NEW YORK (GenomeWeb News) — A consortium of French and Italian researchers has sequenced the genome of a wine grape variety and found that it carries additional copies of genes linked to flavor, aroma, as well as the compound found in red wine believed to confer good health.
The draft sequence by the Public Consortium for Grapevine Genome Characterization hints at how vintners cultivated their crops for these desired phenotypes as far back as the Stone Age.
Its findings may also enable scientists to use the genome of Vitis vinifera, a Pinot Noir variety, to identify genes responsible for desired tastes and disease resistance.
For instance, the team found that compared to other flowering plants, grapevines have twice as many genes linked to essential oil production and other compounds responsible for a wine's aroma. They also have more of the genes that produce resveratrol, the compound in red wine associated with certain health benefits.
The draft sequence is the fourth produced for flowering plants, the second for a woody species, and the first for a fruit crop, the scientists wrote in their article, which appears as a Letter in this week’s Nature. The team presented some of their findings at the Plant and Animal Genome conference in San Diego in January, and reported by GenomeWeb Daily News sister publications In Sequence.
Researchers led by Olivier Jaillon and Patrick Wincker of France's National Institute for Scientific Research at the Universite d'Evry “provided unexpected evidence for genome duplication” in a species that had previously been considered as true diploids on the basis of their genetics.
Writing that they selected grapevine “because of its important place in the cultural heritage of humanity,” the scientists sequenced the PN40024 genotype of V. vinifera using a whole-genome shotgun strategy, with all data generated by paired-end sequencing of cloned inserts using Sanger technology on ABI3730xl sequencers.
The team produced a total of 6.2 million end-reads, representing an 8.4-fold coverage of the genome. Within the assembly, performed with Arachne, 316 supercontigs represent putative allelic haplotypes that constitute 11.6 million bases, they wrote in Nature. When considering only one of the haplotypes in each heterozygous region, the assembly consists of 19,577 contigs and 3,514 supercontigs totaling 487 Mb. This value is close to the 475 Mb reported for the grapevine genome size during January’s PAG conference.
In their paper, the team notes that a “striking feature” of the grapevine proteome is the existence of “large families related to wine characteristics, which have a higher gene copy number than in the other sequenced plants.”
For instance, the team has identified 43 genes encoding stilbene synthases, which help synthesize resveratrol, the grapevine phytoalexin linked to the health benefits associated with moderate red wine consumption.
Additionally, the researchers identified 89 functional genes encoding terpene synthases, which drive the synthesis of terpenoids, secondary metabolites believed to be “major components of resins, essential oils, and aromas of the plant.
The team writes that public access to the sequence will help identify genes underlying the agricultural characteristics of this species, including domestication traits. “A selective amplification of genes belonging to the metabolic pathways of terpenes and tannins has occurred in the grapevine genome, in contrast with other plant genomes, the researchers note.
“This suggests that it may become possible to trace the diversity of wine flavors down to the genome level,” they write.
The genome could also enable vintners to devise grape strains less susceptible to the “large diversity of pathogens” that threaten them. Jean Weissenbach, one of the study's authors and director of Genoscope, the French national sequencing center, said the sequence could help devise breeding programs to increase pest resistance.