Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs

Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26–0.32) and linkage disequilibrium (LD, 28.8–58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genomewide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine

Bibliographic Details

Main Authors:	Laucou, Valérie, Launay, ,Amandine, Bacilieri, Roberto, Lacombe, Thierry, Adam-Blondon, Anne-Françoise, Bérard, Aurélie, Chauveau, Aurélie, Andrés, M. Teresa de, Hausmann, Ludger, Ibáñez Marcos, Javier, Le Paslier, Marie Christine, Maghradze, David, Martínez-Zapater, José M., Maul, Erika, Ponnaiah, Maharajah, Töpfer, Reinhard, Péros, Jean Pièrre, Boursiquot, J. M.
Other Authors:	European Commission
Format:	artículo biblioteca
Language:	English
Published:	Public Library of Science 2018-02-08
Online Access:	http://hdl.handle.net/10261/193562 http://dx.doi.org/10.13039/501100000780
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