Palaeogenomic Insights Into the Origins of French Grapevine Diversity
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This is a repository copy of Palaeogenomic insights into the origins of French grapevine diversity. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/147520/ Version: Accepted Version Article: Ramos Madrigal, Jazmín, Runge, Anne Kathrine Wiborg, Bouby, Laurent et al. (14 more authors) (2019) Palaeogenomic insights into the origins of French grapevine diversity. Nature Plants. ISSN 2055-026X https://doi.org/10.1038/s41477-019-0437-5 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Palaeogenomic insights into the origins of French grapevine 1 diversity 2 1 1,2 3 3 Jazmín Ramos-Madrigal , Anne Kathrine Wiborg Runge , Laurent Bouby , 4 1 4 Thierry Lacombe , José Alfredo Samaniego Castruita , Anne-Françoise Adam- 5 6 7 8 5 Blondon , Isabel Figueiral , Charlotte Hallavant , José M. Martínez-Zapater , 9 10 1,11 6 Caroline Schaal , Reinhard Töpfer , Bent Petersen , Thomas Sicheritz- 1,11 4 4 1,12,* 7 Pontén , Patrice This , Roberto Bacilieri , M. Thomas P. Gilbert , Nathan 1,2,13,14* 8 Wales 9 1 10 Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 2 11 Copenhagen, Denmark. BioArCh, Department of Archaeology, University of York, Wentworth 3 12 Way, York YO10 5DD, UK. ISEM - UMR 5554, CNRS-IRD-EPHE-Université Montpellier, Place . 4 13 Eugène Bataillon, CC 065, 34095 Montpellier Cedex, France UMR AGAP, Université Montpellier, 5 14 CIRAD, INRA, Montpellier SupAgro, 2 Place Viala, 34060 Montpellier, France. URGI, Unité de 15 Recherche Génomique-Info, UR1164, INRA, Université Paris-Saclay, Route de Saint-Cyr 78026 6 16 Versailles, France. Inrap, Méditerranée and ISEM - UMR 5554, CNRS-IRD-EPHE-Universi’té 7 17 Montpellier, Place Eugène Bataillon, CC 065, 34095 Montpellier Cedex, France. Bureau d 18 études Hadès, laboratoire TRACES - UMR 5608 (pôle Terrae) - UT2J, 5 allées A. Machado, 31058 8 19 Toulouse Cedex 9, France. Instituto de Ciencias de la Vid y del Vino (CSIC-UR-Gobierno de La 9 20 Rioja), Ctra. de Burgos km 6, 26007 Logroño Spain. GéoArchEon Sarl, Laboratoire Chrono- 21 Environnement - UMR 6249, Université de Franche Comté, 16 route de Gray, 25000 Besançon, 10 22 France. Julius Kühn-Institut Bundesforschungsinstitut für Kulturpflanzen, Institut für 11 23 Rebenzüchtung, Geilweilerhof, D-76833 Siebeldingen, Germany. Centre of Excellence for 24 Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, 12 13 25 Malaysia. NTNU University Museum, 7491 Trondheim, Norway. Department of Plant and 14 26 Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA. 27 Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, 1 * 28 Université Paul Sabatier, 31000 Toulouse, France. e-mail: [email protected] or 29 [email protected] 30 The Eurasian grapevine (Vitis vinifera) has long been important for wine 31 production and a food source. Despite being clonally propagated, modern 32 cultivars exhibit great morphological and genetic diversity, with thousands 33 of varieties described in historic and contemporaneous records. Through 34 historical accounts, some varieties can be traced to the Middle Ages, but the 35 genetic relationships between ancient and modern vines remain unknown. 36 We present target-enriched genome-wide sequencing data from 28 37 archaeological grape seeds dating to the Iron Age, Roman era, and 38 medieval period. When compared to domesticated and wild accessions, we 39 found the archaeological samples were closely related to Western 40 European cultivars used for winemaking today. We identified seeds with 41 identical genetic signatures present at different Roman sites, as well as 42 seeds sharing parent-offspring relationships with varieties grown today. 43 Furthermore, we discovered one seed dated to ~1100 CE was a genetic 44 match to ‘Savagnin Blanc’, providing evidence for 900 years of 45 uninterrupted vegetative propagation. 