التفاصيل البيبلوغرافية
| العنوان: |
Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs. |
| المؤلفون: |
Laucou, Valérie1 valerie.laucou@inra.fr, Launay, Amandine1, Bacilieri, Roberto1, Lacombe, Thierry1,2, Adam-Blondon, Anne-Françoise3, Bérard, Aurélie4, Chauveau, Aurélie4, de Andrés, Maria Teresa5, Hausmann, Ludger6, Ibáñez, Javier7, Le Paslier, Marie-Christine4, Maghradze, David8, Martinez-Zapater, José Miguel7, Maul, Erika6, Ponnaiah, Maharajah4,9, Töpfer, Reinhard6, Péros, Jean-Pierre1, Boursiquot, Jean-Michel1,2 |
| المصدر: |
PLoS ONE. 2/8/2018, Vol. 13 Issue 2, p1-27. 27p. |
| مصطلحات موضوعية: |
*GRAPES, *GENOMES, *WINES, *LINKAGE disequilibrium, *SINGLE nucleotide polymorphisms |
| مستخلص: |
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 genome-wide 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. [ABSTRACT FROM AUTHOR] |
| قاعدة البيانات: |
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