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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Main Authors:	Carrier, Grégory, Le Cunff, Loïc, Dereeper, Alexis, Legrand, Delphine, Sabot, François, Bouchez, Olivier, Audeguin, Laurent, Boursiquot, Jean-Michel, This, Patrice
Format:	Online
Language:	English
Published:	Public Library of Science 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299709/

id	pubmed-3299709
recordtype	oai_dc
spelling	pubmed-32997092012-03-16 Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L. Carrier, Grégory Le Cunff, Loïc Dereeper, Alexis Legrand, Delphine Sabot, François Bouchez, Olivier Audeguin, Laurent Boursiquot, Jean-Michel This, Patrice Research Article 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. Public Library of Science 2012-03-12 /pmc/articles/PMC3299709/ /pubmed/22427919 http://dx.doi.org/10.1371/journal.pone.0032973 Text en Carrier et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Carrier, Grégory Le Cunff, Loïc Dereeper, Alexis Legrand, Delphine Sabot, François Bouchez, Olivier Audeguin, Laurent Boursiquot, Jean-Michel This, Patrice
spellingShingle	Carrier, Grégory Le Cunff, Loïc Dereeper, Alexis Legrand, Delphine Sabot, François Bouchez, Olivier Audeguin, Laurent Boursiquot, Jean-Michel This, Patrice Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L.
author_facet	Carrier, Grégory Le Cunff, Loïc Dereeper, Alexis Legrand, Delphine Sabot, François Bouchez, Olivier Audeguin, Laurent Boursiquot, Jean-Michel This, Patrice
author_sort	Carrier, Grégory
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.
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.
publisher	Public Library of Science
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299709/
_version_	1611512312246566912

Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L.

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