A recently published grapevine genetic study (Y. Dong, et al., Dual domestications and origin of traits in grapevine evolution, Science 379 (6635), pp. 892 - 900, 3/3/23) "has upended the history of how humans first domesticated grapes for winemaking ..." (Melanie Lidman, It's in the DNA, Times of Israel, 3/25/23). I discussed the factors driving this study, as well as its objectives, in a prior post. In this post I describe study preparation efforts, the steps taken to define ancient vine genetic populations, and the stories hidden in the genes of V. sylvestris, the accepted progenitor of V. vinifera.
Data Collection
As discussed in my lead-in post, in 2019 Dr Chen and his lab reached out to colleagues around the world asking them to contribute material towards the study. A total of 3525 samples of genetic material were received at the State Key Laboratory for Conservation and Utilization of Bio-resources of Yunnan Agricultural University. The samples were distributed as follows:
- 2503 Vitis vinifera, 1022 Vitis sylvestris
- 3186 from Eurasian germplasm and private collections
- 2237 V. vinifera, 949 V. sylvestris
- 339 from previously sequenced samples
According to the authors, the sample population “deferentially included old, autochthonous, economically important varieties to maximize the spectrum of genetic diversity." Lidman asserts that Israel's sample submission "... constituted the largest contingent of wild grapes from a single country, or about 10 percent of the total wild grapes sequenced for the study."
According to Karlsruhe Institute of Technology (KIT), (scitechdaily.com, Scientists Determine the Origins of One of the World's Oldest Crops, 4/17/23), it contributed "... its globally unique collection of European wild vines and very old medieval species" to the study. It also connected the research team with the Ukraine researchers who had fled Crimea -- along with the vines from the Magarach collection -- after the 2014 Russian annexation.
Data Cleanup
In this phase of the study the team "weeded out clones, mutants, synonyms, homonyms and duplicates," ending up with 2448 grapevines (1604 V. vinifera and 844 V. sylvestris) and 498 distinct genotypes.
Categorization
The team first utilized Principal Component Analysis as a mechanism for determining whether "viticultural region" was a key element in defining grapevine diversity; according to the results of the analysis, it was not.
The team subsequently "leveraged genetic ancestry information from an unsupervised ADMIXTURE analysis" (ed., a method of inferring geographical origins based on an analysis of genetic ancestry) to categorize the core accessions. The findings from this analysis were as follows:
- The hierarchical clustering of ancestry components identifies four V. sylvestris groups from distinct geographic regions
- Western Asia
- Caucasus
- Central Europe
- Iberian Peninsula
- V. sylvestris accessions collected from other regions show admixed genetic structures
- For cultivated grapevines, six genetic ancestries could designate six distinctive groups, all covering a broad range of geographic regions
- Accessions with pure ancestries helped to "ascribe" names to these groups
- CG1 -- Western Asian table grapevines
- CG2 -- Caucasian wine grapevines
- CG3 -- Muscat grapevines
- CG4 -- Balkan wine grapevines
- CG5 -- Iberian wine grapevines
- CG6 -- Western European wine grapevines
"The four sylvestris and six vinifera groups formed identifiable clusters in the PCA plots and were thus suitable for population genomic investigations."
The V. sylvestris Story
Based on “genetic ancestries and the occupied ecological niches in the western Eurasia continent, the team designated the V. sylvestris accession from Western Asia and the Caucusus as the eastern ecotype and the accession in Central Europe and the Iberian Peninsula as the western ecotype. The similarities and differences between accessions drive this designation. For example, “both nucleotide diversity and individual heterozygosity show that the western ecotype has significantly reduced variation compared with its eastern counterpart.”
In tracing the sylvestris genetic history, the authors show that the eastern sylvestris (Syl-E in their parlance) flourished in its range from approximately 1.5 million years to 800 000 years ago. The Pleistocene was a time of changing climate cycles, however, and the population experienced a bottleneck between 800,000 and 400,000 years ago.
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| Illustration of a population bottleneck (Source: alevelbiology.co.uk) |
Somewhere between 400,000 and 200,000 years ago there was a divergence in Syl-E, giving rise to Syl-W. According to the analysis, the geographical split which drove the divergence was gradual. The Syl-W grouping experienced its own population bottleneck 400,000 - 150,000 years ago.
The last glacial cycle ran from 115,000 to 11,700 years ago and was characterized by ”global climate trending towards drier and colder conditions.” It was during this period — approximately 56,000 years ago -- that the Syl-E ecotype split into the Syl-E1 and Syl-E2 designates. It was also during this period (approximately 40,000 years ago) that there was a system-wide bottleneck which drove vine population to between 10,000 and 40,000. Syl-W experienced its own divergence, designated by the study team as Syl-W1 and Syl-W2.
In my next post I will take up the tale of V. vinifera, as told by the genes.
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