46 47 1–3 48 Since its domesticationVitis in viniferaSouthwestern Asia more than 6000 years ago , the 49 Eurasian grapevine ( L.) has become one of the world’s most widely 50 produced and economically valuable fruit crops. Although grapevine products 51 are widely consumed as table grapes, dried raisins, fruit preserves, and cooked 52 leaves, both archaeological and historical evidence indicates that wine has been 2 4,5 53 its primary use . A key unresolved question in ancient viniculture is the origin 6 54 and proliferation of vegetative propagation . Like many other fruit crops, 55 grapevine is grown almost exclusively as clonal lineages, wherein favored 56 varieties are maintained through horticultural techniques like grafting, layering, 7,8 57 and planting of shoots . These methods take advantage of its natural ability to 58 reproduce asexually under certain conditions, and ultimately enable the 59 establishment of genetic clones of valuable cultivars. With vegetative 60 propagation, viniculturists can consistently harvest berries with a desired flavor 61 profile, and with relatively limited effort, have the potential to expand cultivars 62 to new vineyards and distant regions. The alternative approach of sowing seeds 63 is unreliable because grapevine genomes are highly heterozygous and 64 individuals grown from seed are highly diverse in quality, yield, phenotype, and 8 65 phenology . Moreover, winemakers have to wait from three to five years until 9 66 vines reach maturity , before it is possible to assess berry quality and yield. 67 Thus, clonal lineages of high-quality vines have become indispensable in modern 68 viniculture. Discovering the antiquity of vegetative propagation technologies and 69 the unique histories of individual grapevine varieties will mark a major 70 advancement in our understanding of ancient viniculture, provide a means to 71 investigate longstanding local agricultural traditions, and gene.g.erate pertinent 72 information for future development of breeding schemes ( through better 73 understanding why some varieties have been more successful than others, or 74 adding historical value to present-day cultivars). 75 76 The history of winemaking in France provides a useful model to explore how 77 vegetative propagation helped establish ancient vineyards, and how those 3 ’ 78 actions ultimately shaped the economy and landscape of one of the world s 79 most esteemed winegrowing countries. Written sources and archaeologicalMassalia 80 records indicate vineyards were first planted at the Greek colony of , th 10,11 81 present day Marseille, during the 6 century BCE . Winemaking subsequently 12 82 spread along the Mediterranean coast , but it was not until end of the first 83 century BCE that Romans greatly increased wine production across southern 10 13 84 France . Roman authors, including Pliny the Elder in the first century CE ( : 85 Book XIV), discussed grafting and grapevine varieties, thereby demonstrating 86 their proficiency in vegetative propagation techniques. While Pliny describes 91 87 varieties, it is currently impossible to link Roman names to modern grapevines; 88 however, it is frequently speculated that some living varieties were grown by the 9 89 Romans, and that those genetic clones have been maintained for two millennia . 90 After the fall of the Roman Empire, winemaking traditions continued in France, 91 and by the Middle Ages, contemporary variety names appear in written records 14 92 . Even though historic names are still used today, it remains unknown whether 93 the same genetic clone has been maintained, or if names have been assigned to 94 other lineages. 95 96 Archaeobotanical remains, in particular seeds, have the potential to shed new 97 light on the legacy of French grapevine varieties, and more generally on the 98 history of viniculture. Using morphometric analyses of seedV. vinifera shape, researchers 99 viniferahave shown seeds from most domesticated grapevines ( V.subsp. vinifera 100 sylvestris) can be distinguished from those producedet byal. wild vines ( 15,16 10 101 subsp. ) . With this approach, Bouby determined that early 102 Roman sites in Southern France (50 BCE–225 CE) contained greater numbers of 4 103 morphologically wild seeds than the following period (225–600 CE), raising the 104 question of whether Romans collected and cultivated wild berries for 105 winemaking. Through this time series, seed shapes tended toward domesticated 106 morphotypes, a finding the authors hypothesize represents a combination of 107 continued selective pressures with a sporadic incorporation of native varieties 108 through sexual reproduction. While these interpretations are thought provoking, 109 the authors also recognize critiques that some wild and domesticated vines 110 produce morphologically indistinguishable seeds. 111 112 One of the most promising avenues of research for ancient viniculture is 113 palaeogenomic (or