Palaeogenomic insights into the origins of French grapevine diversity

Abstract

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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Fig. 1: Genetic affinities between archaeological grape seeds and modern V.vinifera accessions.
Fig. 2: Geographical distribution and relationships between the distinct genetic types of archaeological samples.
Fig. 3: Genetic origins of ancient and historic French grapevine varieties.

Data availability

Sequencing data produced in this study are available at the NCBI Sequence Read Archive under the reference PRJNA489970. Genotype data are available in the figshare repository at: https://doi.org/10.6084/m9.figshare.7610987.

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Acknowledgements

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.

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The project was conceived by N.W., M.T.P.G., R.B. and L.B., and headed by N.W. and M.T.P.G. J.A.S.C., A.K.W.R, R.B. and N.W. designed the experimental enrichment methodology with input from J.M.M.-Z., R.T. and A.-F.A.-B. A.K.W.R. processed the aDNA with input from N.W. J.R.-M., A.K.W.R., R.B. and N.W. designed the analysis strategy. J.R.-M. performed the bioinformatic analysis with assistance from B.P. and T.S.-P. and input from N.W., M.T.P.G. and R.B. J.R.-M., N.W., M.T.P.G., R.B., L.B., T.L. and P.T. interpreted the results. L.B., I.F., C.S. and C.H. curated the archaeological material. J.R.-M., N.W. and M.T.P.G. wrote the manuscript with input from R.B., L.B. and T.L. and the other authors. All authors revised, edited and accepted the manuscript. Primary funding was acquired by M.T.P.G.

Corresponding authors

Correspondence to M. Thomas P. Gilbert or Nathan Wales.

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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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Supplementary Methods, Supplementary References, Supplementary Figures 1–13, and Supplementary Tables 1–7.

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Ramos-Madrigal, J., Runge, A.K.W., Bouby, L. et al. Palaeogenomic insights into the origins of French grapevine diversity. Nat. Plants 5, 595–603 (2019). https://doi.org/10.1038/s41477-019-0437-5

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