so, they explained, there is still interest in creating grapes with improved traits, including resistance to pests and disease — a task that they say can be streamlined by learning more about the genetic profiles underlying specific plant features.

"[A]n environmentally sustainable grape-growing industry will rely on accessing and using the grape's tremendous genetic diversity to develop disease-resistant grape cultivars through marker-assisted breeding," they wrote.

To explore the effects of domestication on grape genetic diversity and gain insights into the relationships between existing grape cultivars, the team used a Vitis9KSNP array to genotype 950 accessions belonging to the domesticated V. vinifera subspecies vinifera and 59 accessions from the wild subspecies sylvestris.

The array was designed using data on more than 70,000 SNPs in the grape genome, the team noted, and assesses nearly 9,000 validated SNPs. The samples tested in the current study were obtained from the USDA's grape germplasm collection.

Using this genotyping approach, the researchers found that the USDA germplasm collection houses at least 583 unique cultivars in the domesticated vinifera subspecies. Most of these were first-degree relatives to one or more of the other domestic cultivars, with more than half of the unique domestic cultivars — some 58 percent — falling into a shared pedigree.

In general, the researchers found that table grapes tended to be more closely related to one another than to wine grape and vice versa. Grapes from the same parts of the world also tended to cluster with one another.

Overall, the team's genetic results were consistent with the notion that grapes were first domesticated in the Near East before spreading to Western Europe and elsewhere, where they mixed with other wild grapes.

This domestication does not seem to have dramatic effects on the genetic diversity within grapes, the researchers reported, though they did see declines in haplotype diversity and linkage disequilibrium in domesticated grapes compared to their wild counterparts.

The maintenance of genetic diversity is promising for future grape breeding prospects, the researchers explained. But, they argued, the same vegetative propagation practices — in which new plants are created using bits of existing plants — that have helped preserve this diversity have also hindered the development of new cultivars through crossing.

"[T]he last several thousand years of grape breeding explored only a small fraction of possible genetic combinations," they wrote, arguing that "future marker-assisted breeding efforts … have tremendous diversity at their disposal to produce desirable wine and table grapes with resistance to existing and future pathogens."

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