The Eurasian grapevine (Vitis vinifera) has long been important for wine production as well as being a food source. Despite being clonally propagated, modern cultivars exhibit great morphological and genetic diversity, with thousands of varieties described in historic and contemporaneous records. Through historical accounts, some varieties can be traced to the Middle Ages, but the genetic relationships between ancient and modern vines remain unknown. We present target-enriched genome-wide sequencing data from 28 archaeological grape seeds dating to the Iron Age, Roman era and medieval period. When compared with domesticated and wild accessions, we found that the archaeological samples were closely related to western European cultivars used for winemaking today. We identified seeds with identical genetic signatures present at different Roman sites, as well as seeds sharing parent–offspring relationships with varieties grown today. Furthermore, we discovered that one seed dated to ~1100 ce was a genetic match to ‘Savagnin Blanc’, providing evidence for 900 years of uninterrupted vegetative propagation.
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Peer Review Information: Nature Plants thanks David Caramelli, Elizabeth Zimmer and other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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Myles, S. et al. Genetic structure and domestication history of the grape. Proc. Natl Acad. Sci. USA 108, 3530–3535 (2011).
Olmo, H. P. in Evolution of Crop Plants (eds Smartt, J. & Simmonds, N. W.) 485–490 (Longman Scientific & Technical, 1995).
Zohary, D., Hopf, M. & Weiss, E. Domestication of Plants in the Old World: The Origin and Spread of Domesticated Plants in South-west Asia, Europe, and the Mediterranean Basin (Oxford Univ. Press, 2012).
McGovern, P. E. Ancient Wine: the Search for the Origins of Viniculture (Princeton Univ. Press, 2003).
McGovern, P. et al. Early Neolithic wine of Georgia in the South Caucasus. Proc. Natl Acad. Sci. USA 114, E10309–E10318 (2017).
Goldschmidt, E. E. The evolution of fruit tree productivity: a review. Econ. Bot. 67, 51–62 (2013).
Hartmann, H. T., Kester, D. E. & Davies, F. T. Plant Propagation: Principles and Practices (Prentice-Hall, 1997).
Janick, J. in Plant Breeding Reviews (ed. Janick, J.) 255–321 (John Wiley & Sons, 2010).
This, P., Lacombe, T. & Thomas, M. Historical origins and genetic diversity of wine grapes. Trends Genet. 22, 511–519 (2006).
Bouby, L. et al. Bioarchaeological insights into the process of domestication of grapevine (Vitis vinifera L.) during Roman times in southern France. PLoS ONE 8, e63195 (2013).
Renfrew, J. M. in Wine: A Scientific Exploration (eds Sandler, M. & Pinder, R.) 56–69 (CRC Press, 2003).
McGovern, P. E. et al. Beginning of viniculture in France. Proc. Natl Acad. Sci. USA 110, 10147–10152 (2013).
Bostock, J. & Riley, H. T. The Natural History of Pliny (Taylor and Francis, 1855).
Royer, C. in La Vigne et le Vin (ed. La Manufacture et la Cite des Sciences et de l’industrie) 15–25 (Graficas, 1988).
Figueiral, I., Bouby, L., Buffat, L., Petitot, H. & Terral, J.-F. Archaeobotany, vine growing and wine producing in Roman southern France: the site of Gasquinoy (Béziers, Hérault). J. Archaeol. Sci. 37, 139–149 (2010).
Terral, J.-F. et al. Evolution and history of grapevine (Vitis vinifera) under domestication: new morphometric perspectives to understand seed domestication syndrome and reveal origins of ancient European cultivars. Ann. Bot. 105, 443–455 (2010).
Bacilieri, R. et al. Potential of combining morphometry and ancient DNA information to investigate grapevine domestication. Veg. Hist. Archaeobot. 26, 345–356 (2016).
Cappellini, E. et al. A multidisciplinary study of archaeological grape seeds. Naturwissenschaften 97, 205–217 (2010).
Manen, J.-F. et al. Microsatellites from archaeological Vitis vinifera seeds allow a tentative assignment of the geographical origin of ancient cultivars. J. Archaeol. Sci. 30, 721–729 (2003).
Wales, N. et al. The limits and potential of paleogenomic techniques for reconstructing grapevine domestication. J. Archaeol. Sci. 72, 57–70 (2016).
Laucou, V. et al. Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs. PLoS ONE 13, e0192540 (2018).
Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007).
Malaspinas, A.-S. et al. bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). Bioinformatics 30, 2962–2964 (2014).
Zhou, Y., Massonnet, M., Sanjak, J. S., Cantu, D. & Gaut, B. S. Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication. Proc. Natl Acad. Sci. USA 114, 11715–11720 (2017).
Di Genova, A. et al. Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants. BMC Plant Biol. 14, 7 (2014).
Cardone, M. F. et al. Inter-varietal structural variation in grapevine genomes. Plant J. 88, 648–661 (2016).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Jørsboe, E., Hanghøj, K. & Albrechtsen, A. fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample. Bioinformatics 33, 3148–3150 (2017).
