Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L.
Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior...
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doaj-eb360fa5ca0c4fa3a7fd1a266fdd1b9d2020-11-25T01:46:41ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0173e3297310.1371/journal.pone.0032973Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L.Grégory CarrierLoïc Le CunffAlexis DereeperDelphine LegrandFrançois SabotOlivier BouchezLaurent AudeguinJean-Michel BoursiquotPatrice ThisThrough multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France.http://europepmc.org/articles/PMC3299709?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Grégory Carrier Loïc Le Cunff Alexis Dereeper Delphine Legrand François Sabot Olivier Bouchez Laurent Audeguin Jean-Michel Boursiquot Patrice This |
spellingShingle |
Grégory Carrier Loïc Le Cunff Alexis Dereeper Delphine Legrand François Sabot Olivier Bouchez Laurent Audeguin Jean-Michel Boursiquot Patrice This Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. PLoS ONE |
author_facet |
Grégory Carrier Loïc Le Cunff Alexis Dereeper Delphine Legrand François Sabot Olivier Bouchez Laurent Audeguin Jean-Michel Boursiquot Patrice This |
author_sort |
Grégory Carrier |
title |
Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. |
title_short |
Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. |
title_full |
Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. |
title_fullStr |
Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. |
title_full_unstemmed |
Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. |
title_sort |
transposable elements are a major cause of somatic polymorphism in vitis vinifera l. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2012-01-01 |
description |
Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France. |
url |
http://europepmc.org/articles/PMC3299709?pdf=render |
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