Palaeogenomic insights into the origins of French grapevine diversity

Ramos‐Madrigal, Jazmín; Runge, Anne Kathrine Wiborg; Bouby, Laurent; Lacombe, Thierry; Castruita, José Alfredo Samaniego; Adam-Blondon, Anne-Françoise; Figueiral, Isabel; Hallavant, Charlotte; Martı́nez-Zapater, José M.; Schaal, Caroline; Töpfer, Reinhard; Petersen, Bent; Sicheritz-Pontén, Thomas; This, Patrice; Baciliéri, Roberto; Gilbert, M. Thomas P.; Wales, Nathan

doi:10.1038/s41477-019-0437-5

Cited by 99 publications

(95 citation statements)

References 48 publications

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“…Savagnin has had a strong impact in the genetic composition of Western and Central European varieties producing many descendants (Lacombe et al, 2013). In addition, two offspring varieties of Savagnin, Alfrocheiro, and Bastardo, were found to contribute several offspring to the Portuguese germplasm (Cunha et al, 2015;Ramos-Madrigal et al, 2019; Figure 5A and Supplementary Table 5). The dissemination of Savagnin and Bastardo, the later already referred by Fernandes (1532) in the Douro region, could be explained by the extended medieval network formed by the Benedictines and Cistercians monasteries all over Europe.…”

Section: Portuguese Grapevine Varieties Are Structured In Three Majormentioning

confidence: 99%

“…One of these varieties is the unexpected case of Branco Desconhecido (Figure 5A), an offspring of Furmint and Kadarka Bela, two Hungarian grapevine varieties. A different case is that of Savagnin, a very old and disseminated variety (105 synonyms in VIVC) that has been cultivated at least during the last 900 years (Ramos-Madrigal et al, 2019). Savagnin has had a strong impact in the genetic composition of Western and Central European varieties producing many descendants (Lacombe et al, 2013).…”

Section: Portuguese Grapevine Varieties Are Structured In Three Majormentioning

confidence: 99%

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Genetic Relationships Among Portuguese Cultivated and Wild Vitis vinifera L. Germplasm

et al. 2020

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The domesticated grapevine spread along the Mediterranean basin from the primary Near East domestication area, where the greatest genetic diversity is found in its ancestor, the wild vine populations. Portuguese wild populations are on the southwestern fringe of the distribution of the Vitis vinifera L. ssp. sylvestris (C.C. Gmel.) Hegi in Europe. During the last Glacial Period they became isolated from the previous continuum that had been the territory of wild vine populations. Archaeological remains of domesticated vinifera grapevines in Portugal date back from 795 Before Common Era (BCE) in the lower Tagus river basin. In this work, 258 Portuguese vinifera varieties and sylvestris plants were characterized using 261 single nucleotide polymorphism (SNP) markers. The study of the genetic diversity of this local germplasm, its population structure and kinship, all framed in their historical and geographical backgrounds, revealed a complex network of first-degree relationships, where only Iberian varieties are involved. Some Iberian genotypes, like Alfrocheiro (Bruñal, in Spain), Sarigo (Cayetana Blanca), Mourisco Branco (Hebén), Amaral (Caiño Bravo), and Marufo (Moravia Dulce) are ancestors of a considerable fraction of all the autochthonous analyzed varieties. A part of the diversity developed was mostly local in some cases as shown by the closeness of several varieties (Vinhos Verdes) to the wild cluster in different analyses. Besides, several evidences of introgression of domesticated germplasm into wild vines was found, substantiating the high risk of genetic contamination of the sylvestris subspecies. All these findings together to the known matching between the wild maternal lineage of the Iberian Peninsula and an important number of Portuguese grapevine varieties (chlorotype A), point out that some of these varieties derive, directly or indirectly, from originally local wild populations, supporting the possible occurrence of secondary events of local domestication, or, at least, of an introgression process of wild into cultivated grapevines.