Manichaikul, A. et al. Robust relationship inference in genome-wide association studies. Bioinformatics 26, 2867–2873 (2010).
Korneliussen, T. S. & Moltke, I. NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data. Bioinformatics 31, 4009–4011 (2015).
Bleckmann, A., Alter, S. & Dresselhaus, T. The beginning of a seed: regulatory mechanisms of double fertilization. Front. Plant Sci. 5, 452 (2014).
Ebadi, A., Sedgley, M., May, P. & Coombe, B. G. Seed development and abortion in Vitis vinifera L., cv. Chardonnay. Int. J. Plant Sci. 157, 703–712 (1996).
Cadot, Y., Miñana-Castelló, M. T. & Chevalier, M. Anatomical, histological, and histochemical changes in grape seeds from Vitis vinifera L. cv Cabernet franc during fruit development. J. Agric. Food Chem. 54, 9206–9215 (2006).
Boursiquot, J. in Le Château-Chalon: un Vin, son Terroir et ses Hommes (eds Berthet-Bondet J. & Roulière-Lambert M.-J.) 46–55 (Mêta Jura, 2013).
Lacombe, T. et al. Large-scale parentage analysis in an extended set of grapevine cultivars (Vitis vinifera L.). Theor. Appl. Genet. 126, 401–414 (2013).
Regner, R., Stadlhuber, A. & Kaserer, H. Considerations about the evolution of grapevine and the role of Traminer. Acta Hortic. 528, 179–184 (2000).
Bowers, J. E., Siret, R., Meredith, C. P., This, P. & Boursiquot, J.-M. A single pair of parents proposed for a group of grapevine varieties in northeastern France. Acta Hortic. 5281, 129–132 (2000).
Galet, P. Dictionnaire Encylcopédique des Cépages et de leurs Synonymes (Libre et Solidaire, 2015).
Périsset, Z. Histoire de la Vigne et du Vin en Valais: des Origines à nos Jours (Infolio, 2010).
Robinson, J., Harding, J. & Vouillamoz, J. Wine Grapes: A Complete Guide to 1,368 Vine Varieties, including their Origins and Flavours (Ecco, 2012).
Mascher, M. et al. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat. Genet. 48, 1089–1093 (2016).
Ramos-Madrigal, J. et al. Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication. Curr. Biol. 26, 3195–3201 (2016).
Vallebueno-Estrada, M. et al. The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding. Proc. Natl Acad. Sci. USA 113, 14151–14156 (2016).
Malenica, N. et al. Whole genome amplification and microsatellite genotyping of herbarium DNA revealed the identity of an ancient grapevine cultivar. Naturwissenschaften 98, 763–772 (2011).
Fuller, D. Q. Long and attenuated: comparative trends in the domestication of tree fruits. Veg. Hist. Archaeobot. 27, 165–176 (2018).
Wales, N., Andersen, K., Cappellini, E., Ávila-Arcos, M. C. & Gilbert, M. T. P. Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains. PLoS ONE 9, e86827 (2014).
Wales, N. et al. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA. Biotechniques 59, 368–371 (2015).
Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).
Canaguier, A. et al. A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3). Genom. Data 14, 56–62 (2017).
Jansen, R. K. et al. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol. Biol. 6, 32 (2006).
Goremykin, V. V., Salamini, F., Velasco, R. & Viola, R. Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol. Biol. Evol. 26, 99–110 (2008).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Schubert, M. et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012).
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Vitis International Variety Catalogue (JKI, accessed 7 January 2019); www.vivc.de
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15, 356 (2014).
Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).
We thank the Danish National High-throughput Sequencing Centre for assistance in generating the sequencing data. This project was funded by the Danish Council for Independent Research (10–081390) and the Danish National Research Foundation (DNRF94). L.B. and R.B. were supported by the French National Agency of Research (VINICULTURE project—ANR-16-CE27–0013). We thank the following scientific and technical directors and corresponding institutions for providing the archaeological material used in this project as well as contextual information: P. Blanchard (Inrap, site: La Madeleine), E. Verdel (Isère Patrimoine, site: Colletière), H. Pomarèdes (Inrap, sites: Mas de Vignoles XIV and La Lesse-Espagnac), O. Ginouvez (Inrap, site: Terrasses de Montfau), R. Bourgaut (Communauté d’Agglomération du Bassin de Thau, site: Roumèges), P. Flotte (Archéologie Alsace, site: Horbourg-Wihr), M. Compan (Inrap, site: Mont Ferrier), I. Daveau (Inrap, site: Cougourlude) and C. Tardy (Inrap). We are also grateful to the GrapeReSeq consortium for early access to the genotype data. Finally, we thank J. V. Moreno-Mayar, S. Gopalakrishnan, F. G. Vieira, D. Maghradze and A. Schlumbaum for their helpful discussion.