NEW YORK – Using genome sequencing and resequencing, a team from Yunnan Agricultural University, the Chinese Academy of Sciences, and elsewhere has untangled new insights in the history of the grapevine (Vitis vinifera) plant, tracing the plant's domestication to concurrent events in Western Asia and the Caucasus region.
"The foundation of all old models was the assumption that there was only one domestication event," co-senior and co-corresponding author Wei Chen, a researcher at Yunnan Agricultural University, explained in an email. "Following this assumption, when people chose different grapes for the analysis, they reached different conclusions on domestication location."
In contrast, the team's genomic research on the cultivated grapevine subspecies V. vinifera ssp. vinifera (known as V. vinifera) and the wild progenitor subspecies V. vinifera ssp. sylvestris (V. sylvestris) highlighted two domestication events that took place at roughly the same time in Western Asia and the Caucasus region, while refining the timeframe for these domestication events. The results appeared in Science on Thursday.
"Our systematic genomic survey of V. sylvestris and V. vinifera accessions paints a defined picture of grapevine evolutionary history, which echoes key events in the history of world climate change and human migration," the authors wrote.
After putting together a chromosome-level reference genome for the wild grapevine progenitor subspecies Vitis sylvestris, the researchers analyzed the genome assembly alongside new and available resequencing data for more than 3,500 other grapevine representatives, including 1,022 V. sylvestris and 2,503 V. vinifera accessions.
"This dataset includes not only wild grapes covering major habitats, but also old and unique cultivated grapes from major viticulture regions," Chen said.
Based on millions of SNPs and small insertion or deletion variants found in the sequences, the team saw nearly 500 different grapevine genotypes, along with four geographically distinct V. sylvestris genetic clusters and half a dozen V. vinifera clusters that fell roughly along a gradient stretching from Western Asia to Europe.
Bringing in geological and archaeological clues, meanwhile, the investigators traced grapevine evolutionary history back to the Pleistocene period, when they speculated that humans relied on the plants to some extent without cultivating them systematically.
In particular, the authors suggested that it is "highly likely that modern humans extensively used grapevines as an energy source from the late Pleistocene, but the harsh climate was not suited for agriculture."
Based on population bottleneck patterns and other data, the team estimated that V. vinifera domestication took place roughly 6,900 to 11,000 years ago in the Caucasus and Western Asia, where V. vinifera initially appeared to be cultivated for wine production and table grape uses, respectively.
"These data collectively support a dual origin of V. vinifera and reject the population theory of a single primary domestication center," the authors reported, noting that an estimated population divergence time of roughly 11,000 years ago indicated that "domestication events took place concurrently around the advent of agriculture."
From there, the team reported, the plants — particularly those associated with domestication in Western Asia or the Near East — moved with humans and along trade to other parts of the world, continuing to diversify and occasionally mix further with V. sylvestris along the way.
The study also provided an opportunity to consider genetic factors corresponding to grapevine traits of interest, ranging from berry skin coloring to the production of a specific "muscat" aroma and flavor, linking the latter trait to SNPs on chromosomes 5 and 18.
More broadly, the team anticipates that other investigators "can use this dataset to identify genetic variations underlying desirable traits, improve grape quality, and help molecular breeding programs," Chen said, noting that the sequence collection "will help the whole field prepare for the challenges of climate change to our essential vine."
In a related perspectives article in Science, the University of Warwick's Robin Allaby suggested that the grapevine genome collection "will provide insight into the finer points of grape evolution for some time to come."
Even so, Allaby noted that the current study "does not stray into the effects of structural variation in the genome," and argued that the "next big step will be to integrate these data into a structural landscape."