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Section: Portuguese Grapevine Varieties Are Structured In Three Majormentioning

confidence: 99%

Section: Portuguese Grapevine Varieties Are Structured In Three Majormentioning

confidence: 99%

Genetic Relationships Among Portuguese Cultivated and Wild Vitis vinifera L. Germplasm

et al. 2020

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“…Traminer, is a very spread European variety which cultivation dates back at least 900 years [47]. Although Savagnin was not included in the study, its color mutant (Gewuerztraminer) was, and showed a very high value for the fruitset rate too (90.8%).…”

Section: Variation For Reproductive Performance Variablesmentioning

confidence: 99%

Cultivated Grapevine Displays a Great Diversity for Reproductive Performance Variables

2019

Crop Breed Genet Genom.

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Background: There are thousands of grapevine varieties that display a wide range of variation for traits like grape use (wine, table grape or both), color or ripening time, but little is known about their reproductive performance, especially flowering and fruitset (conversion from flower to fruit). Works focused at the study of these traits in grapevine evaluated one or few varieties and used different methodologies making comparisons difficult. This study aimed to characterize the reproductive performance of 120 varieties and its stability over two seasons using a precise methodology. Methods: Reproductive performance was determined through counting flowers and berries in the same inflorescences/bunches (10 per variety), for which a new methodology of image analysis of scanned calyptras was developed. Varieties were classified according to their reproductive performance. Results: A great diversity was found for most variables including fruitset and number of flowers. Large differences between varieties were observed both in values and in stability among seasons. The varieties clustered in three main classes that displayed significant differences not only for the reproductive performance variables used for the clustering but for most the variables studied. Varieties in these classes showed a nonrandom distribution regarding the grape use and the genetic structure based on molecular markers. Conclusions: This is the largest study of reproductive performance variables such as fruitset ever done in grapevine. It provides specific values for many varieties for the first time, useful for breeding programs. The clustering based on these variables is related with those based on use and geographical origin.

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“…By extension, when other taxa and other archeological and environmental contexts will be included, the production of larger ancient sequence datasets will help researchers characterize the epigenetic response of plant species to many other selective pressures, including climate change, pollution, and more (Allaby et al, 2015;Gutaker and Burbano, 2017). Unless candidate loci of interest or predefined sets of CG, CHG, and CHH loci are specifically targeted (e.g., through in solution DNA capture, Ramos-Madrigal et al, 2019), reaching this goal will, however, require massive sequencing efforts. It is crucial to keep in mind that (1) ancient DNA analyses are destructive, (2) archeological material represent a finite resource, and that (3) C deamination inflate sequencing errors and can, thus, impact downstream analyses.…”

Section: Discussionmentioning

confidence: 99%

Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage

2020

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The ultra-short DNA molecules still preserved in archeological remains can provide invaluable genetic information about past individuals, species, and communities within the half to 1-million-year time range. The sequence data are, however, generally affected by post-mortem DNA damage and include specific patterns of nucleotide misincorporations, which can help data authentication. Recent work in ancient mammals has shown that such patterns can also help assess past levels of DNA methylation in CpG contexts. Despite pioneering work in barley and sorghum, ancient epigenetic marks have received limited attention in plants and it remains unknown whether ancient epigenetic signatures can be retrieved in any of the three main sequence contexts (CG, CHG, and CHH). To address this question, we extended a statistical methylation score originally proposed to trace cytosine methylation in mammal sequence data to accommodate the three methylation contexts common in plants. We applied this score to a range of tissues (wood, cobs, and grains) and species (oak, maize, and barley), spanning both desiccated and waterlogged archeological samples. Ancient sequence data obtained for USER-treated DNA extracts yielded methylation scores on par with DNA methylation levels of modern organellar and nuclear genomes. At the quantitative level, scores were (1) positively correlated to post-mortem cytosine deamination, and (2) replicated relative contributions of CG, CHG, and CHH contexts to DNA methylation assessed by bisulfite DNA sequencing of modern plant tissues. This demonstrates that genuine DNA methylation signatures can be characterized in ancient plant remains, which opens new avenues for investigating the plant evolutionary response to farming, pollution, epidemics, and changing environmental conditions.

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Palaeogenomic insights into the origins of French grapevine diversity

Cited by 99 publications

References 48 publications

Genetic Relationships Among Portuguese Cultivated and Wild Vitis vinifera L. Germplasm

Genetic Relationships Among Portuguese Cultivated and Wild Vitis vinifera L. Germplasm

Cultivated Grapevine Displays a Great Diversity for Reproductive Performance Variables

Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage

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